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Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria ME, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv 2024:2023.04.02.535219. [PMID: 37066352 PMCID: PMC10103973 DOI: 10.1101/2023.04.02.535219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Knowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state Regulatory Potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbored distinctive transcription factor binding motifs that were similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we showed that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.
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Affiliation(s)
- Guanjue Xiang
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215
| | - Xi He
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Belinda M. Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Kathryn J. Isaac
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Dylan J. Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Camden Jansen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Alexander Q. Wixom
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - April Cockburn
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Amber Miller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Qian Qi
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Yanghua He
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai`i at Mānoa, Honolulu, HI 96822, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Jens Lichtenberg
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892
| | - Elisabeth F. Heuston
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892
| | - Stacie M. Anderson
- Flow Cytometry Core, National Human Genome Research Institute, Bethesda, MD 20892
| | - Jing Luan
- Department of Pediatrics, Children’s Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marit W. Vermunt
- Department of Pediatrics, Children’s Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL 60611
| | - Michael E.G. Sauria
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - Berthold Göttgens
- Welcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jim R. Hughes
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Douglas R. Higgs
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Mitchell J. Weiss
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Yong Cheng
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Gerd A. Blobel
- Department of Pediatrics, Children’s Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - David M. Bodine
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892
| | - Yu Zhang
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
| | - Qunhua Li
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
- Center for Computational Biology and Bioinformatics, Genome Sciences Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Computational Biology and Bioinformatics, Genome Sciences Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Computational Biology and Bioinformatics, Genome Sciences Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802
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2
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Pagnamenta AT, Camps C, Giacopuzzi E, Taylor JM, Hashim M, Calpena E, Kaisaki PJ, Hashimoto A, Yu J, Sanders E, Schwessinger R, Hughes JR, Lunter G, Dreau H, Ferla M, Lange L, Kesim Y, Ragoussis V, Vavoulis DV, Allroggen H, Ansorge O, Babbs C, Banka S, Baños-Piñero B, Beeson D, Ben-Ami T, Bennett DL, Bento C, Blair E, Brasch-Andersen C, Bull KR, Cario H, Cilliers D, Conti V, Davies EG, Dhalla F, Dacal BD, Dong Y, Dunford JE, Guerrini R, Harris AL, Hartley J, Hollander G, Javaid K, Kane M, Kelly D, Kelly D, Knight SJL, Kreins AY, Kvikstad EM, Langman CB, Lester T, Lines KE, Lord SR, Lu X, Mansour S, Manzur A, Maroofian R, Marsden B, Mason J, McGowan SJ, Mei D, Mlcochova H, Murakami Y, Németh AH, Okoli S, Ormondroyd E, Ousager LB, Palace J, Patel SY, Pentony MM, Pugh C, Rad A, Ramesh A, Riva SG, Roberts I, Roy N, Salminen O, Schilling KD, Scott C, Sen A, Smith C, Stevenson M, Thakker RV, Twigg SRF, Uhlig HH, van Wijk R, Vona B, Wall S, Wang J, Watkins H, Zak J, Schuh AH, Kini U, Wilkie AOM, Popitsch N, Taylor JC. Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases. Genome Med 2023; 15:94. [PMID: 37946251 PMCID: PMC10636885 DOI: 10.1186/s13073-023-01240-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25-30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing.
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Affiliation(s)
- Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Carme Camps
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edoardo Giacopuzzi
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Human Technopole, Viale Rita Levi Montalcini 1, 20157, Milan, Italy
| | - John M Taylor
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mona Hashim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Eduardo Calpena
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Pamela J Kaisaki
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Akiko Hashimoto
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jing Yu
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edward Sanders
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Ron Schwessinger
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- University Medical Center Groningen, Groningen University, PO Box 72, 9700 AB, Groningen, The Netherlands
| | - Helene Dreau
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Matteo Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Lukas Lange
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Yesim Kesim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Vassilis Ragoussis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Dimitrios V Vavoulis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Holger Allroggen
- Neurosciences Department, UHCW NHS Trust, Clifford Bridge Road, Coventry, CV2 2DX, UK
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK
| | - Benito Baños-Piñero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - David Beeson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Tal Ben-Ami
- Pediatric Hematology-Oncology Unit, Kaplan Medical Center, Rehovot, Israel
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Celeste Bento
- Hematology Department, Hospitais da Universidade de Coimbra, Coimbra, Portugal
| | - Edward Blair
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Katherine R Bull
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Holger Cario
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Eythstrasse 24, 89075, Ulm, Germany
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Valerio Conti
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - E Graham Davies
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Fatima Dhalla
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7TY, UK
| | - Beatriz Diez Dacal
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Yin Dong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - James E Dunford
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Adrian L Harris
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Jane Hartley
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Georg Hollander
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Kassim Javaid
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Maureen Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Pharmacy Hall North, Room 731, 20 N. Pine Street, Baltimore, MD, 21201, USA
| | - Deirdre Kelly
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Dominic Kelly
- Children's Hospital, OUH NHS Foundation Trust, NIHR Oxford BRC, Headley Way, Oxford, OX3 9DU, UK
| | - Samantha J L Knight
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Alexandra Y Kreins
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Erika M Kvikstad
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Craig B Langman
- Feinberg School of Medicine, Northwestern University, 211 E Chicago Avenue, Chicago, IL, MS37, USA
| | - Tracy Lester
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Kate E Lines
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Simon R Lord
- Early Phase Clinical Trials Unit, Department of Oncology, University of Oxford, Cancer and Haematology Centre, Level 2 Administration Area, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Xin Lu
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Sahar Mansour
- St George's University Hospitals NHS Foundation Trust, Blackshore Road, Tooting, London, SW17 0QT, UK
| | - Adnan Manzur
- MRC Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Brian Marsden
- Nuffield Department of Medicine, Kennedy Institute, University of Oxford, Oxford, OX3 7BN, UK
| | - Joanne Mason
- Yourgene Health Headquarters, Skelton House, Lloyd Street North, Manchester Science Park, Manchester, M15 6SH, UK
| | - Simon J McGowan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Davide Mei
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Hana Mlcochova
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Steven Okoli
- Imperial College NHS Trust, Department of Haematology, Hammersmith Hospital, Du Cane Road, London, W12 0HS, UK
| | - Elizabeth Ormondroyd
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Lilian Bomme Ousager
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacqueline Palace
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Smita Y Patel
- Clinical Immunology, John Radcliffe Hospital, Level 4A, Oxford, OX3 9DU, UK
| | - Melissa M Pentony
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Chris Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Aboulfazl Rad
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
| | - Archana Ramesh
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Simone G Riva
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Irene Roberts
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Noémi Roy
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Level 4, Haematology, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Outi Salminen
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Kyleen D Schilling
- Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Arjune Sen
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Conrad Smith
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mark Stevenson
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Rajesh V Thakker
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Holm H Uhlig
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Richard van Wijk
- UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Barbara Vona
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Steven Wall
- Oxford Craniofacial Unit, John Radcliffe Hospital, Level LG1, West Wing, Oxford, OX3 9DU, UK
| | - Jing Wang
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hugh Watkins
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Jaroslav Zak
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Usha Kini
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Andrew O M Wilkie
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Niko Popitsch
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter(VBC), Dr.-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK.
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3
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Downes DJ, Smith AL, Karpinska MA, Velychko T, Rue-Albrecht K, Sims D, Milne TA, Davies JOJ, Oudelaar AM, Hughes JR. Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nat Protoc 2023; 18:3155. [PMID: 37369851 DOI: 10.1038/s41596-023-00860-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Taras Velychko
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Kevin Rue-Albrecht
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David Sims
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Haematology Theme, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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4
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Preston AE, Frost JN, Badat M, Teh M, Armitage AE, Norfo R, Wideman SK, Hanifi M, White N, Roy N, Ghesquiere B, Babbs C, Kassouf M, Davies J, Hughes JR, Beagrie R, Higgs DR, Drakesmith H. Ancient genomic linkage couples metabolism with erythroid development. bioRxiv 2023:2023.09.25.558944. [PMID: 37808769 PMCID: PMC10557585 DOI: 10.1101/2023.09.25.558944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Generation of mature cells from progenitors requires tight coupling of differentiation and metabolism. During erythropoiesis, erythroblasts are required to massively upregulate globin synthesis then clear extraneous material and enucleate to produce erythrocytes1-3. Nprl3 has remained in synteny with the α-globin genes for >500 million years4, and harbours the majority of the α-globin enhancers5. Nprl3 is a highly conserved inhibitor of mTORC1, which controls cellular metabolism. However, whether Nprl3 itself serves an erythroid role is unknown. Here, we show that Nprl3 is a key regulator of erythroid metabolism. Using Nprl3-deficient fetal liver and adult competitive bone marrow - fetal liver chimeras, we show that NprI3 is required for sufficient erythropoiesis. Loss of Nprl3 elevates mTORC1 signalling, suppresses autophagy and disrupts erythroblast glycolysis and redox control. Human CD34+ progenitors lacking NPRL3 produce fewer enucleated cells and demonstrate dysregulated mTORC1 signalling in response to nutrient availability and erythropoietin. Finally, we show that the α-globin enhancers upregulate NprI3 expression, and that this activity is necessary for optimal erythropoiesis. Therefore, the anciently conserved linkage of NprI3, α-globin and their associated enhancers has enabled coupling of metabolic and developmental control in erythroid cells. This may enable erythropoiesis to adapt to fluctuating nutritional and environmental conditions.
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Affiliation(s)
- Alexandra E Preston
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Joe N Frost
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Mohsin Badat
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Megan Teh
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Andrew E Armitage
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ruggiero Norfo
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Sarah K Wideman
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Muhammad Hanifi
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Natasha White
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Noémi Roy
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Bart Ghesquiere
- Metabolomics Expertise Center, VIB Center for Cancer Biology, 3000 Leuven, Belgium
- Metabolomics Expertise Center, Department of Oncology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Mira Kassouf
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - James Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rob Beagrie
- Chromatin and Disease Group, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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5
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Riva SG, Georgiades E, Gur ER, Baxter M, Hughes JR. CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data. J Vis Exp 2023. [PMID: 37811941 DOI: 10.3791/65633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
Assay for transposase-accessible chromatin (ATAC) and chromatin immunoprecipitation (ChIP), coupled with next-generation sequencing (NGS), have revolutionized the study of gene regulation. A lack of standardization in the analysis of the highly dimensional datasets generated by these techniques has made reproducibility difficult to achieve, leading to discrepancies in the published, processed data. Part of this problem is due to the diverse range of bioinformatic tools available for the analysis of these types of data. Secondly, a number of different bioinformatic tools are required sequentially to convert raw data into a fully processed and interpretable output, and these tools require varying levels of computational skills. Furthermore, there are many options for quality control that are not uniformly employed during data processing. We address these issues with a complete assay for transposase-accessible chromatin sequencing (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) upstream pipeline (CATCH-UP), an easy-to-use, Python-based pipeline for the analysis of bulk ChIP-seq and ATAC-seq datasets from raw fastq files to visualizable bigwig tracks and peaks calls. This pipeline is simple to install and run, requiring minimal computational knowledge. The pipeline is modular, scalable, and parallelizable on various computing infrastructures, allowing for easy reporting of methodology to enable reproducible analysis of novel or published datasets.
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Affiliation(s)
- Simone G Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford;
| | - Emily Georgiades
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford
| | - E Ravza Gur
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford
| | - Matthew Baxter
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford
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6
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Torres JM, Sun H, Nylander V, Downes DJ, van de Bunt M, McCarthy MI, Hughes JR, Gloyn AL. Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells. Wellcome Open Res 2023; 8:165. [PMID: 37736013 PMCID: PMC10509606 DOI: 10.12688/wellcomeopenres.18653.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 09/23/2023] Open
Abstract
Background: Resolving causal genes for type 2 diabetes at loci implicated by genome-wide association studies (GWAS) requires integrating functional genomic data from relevant cell types. Chromatin features in endocrine cells of the pancreatic islet are particularly informative and recent studies leveraging chromosome conformation capture (3C) with Hi-C based methods have elucidated regulatory mechanisms in human islets. However, these genome-wide approaches are less sensitive and afford lower resolution than methods that target specific loci. Methods: To gauge the extent to which targeted 3C further resolves chromatin-mediated regulatory mechanisms at GWAS loci, we generated interaction profiles at 23 loci using next-generation (NG) capture-C in a human beta cell model (EndoC-βH1) and contrasted these maps with Hi-C maps in EndoC-βH1 cells and human islets and a promoter capture Hi-C map in human islets. Results: We found improvements in assay sensitivity of up to 33-fold and resolved ~3.6X more chromatin interactions. At a subset of 18 loci with 25 co-localised GWAS and eQTL signals, NG Capture-C interactions implicated effector transcripts at five additional genetic signals relative to promoter capture Hi-C through physical contact with gene promoters. Conclusions: High resolution chromatin interaction profiles at selectively targeted loci can complement genome- and promoter-wide maps.
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Affiliation(s)
- Jason M. Torres
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, England, OX3 7BN, UK
| | - Han Sun
- Department of Pediatrics, Division of Endocrinology and Diabetes, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Vibe Nylander
- Oxford Centre for Diabetes Endocrinology & Metabolism, University of Oxford, Oxford, England, OX3 7L3, UK
| | - Damien J. Downes
- Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9D2, UK
| | - Martijn van de Bunt
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, England, OX3 7BN, UK
- Oxford Centre for Diabetes Endocrinology & Metabolism, University of Oxford, Oxford, England, OX3 7L3, UK
- Present address: Cytoki Pharma ApS, Tuborg Boulevard 12, Hellerup, DK-2900, Denmark
| | - Mark I. McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, England, OX3 7BN, UK
- Oxford Centre for Diabetes Endocrinology & Metabolism, University of Oxford, Oxford, England, OX3 7L3, UK
- Present address: OMNI Human Genetics, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jim R. Hughes
- Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9D2, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9D2, UK
| | - Anna L. Gloyn
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, England, OX3 7BN, UK
- Department of Pediatrics, Division of Endocrinology and Diabetes, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Oxford Centre for Diabetes Endocrinology & Metabolism, University of Oxford, Oxford, England, OX3 7L3, UK
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7
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Turkalj S, Jakobsen NA, Groom A, Metzner M, Riva SG, Gür ER, Usukhbayar B, Salazar MA, Hentges LD, Mickute G, Clark K, Sopp P, Davies JOJ, Hughes JR, Vyas P. GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell Stem Cell 2023; 30:722-740.e11. [PMID: 37146586 DOI: 10.1016/j.stem.2023.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.
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Affiliation(s)
- Sven Turkalj
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Niels Asger Jakobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angus Groom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Marlen Metzner
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Simone G Riva
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - E Ravza Gür
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Batchimeg Usukhbayar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Mirian Angulo Salazar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Lance D Hentges
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gerda Mickute
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Kevin Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Oxford Centre for Haematology, NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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8
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Hentges LD, Sergeant MJ, Cole CB, Downes DJ, Hughes JR, Taylor S. LanceOtron: a deep learning peak caller for genome sequencing experiments. Bioinformatics 2022; 38:4255-4263. [PMID: 35866989 PMCID: PMC9477537 DOI: 10.1093/bioinformatics/btac525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/10/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Genome sequencing experiments have revolutionized molecular biology by allowing researchers to identify important DNA-encoded elements genome wide. Regions where these elements are found appear as peaks in the analog signal of an assay's coverage track, and despite the ease with which humans can visually categorize these patterns, the size of many genomes necessitates algorithmic implementations. Commonly used methods focus on statistical tests to classify peaks, discounting that the background signal does not completely follow any known probability distribution and reducing the information-dense peak shapes to simply maximum height. Deep learning has been shown to be highly accurate for many pattern recognition tasks, on par or even exceeding human capabilities, providing an opportunity to reimagine and improve peak calling. RESULTS We present the peak calling framework LanceOtron, which combines deep learning for recognizing peak shape with multifaceted enrichment calculations for assessing significance. In benchmarking ATAC-seq, ChIP-seq and DNase-seq, LanceOtron outperforms long-standing, gold-standard peak callers through its improved selectivity and near-perfect sensitivity. AVAILABILITY AND IMPLEMENTATION A fully featured web application is freely available from LanceOtron.molbiol.ox.ac.uk, command line interface via python is pip installable from PyPI at https://pypi.org/project/lanceotron/, and source code and benchmarking tests are available at https://github.com/LHentges/LanceOtron. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lance D Hentges
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Martin J Sergeant
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Christopher B Cole
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jim R Hughes
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Stephen Taylor
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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9
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Downes DJ, Hughes JR. Natural and Experimental Rewiring of Gene Regulatory Regions. Annu Rev Genomics Hum Genet 2022; 23:73-97. [PMID: 35472292 DOI: 10.1146/annurev-genom-112921-010715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription of genes is controlled primarily by cis-regulatory elements: promoters, enhancers, and insulators. The medical importance of this key biological process can be seen by the frequency with which mutations and inherited variants that alter cis-regulatory elements lead to monogenic and complex diseases and cancer. Here, we provide an overview of the methods available to characterize and perturb gene regulatory circuits. We then highlight mechanisms through which regulatory rewiring contributes to disease, and conclude with a perspective on how our understanding of gene regulation can be used to improve human health.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
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10
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Pavlaki I, Shapiro M, Pisignano G, Jones SME, Telenius J, Muñoz-Descalzo S, Williams RJ, Hughes JR, Vance KW. Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells. PLoS Genet 2022; 18:e1010230. [PMID: 35709096 PMCID: PMC9202886 DOI: 10.1371/journal.pgen.1010230] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 11/19/2022] Open
Abstract
Central nervous system-expressed long non-coding RNAs (lncRNAs) are often located in the genome close to protein coding genes involved in transcriptional control. Such lncRNA-protein coding gene pairs are frequently temporally and spatially co-expressed in the nervous system and are predicted to act together to regulate neuronal development and function. Although some of these lncRNAs also bind and modulate the activity of the encoded transcription factors, the regulatory mechanisms controlling co-expression of neighbouring lncRNA-protein coding genes remain unclear. Here, we used high resolution NG Capture-C to map the cis-regulatory interaction landscape of the key neuro-developmental Paupar-Pax6 lncRNA-mRNA locus. The results define chromatin architecture changes associated with high Paupar-Pax6 expression in neurons and identify both promoter selective as well as shared cis-regulatory-promoter interactions involved in regulating Paupar-Pax6 co-expression. We discovered that the TCF7L2 transcription factor, a regulator of chromatin architecture and major effector of the Wnt signalling pathway, binds to a subset of these candidate cis-regulatory elements to coordinate Paupar and Pax6 co-expression. We describe distinct roles for Paupar in Pax6 expression control and show that the Paupar DNA locus contains a TCF7L2 bound transcriptional silencer whilst the Paupar transcript can act as an activator of Pax6. Our work provides important insights into the chromatin interactions, signalling pathways and transcription factors controlling co-expression of adjacent lncRNAs and protein coding genes in the brain.
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Affiliation(s)
- Ioanna Pavlaki
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Michael Shapiro
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Giuseppina Pisignano
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - Jelena Telenius
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia Muñoz-Descalzo
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Universidad Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Robert J. Williams
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Keith W. Vance
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- * E-mail:
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11
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Herrmann JC, Beagrie RA, Hughes JR. Making connections: enhancers in cellular differentiation. Trends Genet 2022; 38:395-408. [PMID: 34753603 DOI: 10.1016/j.tig.2021.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 01/23/2023]
Abstract
Deciphering the process by which hundreds of distinct cell types emerge from a single zygote to form a complex multicellular organism remains one of the greatest challenges in biological research. Enhancers are known to be central to cell type-specific gene expression, yet many questions regarding how these genomic elements interact both temporally and spatially with other cis- and trans-acting factors to control transcriptional activity during differentiation and development remain unanswered. Here, we review our current understanding of the role of enhancers and their interactions in this context and highlight recent progress achieved with experimental methods of unprecedented resolution.
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Affiliation(s)
- Jennifer C Herrmann
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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12
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Owens DDG, Anselmi G, Oudelaar AM, Downes DJ, Cavallo A, Harman JR, Schwessinger R, Bucakci A, Greder L, de Ornellas S, Jeziorska D, Telenius J, Hughes JR, de Bruijn MFTR. Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development. Nat Commun 2022; 13:773. [PMID: 35140205 PMCID: PMC8828719 DOI: 10.1038/s41467-022-28376-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/12/2022] [Indexed: 01/22/2023] Open
Abstract
The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation of Runx1 in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures. Runx1 resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility, Runx1 enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increase in the TAD, along with initiation of Runx1 expression from the P2 promoter. Differentiation to hematopoietic progenitor cells is associated with the formation of tissue-specific sub-TADs over Runx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from both Runx1 promoters. Deletion of promoter-proximal CTCF sites at the sub-TAD boundaries has no obvious effects on E-P interactions but leads to partial loss of domain structure, mildly affects gene expression, and delays hematopoietic development. Together, our analysis of gene regulation at a large multi-promoter developmental gene reveals that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression.
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Affiliation(s)
- Dominic D G Owens
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Giorgio Anselmi
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Damien J Downes
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Alessandro Cavallo
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Joe R Harman
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Akin Bucakci
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lucas Greder
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sara de Ornellas
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Physical and Theoretical Chemistry Building, Department of Chemistry, University of Oxford, Oxford, UK
| | - Danuta Jeziorska
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jelena Telenius
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Marella F T R de Bruijn
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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13
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Downes DJ, Smith AL, Karpinska MA, Velychko T, Rue-Albrecht K, Sims D, Milne TA, Davies JOJ, Oudelaar AM, Hughes JR. Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture. Nat Protoc 2022; 17:445-475. [PMID: 35121852 PMCID: PMC7613269 DOI: 10.1038/s41596-021-00651-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/27/2021] [Indexed: 12/16/2022]
Abstract
Chromosome conformation capture (3C) methods measure the spatial proximity between DNA elements in the cell nucleus. Many methods have been developed to sample 3C material, including the Capture-C family of protocols. Capture-C methods use oligonucleotides to enrich for interactions of interest from sequencing-ready 3C libraries. This approach is modular and has been adapted and optimized to work for sampling of disperse DNA elements (NuTi Capture-C), including from low cell inputs (LI Capture-C), as well as to generate Hi-C like maps for specific regions of interest (Tiled-C) and to interrogate multiway interactions (Tri-C). We present the design, experimental protocol and analysis pipeline for NuTi Capture-C in addition to the variations for generation of LI Capture-C, Tiled-C and Tri-C data. The entire procedure can be performed in 3 weeks and requires standard molecular biology skills and equipment, access to a next-generation sequencing platform, and basic bioinformatic skills. Implemented with other sequencing technologies, these methods can be used to identify regulatory interactions and to compare the structural organization of the genome in different cell types and genetic models.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Taras Velychko
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Kevin Rue-Albrecht
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David Sims
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Haematology Theme, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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14
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Abstract
Tri-C is a chromosome conformation capture (3C) approach that can efficiently identify multiway chromatin interactions with viewpoints of interest. As opposed to pair-wise interactions identified in methods such as Hi-C, 4C, and Capture-C, the detection of multiway interactions allows researchers to investigate how multiple cis-regulatory elements interact together in higher-order structures in single nuclei and address questions regarding structural cooperation between these elements. Here, we describe the procedure for designing and performing a Tri-C experiment.
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Affiliation(s)
- A Marieke Oudelaar
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Damien J Downes
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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15
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Downes DJ, Cross AR, Hua P, Roberts N, Schwessinger R, Cutler AJ, Munis AM, Brown J, Mielczarek O, de Andrea CE, Melero I, Gill DR, Hyde SC, Knight JC, Todd JA, Sansom SN, Issa F, Davies JOJ, Hughes JR. Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. Nat Genet 2021; 53:1606-1615. [PMID: 34737427 PMCID: PMC7611960 DOI: 10.1038/s41588-021-00955-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 09/22/2021] [Indexed: 12/21/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) disease (COVID-19) pandemic has caused millions of deaths worldwide. Genome-wide association studies identified the 3p21.31 region as conferring a twofold increased risk of respiratory failure. Here, using a combined multiomics and machine learning approach, we identify the gain-of-function risk A allele of an SNP, rs17713054G>A, as a probable causative variant. We show with chromosome conformation capture and gene-expression analysis that the rs17713054-affected enhancer upregulates the interacting gene, leucine zipper transcription factor like 1 (LZTFL1). Selective spatial transcriptomic analysis of lung biopsies from patients with COVID-19 shows the presence of signals associated with epithelial-mesenchymal transition (EMT), a viral response pathway that is regulated by LZTFL1. We conclude that pulmonary epithelial cells undergoing EMT, rather than immune cells, are likely responsible for the 3p21.31-associated risk. Since the 3p21.31 effect is conferred by a gain-of-function, LZTFL1 may represent a therapeutic target.
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Affiliation(s)
- Damien J Downes
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Amy R Cross
- Nuffield Department of Surgical Sciences, Transplantation Research and Immunology Group,University of Oxford, Oxford, UK
| | - Peng Hua
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine Centre for Computational Biology, University of Oxford, Oxford, UK
| | - Antony J Cutler
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Immunology Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Altar M Munis
- Department of Medicine, Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe University of Oxford, Oxford, UK
| | - Jill Brown
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Olga Mielczarek
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Carlos E de Andrea
- Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ignacio Melero
- Division of Immunology and Immunotherapy, Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Deborah R Gill
- Department of Medicine, Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe University of Oxford, Oxford, UK
| | - Stephen C Hyde
- Department of Medicine, Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe University of Oxford, Oxford, UK
| | - Julian C Knight
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - John A Todd
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, Transplantation Research and Immunology Group,University of Oxford, Oxford, UK
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - James O J Davies
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK.
| | - Jim R Hughes
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine Centre for Computational Biology, University of Oxford, Oxford, UK.
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16
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King AJ, Songdej D, Downes DJ, Beagrie RA, Liu S, Buckley M, Hua P, Suciu MC, Marieke Oudelaar A, Hanssen LLP, Jeziorska D, Roberts N, Carpenter SJ, Francis H, Telenius J, Olijnik AA, Sharpe JA, Sloane-Stanley J, Eglinton J, Kassouf MT, Orkin SH, Pennacchio LA, Davies JOJ, Hughes JR, Higgs DR, Babbs C. Reactivation of a developmentally silenced embryonic globin gene. Nat Commun 2021; 12:4439. [PMID: 34290235 PMCID: PMC8295333 DOI: 10.1038/s41467-021-24402-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/12/2021] [Indexed: 12/26/2022] Open
Abstract
The α- and β-globin loci harbor developmentally expressed genes, which are silenced throughout post-natal life. Reactivation of these genes may offer therapeutic approaches for the hemoglobinopathies, the most common single gene disorders. Here, we address mechanisms regulating the embryonically expressed α-like globin, termed ζ-globin. We show that in embryonic erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD (topologically associating domain) of open, acetylated chromatin and interacts with the α-globin super-enhancer. By contrast, in adult erythroid cells, the ζ-gene is packaged within a small (~10 kb) sub-domain of hypoacetylated, facultative heterochromatin within the acetylated sub-TAD and that it no longer interacts with its enhancers. The ζ-gene can be partially re-activated by acetylation and inhibition of histone de-acetylases. In addition to suggesting therapies for severe α-thalassemia, these findings illustrate the general principles by which reactivation of developmental genes may rescue abnormalities arising from mutations in their adult paralogues.
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Affiliation(s)
- Andrew J King
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Duantida Songdej
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Division of Hematology/Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Siyu Liu
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Megan Buckley
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Maria C Suciu
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Lars L P Hanssen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Danuta Jeziorska
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stephanie J Carpenter
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Helena Francis
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Aude-Anais Olijnik
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jacqueline A Sharpe
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jacqueline Sloane-Stanley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jennifer Eglinton
- National Haemoglobinopathy Reference Laboratory, Department of Haematology, Level 4, John Radcliffe Hospital, Oxford, UK
| | - Mira T Kassouf
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stuart H Orkin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA
| | - Len A Pennacchio
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
| | - James O J Davies
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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17
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Hua P, Badat M, Hanssen LLP, Hentges LD, Crump N, Downes DJ, Jeziorska DM, Oudelaar AM, Schwessinger R, Taylor S, Milne TA, Hughes JR, Higgs DR, Davies JOJ. Defining genome architecture at base-pair resolution. Nature 2021; 595:125-129. [PMID: 34108683 DOI: 10.1038/s41586-021-03639-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/13/2021] [Indexed: 12/16/2022]
Abstract
In higher eukaryotes, many genes are regulated by enhancers that are 104-106 base pairs (bp) away from the promoter. Enhancers contain transcription-factor-binding sites (which are typically around 7-22 bp), and physical contact between the promoters and enhancers is thought to be required to modulate gene expression. Although chromatin architecture has been mapped extensively at resolutions of 1 kilobase and above; it has not been possible to define physical contacts at the scale of the proteins that determine gene expression. Here we define these interactions in detail using a chromosome conformation capture method (Micro-Capture-C) that enables the physical contacts between different classes of regulatory elements to be determined at base-pair resolution. We find that highly punctate contacts occur between enhancers, promoters and CCCTC-binding factor (CTCF) sites and we show that transcription factors have an important role in the maintenance of the contacts between enhancers and promoters. Our data show that interactions between CTCF sites are increased when active promoters and enhancers are located within the intervening chromatin. This supports a model in which chromatin loop extrusion1 is dependent on cohesin loading at active promoters and enhancers, which explains the formation of tissue-specific chromatin domains without changes in CTCF binding.
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Affiliation(s)
- Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mohsin Badat
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lars L P Hanssen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lance D Hentges
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Danuta M Jeziorska
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen Taylor
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Doug R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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18
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Sergeant MJ, Hughes JR, Hentges L, Lunter G, Downes DJ, Taylor S. Multi Locus View: an extensible web-based tool for the analysis of genomic data. Commun Biol 2021; 4:623. [PMID: 34035422 PMCID: PMC8149710 DOI: 10.1038/s42003-021-02097-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/31/2021] [Indexed: 01/10/2023] Open
Abstract
Tracking and understanding data quality, analysis and reproducibility are critical concerns in the biological sciences. This is especially true in genomics where next generation sequencing (NGS) based technologies such as ChIP-seq, RNA-seq and ATAC-seq are generating a flood of genome-scale data. However, such data are usually processed with automated tools and pipelines, generating tabular outputs and static visualisations. Interpretation is normally made at a high level without the ability to visualise the underlying data in detail. Conventional genome browsers are limited to browsing single locations and do not allow for interactions with the dataset as a whole. Multi Locus View (MLV), a web-based tool, has been developed to allow users to fluidly interact with genomics datasets at multiple scales. The user is able to browse the raw data, cluster, and combine the data with other analysis and annotate the data. User datasets can then be shared with other users or made public for quick assessment from the academic community. MLV is publically available at https://mlv.molbiol.ox.ac.uk .
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Affiliation(s)
- Martin J Sergeant
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lance Hentges
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gerton Lunter
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- University Medical Centre Groningen, Department of Epidemiology, University of Groningen, Groningen, The Netherlands
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stephen Taylor
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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19
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Larke MSC, Schwessinger R, Nojima T, Telenius J, Beagrie RA, Downes DJ, Oudelaar AM, Truch J, Graham B, Bender MA, Proudfoot NJ, Higgs DR, Hughes JR. Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Mol Cell 2021; 81:983-997.e7. [PMID: 33539786 PMCID: PMC7612206 DOI: 10.1016/j.molcel.2021.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 09/25/2020] [Accepted: 01/02/2021] [Indexed: 12/16/2022]
Abstract
Gene transcription occurs via a cycle of linked events, including initiation, promoter-proximal pausing, and elongation of RNA polymerase II (Pol II). A key question is how transcriptional enhancers influence these events to control gene expression. Here, we present an approach that evaluates the level and change in promoter-proximal transcription (initiation and pausing) in the context of differential gene expression, genome-wide. This combinatorial approach shows that in primary cells, control of gene expression during differentiation is achieved predominantly via changes in transcription initiation rather than via release of Pol II pausing. Using genetically engineered mouse models, deleted for functionally validated enhancers of the α- and β-globin loci, we confirm that these elements regulate Pol II recruitment and/or initiation to modulate gene expression. Together, our data show that gene expression during differentiation is regulated predominantly at the level of initiation and that enhancers are key effectors of this process.
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Affiliation(s)
- Martin S C Larke
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Julia Truch
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Bryony Graham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - M A Bender
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Douglas R Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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20
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Downes DJ, Beagrie RA, Gosden ME, Telenius J, Carpenter SJ, Nussbaum L, De Ornellas S, Sergeant M, Eijsbouts CQ, Schwessinger R, Kerry J, Roberts N, Shivalingam A, El-Sagheer A, Oudelaar AM, Brown T, Buckle VJ, Davies JOJ, Hughes JR. High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nat Commun 2021; 12:531. [PMID: 33483495 PMCID: PMC7822813 DOI: 10.1038/s41467-020-20809-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023] Open
Abstract
Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical limitations, generation of reproducible high-resolution interaction profiles has not been achieved at genome-wide scale. Here, to overcome this barrier, we systematically test each step of 3C and report two improvements over current methods. We show that up to 30% of reporter events generated using the popular in situ 3C method arise from ligations between two individual nuclei, but this noise can be almost entirely eliminated by isolating intact nuclei after ligation. Using Nuclear-Titrated Capture-C, we generate reproducible high-resolution genome-wide 3C interaction profiles by targeting 8055 gene promoters in erythroid cells. By pairing high-resolution 3C interaction calls with nascent gene expression we interrogate the role of promoter hubs and super-enhancers in gene regulation.
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Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Matthew E Gosden
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jelena Telenius
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stephanie J Carpenter
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lea Nussbaum
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sara De Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Martin Sergeant
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chris Q Eijsbouts
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jon Kerry
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Arun Shivalingam
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Afaf El-Sagheer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tom Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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21
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Long HK, Osterwalder M, Welsh IC, Hansen K, Davies JOJ, Liu YE, Koska M, Adams AT, Aho R, Arora N, Ikeda K, Williams RM, Sauka-Spengler T, Porteus MH, Mohun T, Dickel DE, Swigut T, Hughes JR, Higgs DR, Visel A, Selleri L, Wysocka J. Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder. Cell Stem Cell 2020; 27:765-783.e14. [PMID: 32991838 PMCID: PMC7655526 DOI: 10.1016/j.stem.2020.09.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 01/09/2023]
Abstract
Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence (PRS). Leveraging a human stem cell differentiation model, we identify two clusters of enhancers within the PRS-associated region that regulate SOX9 expression during a restricted window of facial progenitor development at distances up to 1.45 Mb. Enhancers within the 1.45 Mb cluster exhibit highly synergistic activity that is dependent on the Coordinator motif. Using mouse models, we demonstrate that PRS phenotypic specificity arises from the convergence of two mechanisms: confinement of Sox9 dosage perturbation to developing facial structures through context-specific enhancer activity and heightened sensitivity of the lower jaw to Sox9 expression reduction. Overall, we characterize the longest-range human enhancers involved in congenital malformations, directly demonstrate that PRS is an enhanceropathy, and illustrate how small changes in gene expression can lead to morphological variation.
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Affiliation(s)
- Hannah K Long
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian C Welsh
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Karissa Hansen
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Yiran E Liu
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mervenaz Koska
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander T Adams
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Robert Aho
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kazuya Ikeda
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Ruth M Williams
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Tim Mohun
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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22
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Schwessinger R, Gosden M, Downes D, Brown RC, Oudelaar AM, Telenius J, Teh YW, Lunter G, Hughes JR. DeepC: predicting 3D genome folding using megabase-scale transfer learning. Nat Methods 2020; 17:1118-1124. [PMID: 33046896 PMCID: PMC7610627 DOI: 10.1038/s41592-020-0960-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/20/2020] [Indexed: 01/29/2023]
Abstract
Predicting the impact of noncoding genetic variation requires interpreting it in the context of three-dimensional genome architecture. We have developed deepC, a transfer-learning-based deep neural network that accurately predicts genome folding from megabase-scale DNA sequence. DeepC predicts domain boundaries at high resolution, learns the sequence determinants of genome folding and predicts the impact of both large-scale structural and single base-pair variations.
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Affiliation(s)
- Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Matthew Gosden
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Damien Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Richard C Brown
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jelena Telenius
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Yee Whye Teh
- Department of Statistics, University of Oxford, Oxford, UK
| | - Gerton Lunter
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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23
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Olijnik AA, Roy NBA, Scott C, Marsh JA, Brown J, Lauschke K, Ask K, Roberts N, Downes DJ, Brolih S, Johnson E, Xella B, Proven M, Hipkiss R, Ryan K, Frisk P, Mäkk J, Stattin ELM, Sadasivam N, McIlwaine L, Hill QA, Renella R, Hughes JR, Gibbons RJ, Groth A, McHugh PJ, Higgs DR, Buckle VJ, Babbs C. Genetic and functional insights into CDA-I prevalence and pathogenesis. J Med Genet 2020; 58:185-195. [PMID: 32518175 DOI: 10.1136/jmedgenet-2020-106880] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/05/2020] [Accepted: 04/02/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND Congenital dyserythropoietic anaemia type I (CDA-I) is a hereditary anaemia caused by biallelic mutations in the widely expressed genes CDAN1 and C15orf41. Little is understood about either protein and it is unclear in which cellular pathways they participate. METHODS Genetic analysis of a cohort of patients with CDA-I identifies novel pathogenic variants in both known causative genes. We analyse the mutation distribution and the predicted structural positioning of amino acids affected in Codanin-1, the protein encoded by CDAN1. Using western blotting, immunoprecipitation and immunofluorescence, we determine the effect of particular mutations on both proteins and interrogate protein interaction, stability and subcellular localisation. RESULTS We identify six novel CDAN1 mutations and one novel mutation in C15orf41 and uncover evidence of further genetic heterogeneity in CDA-I. Additionally, population genetics suggests that CDA-I is more common than currently predicted. Mutations are enriched in six clusters in Codanin-1 and tend to affect buried residues. Many missense and in-frame mutations do not destabilise the entire protein. Rather C15orf41 relies on Codanin-1 for stability and both proteins, which are enriched in the nucleolus, interact to form an obligate complex in cells. CONCLUSION Stability and interaction data suggest that C15orf41 may be the key determinant of CDA-I and offer insight into the mechanism underlying this disease. Both proteins share a common pathway likely to be present in a wide variety of cell types; however, nucleolar enrichment may provide a clue as to the erythroid specific nature of CDA-I. The surprisingly high predicted incidence of CDA-I suggests that better ascertainment would lead to improved patient care.
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Affiliation(s)
- Aude-Anais Olijnik
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Noémi B A Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Caroline Scott
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jill Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Karin Lauschke
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Katrine Ask
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Eli Lilly Danmark, Herlev, Denmark
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sanja Brolih
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Barbara Xella
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Molecular Haematology Laboratory, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ria Hipkiss
- Molecular Haematology Laboratory, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kate Ryan
- Haematology Department, Manchester University NHS Foundation Trust, Manchester, UK
| | - Per Frisk
- Department of Women's and Children's Health, Uppsala University and Uppsala University Childrens' Hospital, Uppsala, Sweden
| | - Johan Mäkk
- Centre for Health Development, Västmanland Region, Uppsala University, Uppsala, Sweden
| | | | - Nandini Sadasivam
- Haematology Department, Manchester University NHS Foundation Trust, Manchester, UK
| | - Louisa McIlwaine
- Department of Haematology, NHS Trust Greater Glasgow and Clyde, Glasgow, UK
| | - Quentin A Hill
- Department of Haematology, St James's University Hospital, Leeds, UK
| | - Raffaele Renella
- Pediatric Hematology-Oncology Laboratory, Lausanne University Hospital and University of Lausanne, Lausanne, VD, Switzerland
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,The Novo Nordisk Center for Protein Research (CPR), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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24
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Gillespie MA, Palii CG, Sanchez-Taltavull D, Shannon P, Longabaugh WJR, Downes DJ, Sivaraman K, Espinoza HM, Hughes JR, Price ND, Perkins TJ, Ranish JA, Brand M. Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis. Mol Cell 2020; 78:960-974.e11. [PMID: 32330456 PMCID: PMC7344268 DOI: 10.1016/j.molcel.2020.03.031] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/20/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022]
Abstract
Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies, our knowledge about the protein copy number of TFs in the nucleus is limited. Here, by determining the absolute abundances of 103 TFs and co-factors during the course of human erythropoiesis, we provide a dynamic and quantitative scale for TFs in the nucleus. Furthermore, we establish the first gene regulatory network of cell fate commitment that integrates temporal protein stoichiometry data with mRNA measurements. The model revealed quantitative imbalances in TFs' cross-antagonistic relationships that underlie lineage determination. Finally, we made the surprising discovery that, in the nucleus, co-repressors are dramatically more abundant than co-activators at the protein level, but not at the RNA level, with profound implications for understanding transcriptional regulation. These analyses provide a unique quantitative framework to understand transcriptional regulation of cell differentiation in a dynamic context.
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Affiliation(s)
| | - Carmen G Palii
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada
| | - Daniel Sanchez-Taltavull
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada; Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Paul Shannon
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Karthi Sivaraman
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Theodore J Perkins
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
| | - Jeffrey A Ranish
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H8L6, Canada.
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25
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Oudelaar AM, Beagrie RA, Gosden M, de Ornellas S, Georgiades E, Kerry J, Hidalgo D, Carrelha J, Shivalingam A, El-Sagheer AH, Telenius JM, Brown T, Buckle VJ, Socolovsky M, Higgs DR, Hughes JR. Dynamics of the 4D genome during in vivo lineage specification and differentiation. Nat Commun 2020; 11:2722. [PMID: 32483172 PMCID: PMC7264236 DOI: 10.1038/s41467-020-16598-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/13/2020] [Indexed: 02/08/2023] Open
Abstract
Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. Our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity. Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development.
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Affiliation(s)
- A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew Gosden
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sara de Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Emily Georgiades
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jon Kerry
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Hidalgo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School Worcester, Massachusetts, USA
| | - Joana Carrelha
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Oxford, UK
- Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, Egypt
| | - Jelena M Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Merav Socolovsky
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School Worcester, Massachusetts, USA
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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26
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Chiariello AM, Bianco S, Oudelaar AM, Esposito A, Annunziatella C, Fiorillo L, Conte M, Corrado A, Prisco A, Larke MS, Telenius JM, Sciarretta R, Musella F, Buckle VJ, Higgs DR, Hughes JR, Nicodemi M. A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells. Cell Rep 2020; 30:2125-2135.e5. [DOI: 10.1016/j.celrep.2020.01.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 08/13/2019] [Accepted: 01/14/2020] [Indexed: 01/07/2023] Open
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27
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Oudelaar AM, Harrold CL, Hanssen LLP, Telenius JM, Higgs DR, Hughes JR. A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus. Nat Commun 2019; 10:5412. [PMID: 31776347 PMCID: PMC6881440 DOI: 10.1038/s41467-019-13404-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022] Open
Abstract
Specific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements contained within a single chromatin domain are coordinated. Recent technological advances which can detect multi-way chromatin interactions at single alleles can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. Here, we use such an approach to investigate how interactions of the α-globin enhancers are distributed between multiple promoters in a mouse model in which the α-globin domain is extended to include several additional genes. Our data show that gene promoters do not form mutually exclusive interactions with enhancers, but all interact simultaneously in a single complex. These findings suggest that promoters do not structurally compete for interactions with enhancers, but form a regulatory hub structure, which is consistent with recent models of transcriptional activation occurring in non-membrane bound nuclear compartments.
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Affiliation(s)
- A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Caroline L Harrold
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lars L P Hanssen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jelena M Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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28
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Godfrey L, Crump NT, Thorne R, Lau IJ, Repapi E, Dimou D, Smith AL, Harman JR, Telenius JM, Oudelaar AM, Downes DJ, Vyas P, Hughes JR, Milne TA. DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation. Nat Commun 2019; 10:2803. [PMID: 31243293 PMCID: PMC6594956 DOI: 10.1038/s41467-019-10844-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 06/05/2019] [Indexed: 12/26/2022] Open
Abstract
Enhancer elements are a key regulatory feature of many important genes. Several general features including the presence of specific histone modifications are used to demarcate potentially active enhancers. Here we reveal that putative enhancers marked with H3 lysine 79 (H3K79) di or trimethylation (me2/3) (which we name H3K79me2/3 enhancer elements or KEEs) can be found in multiple cell types. Mixed lineage leukemia gene (MLL) rearrangements (MLL-r) such as MLL-AF4 are a major cause of incurable acute lymphoblastic leukemias (ALL). Using the DOT1L inhibitor EPZ-5676 in MLL-AF4 leukemia cells, we show that H3K79me2/3 is required for maintaining chromatin accessibility, histone acetylation and transcription factor binding specifically at KEEs but not non-KEE enhancers. We go on to show that H3K79me2/3 is essential for maintaining enhancer-promoter interactions at a subset of KEEs. Together, these data implicate H3K79me2/3 as having a functional role at a subset of active enhancers in MLL-AF4 leukemia cells.
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Affiliation(s)
- Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ross Thorne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - I-Jun Lau
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Emmanouela Repapi
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Dimitra Dimou
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Alastair L Smith
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joe R Harman
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jelena M Telenius
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - A Marieke Oudelaar
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Jim R Hughes
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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29
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Lim PJ, Duarte TL, Arezes J, Garcia-Santos D, Hamdi A, Pasricha SR, Armitage AE, Mehta H, Wideman S, Santos AG, Santos-Gonçalves A, Morovat A, Hughes JR, Soilleux E, Wang CY, Bayer AL, Klenerman P, Willberg CB, Hartley RC, Murphy MP, Babitt JL, Ponka P, Porto G, Drakesmith H. Nrf2 controls iron homeostasis in haemochromatosis and thalassaemia via Bmp6 and hepcidin. Nat Metab 2019; 1:519-531. [PMID: 31276102 PMCID: PMC6609153 DOI: 10.1038/s42255-019-0063-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Iron is critical for life but toxic in excess because of iron-catalysed formation of pro-oxidants that cause tissue damage in a range of disorders. The Nrf2 transcription factor orchestrates cell-intrinsic protective antioxidant responses, and the peptide hormone hepcidin maintains systemic iron homeostasis, but is pathophysiologically decreased in haemochromatosis and beta-thalassaemia. Here, we show that Nrf2 is activated by iron-induced, mitochondria-derived pro-oxidants and drives Bmp6 expression in liver sinusoid endothelial cells, which in turn increases hepcidin synthesis by neighbouring hepatocytes. In Nrf2 knockout mice, the Bmp6-hepcidin response to oral and parenteral iron is impaired and iron accumulation and hepatic damage are increased. Pharmacological activation of Nrf2 stimulates the Bmp6-hepcidin axis, improving iron homeostasis in haemochromatosis and counteracting the inhibition of Bmp6 by erythroferrone in beta-thalassaemia. We propose that Nrf2 links cellular sensing of excess toxic iron to control of systemic iron homeostasis and antioxidant responses, and may be a therapeutic target for iron-associated disorders.
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Affiliation(s)
- Pei Jin Lim
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Tiago L. Duarte
- Instituto de Biologia Molecular e Celular & Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - João Arezes
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Daniel Garcia-Santos
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Amel Hamdi
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Sant-Rayn Pasricha
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Andrew E. Armitage
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Hema Mehta
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, Oxfordshire, UK
| | - Sarah Wideman
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Ana G. Santos
- Instituto de Biologia Molecular e Celular & Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Andreia Santos-Gonçalves
- Instituto de Biologia Molecular e Celular & Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Alireza Morovat
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, UK
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine. University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Elizabeth Soilleux
- Department of Cellular Pathology, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Chia-Yu Wang
- Nephrology Division, Program in Membrane Biology, Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Abraham L. Bayer
- Nephrology Division, Program in Membrane Biology, Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Paul Klenerman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Oxford NIHR Biomedical Research Centre, The John Radcliffe Hospital, Oxford, UK
| | | | - Richard C. Hartley
- WestCHEM School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Michael P. Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Jodie L. Babitt
- Nephrology Division, Program in Membrane Biology, Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Prem Ponka
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Graça Porto
- Instituto de Biologia Molecular e Celular & Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Haematology Theme Oxford Biomedical Research Centre, Oxford, UK
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30
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Oudelaar AM, Davies JOJ, Hanssen LLP, Telenius JM, Schwessinger R, Liu Y, Brown JM, Downes DJ, Chiariello AM, Bianco S, Nicodemi M, Buckle VJ, Dekker J, Higgs DR, Hughes JR. Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nat Genet 2018; 50:1744-1751. [PMID: 30374068 PMCID: PMC6265079 DOI: 10.1038/s41588-018-0253-2] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/07/2018] [Indexed: 11/09/2022]
Abstract
The promoters of mammalian genes are commonly regulated by multiple distal enhancers, which physically interact within discrete chromatin domains. How such domains form and how the regulatory elements within them interact in single cells is not understood. To address this we developed Tri-C, a new Chromosome Conformation Capture (3C) approach to identify concurrent chromatin interactions at individual alleles. Analysis by Tri-C reveals heterogeneous patterns of single-allele interactions between CTCF boundary elements, indicating that the formation of chromatin domains likely results from a dynamic process. Within these domains, we observe specific higher-order structures involving simultaneous interactions between multiple enhancers and promoters. Such regulatory hubs provide a structural basis for understanding how multiple cis-regulatory elements act together to establish robust regulation of gene expression.
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Affiliation(s)
- A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lars L P Hanssen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jelena M Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Yu Liu
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jill M Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso di Monte Sant'Angelo, Naples, Italy
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso di Monte Sant'Angelo, Naples, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso di Monte Sant'Angelo, Naples, Italy
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK. .,MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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31
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Brown JM, Roberts NA, Graham B, Waithe D, Lagerholm C, Telenius JM, De Ornellas S, Oudelaar AM, Scott C, Szczerbal I, Babbs C, Kassouf MT, Hughes JR, Higgs DR, Buckle VJ. A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions. Nat Commun 2018; 9:3849. [PMID: 30242161 PMCID: PMC6155075 DOI: 10.1038/s41467-018-06248-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 08/24/2018] [Indexed: 11/08/2022] Open
Abstract
Self-interacting chromatin domains encompass genes and their cis-regulatory elements; however, the three-dimensional form a domain takes, whether this relies on enhancer-promoter interactions, and the processes necessary to mediate the formation and maintenance of such domains, remain unclear. To examine these questions, here we use a combination of high-resolution chromosome conformation capture, a non-denaturing form of fluorescence in situ hybridisation and super-resolution imaging to study a 70 kb domain encompassing the mouse α-globin regulatory locus. We show that this region forms an erythroid-specific, decompacted, self-interacting domain, delimited by frequently apposed CTCF/cohesin binding sites early in terminal erythroid differentiation, and does not require transcriptional elongation for maintenance of the domain structure. Formation of this domain does not rely on interactions between the α-globin genes and their major enhancers, suggesting a transcription-independent mechanism for establishment of the domain. However, absence of the major enhancers does alter internal domain interactions. Formation of a loop domain therefore appears to be a mechanistic process that occurs irrespective of the specific interactions within.
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Affiliation(s)
- Jill M Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Nigel A Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Bryony Graham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Dominic Waithe
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Jelena M Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Sara De Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Caroline Scott
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Izabela Szczerbal
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Mira T Kassouf
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK.
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32
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Nussbaum L, Telenius JM, Hill S, Hirschfeld PP, Suciu MC, Downes DJ, Hughes JR. High-Throughput Genotyping of CRISPR/Cas Edited Cells in 96-Well Plates. Methods Protoc 2018; 1:E29. [PMID: 31164571 PMCID: PMC6481090 DOI: 10.3390/mps1030029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 11/27/2022] Open
Abstract
The emergence in recent years of DNA editing technologies-Zinc finger nucleases (ZFNs), transcription activator-like effector (TALE) guided nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/Cas family enzymes, and Base-Editors-have greatly increased our ability to generate hundreds of edited cells carrying an array of alleles, including single-nucleotide substitutions. However, the infrequency of homology-dependent repair (HDR) in generating these substitutions in general requires the screening of large numbers of edited cells to isolate the sequence change of interest. Here we present a high-throughput method for the amplification and barcoding of edited loci in a 96-well plate format. After barcoding, plates are indexed as pools which permits multiplexed sequencing of hundreds of clones simultaneously. This protocol works at high success rate with more than 94% of clones successfully genotyped following analysis.
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Affiliation(s)
- Lea Nussbaum
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK; (L.N.); (J.M.T.); (S.H.); (P.P.H.); (M.C.S.)
| | - Jelena M. Telenius
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK; (L.N.); (J.M.T.); (S.H.); (P.P.H.); (M.C.S.)
- MRC WIMM Center for Computational Biology, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK
| | - Stephanie Hill
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK; (L.N.); (J.M.T.); (S.H.); (P.P.H.); (M.C.S.)
| | - Priscila P. Hirschfeld
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK; (L.N.); (J.M.T.); (S.H.); (P.P.H.); (M.C.S.)
| | - Maria C. Suciu
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK; (L.N.); (J.M.T.); (S.H.); (P.P.H.); (M.C.S.)
- Genomics plc, Oxford OX1 1JD, UK
| | - The WIGWAM Consortium
- Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK;
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Damien J. Downes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK; (L.N.); (J.M.T.); (S.H.); (P.P.H.); (M.C.S.)
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK; (L.N.); (J.M.T.); (S.H.); (P.P.H.); (M.C.S.)
- MRC WIMM Center for Computational Biology, Weatherall Institute of Molecular Medicine, Oxford OX3 9DU, UK
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33
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Hariman H, Grant PJ, Hughes JR, Booth NA, Davies JA, Prentice CRM. Effect of Physiological Concentrations of Vasopressin on Components of the Fibrinolytic System. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1646580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryHigh physiological concentrations of plasma vasopressin (aVP) when achieved by infusion cause an increase in plasma factor VIII coagulant activity and shortening of the euglobulin clot lysis time (ECLT). To investigate the effects of aVP on components of the fibrinolytic pathway and on thrombin generation, t healthy volunteers were infused with saline for 30 min followed by aVP for L hour and blood samples taken every 30 min for measurement of aVR ECtf tissue-type plasminogen activator (t-PA), t-PA inhibition (tPA-I), plasminogen activator inhibitor L (PAI-1 Ag), activated partial thromboplastin time (APTT), fibrinopeptide A (FPA), fibrinopeptide B 15-42 (FPBß 15-42) and crosslinked fibrin breakdown products (XL-FDP). Plasma aVP rose to a median of 75 pg/ml after 90 min and fell to 13.8 pdml 30 min later. The APTT fell from 43.5 to 35 sec (p <0.01) but there was no change in plasma FPA or in XL-FDP. Plasminogen activator activity (106/ECLT2) increased from 25 to 736 units (p <0.01) and t-PA from 200 to 1012 mlU/ml (p <0.01). tPA-I fell from 8.0 to 2.7 IU/ml at 90 min (p <0.05) but PAI-1 Ag remained unchanged. Plasma FPBß 15-42 was 2.4 and 1.2 pmol/ml before infusion with aVP and showed a small rise to 3.5 pmol/ml after 60 min (p <0.05). The results show the effects of aVP on fibrinolysis are mediated by an increase in t-PA. In the absence of thrombin generation the rise in t-PA was not accompanied by changes in XL-FDP.
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Affiliation(s)
- H Hariman
- The University Department of Medicine, The General Infirmary, Leeds, UK
| | - P J Grant
- The University Department of Medicine, The General Infirmary, Leeds, UK
| | - J R Hughes
- The University Department of Medicine, The General Infirmary, Leeds, UK
| | - N A Booth
- The Department of Medicine and Therapeutics, University of Aberdeen, Aberdeen, UK
| | - J A Davies
- The University Department of Medicine, The General Infirmary, Leeds, UK
| | - C R M Prentice
- The University Department of Medicine, The General Infirmary, Leeds, UK
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34
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Oudelaar AM, Davies JOJ, Downes DJ, Higgs DR, Hughes JR. Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C. Nucleic Acids Res 2018; 45:e184. [PMID: 29186505 PMCID: PMC5728395 DOI: 10.1093/nar/gkx1194] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023] Open
Abstract
Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin architecture in rare cell populations. We present a new low-input Capture-C approach that can generate high-quality 3C interaction profiles from 10 000-20 000 cells, depending on the resolution used for analysis. We also present a PCR-free, sequencing-free 3C technique based on NanoString technology called C-String. By comparing C-String and Capture-C interaction profiles we show that the latter are not skewed by PCR amplification. Furthermore, we demonstrate that chromatin interactions detected by Capture-C do not depend on the degree of cross-linking by performing experiments with varying formaldehyde concentrations.
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Affiliation(s)
- A Marieke Oudelaar
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - James O J Davies
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Damien J Downes
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Douglas R Higgs
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jim R Hughes
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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Yan T, Ooi WF, Qamra A, Cheung A, Ma D, Sundaram GM, Xu C, Xing M, Poon L, Wang J, Loh YP, Ho JHJ, Ng JJQ, Ramlee MK, Aswad L, Rozen SG, Ghosh S, Bard FA, Sampath P, Tergaonkar V, Davies JOJ, Hughes JR, Goh E, Bi X, Fullwood MJ, Tan P, Li S. HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis. Nat Commun 2018; 9:100. [PMID: 29311615 PMCID: PMC5758779 DOI: 10.1038/s41467-017-02601-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/13/2017] [Indexed: 02/06/2023] Open
Abstract
The repression of telomerase activity during cellular differentiation promotes replicative aging and functions as a physiological barrier for tumorigenesis in long-lived mammals, including humans. However, the underlying mechanisms remain largely unclear. Here we describe how miR-615-3p represses hTERT expression. mir-615-3p is located in an intron of the HOXC5 gene, a member of the highly conserved homeobox family of transcription factors controlling embryogenesis and development. Unexpectedly, we found that HoxC5 also represses hTERT expression by disrupting the long-range interaction between hTERT promoter and its distal enhancer. The 3'UTR of hTERT and its upstream enhancer region are well conserved in long-lived primates. Both mir-615-3p and HOXC5 are activated upon differentiation, which constitute a feed-forward loop that coordinates transcriptional and post-transcriptional repression of hTERT during cellular differentiation. Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.
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Affiliation(s)
- TingDong Yan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Aditi Qamra
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117597, Singapore
| | - Alice Cheung
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - DongLiang Ma
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Research, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
| | | | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Manjie Xing
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - LaiFong Poon
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Jing Wang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Yan Ping Loh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jess Hui Jie Ho
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Joscelyn Jun Quan Ng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Muhammad Khairul Ramlee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Luay Aswad
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Steve G Rozen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Duke-NUS Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Sujoy Ghosh
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Frederic A Bard
- Institute of Molecular and Cell Biology (IMCB), Singapore, 138673, Singapore
| | - Prabha Sampath
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Institute of Medical Biology (IMB), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology (IMCB), Singapore, 138673, Singapore
| | - James O J Davies
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Eyleen Goh
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117597, Singapore
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Research, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, 20 Biopolis Street, Singapore, 138669, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Institute of Molecular and Cell Biology (IMCB), Singapore, 138673, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117597, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Duke-NUS Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Cellular and Molecular Research, National Cancer Centre, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117597, Singapore.
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Hughes JR, Kaye BM, Beswick AR, Ter Haar G. Complications following laryngeal sacculectomy in brachycephalic dogs. J Small Anim Pract 2017; 59:16-21. [PMID: 29047114 DOI: 10.1111/jsap.12763] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/06/2017] [Accepted: 08/04/2017] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To evaluate the effect of sacculectomy on the immediate postoperative complication rate in dogs affected with brachycephalic obstructive airway syndrome. MATERIALS AND METHODS Retrospective review of clinical records of brachycephalic dogs with everted saccules that underwent surgery for brachycephalic obstructive airway syndrome between 2009 and 2014. Dogs were grouped as those having nares resection and staphylectomy only and those having nares resection, staphylectomy and laryngeal sacculectomy. Complications were scored as mild, moderate or severe. RESULTS In total, 37 dogs were included in the sacculectomy group and 44 in the comparator group. Dogs that had undergone sacculectomy were more likely to develop postoperative complications, with 18 of 37 developing complications, nine of which were moderate to severe. In the group without sacculectomy, nine of 44 dogs developed complications, of which one was severe. Different breed distribution between groups might also impact this outcome. CLINICAL SIGNIFICANCE The results suggest that sacculectomy might increase morbidity following brachycephalic airway surgery, but repeat studies are required to confirm this result. Further information is also required to determine whether the short-term risks of sacculectomy are outweighed by superior long-term functional outcome.
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Affiliation(s)
- J R Hughes
- Department of Veterinary Clinical Sciences, The Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
| | - B M Kaye
- Department of Veterinary Clinical Sciences, The Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
| | - A R Beswick
- Department of Veterinary Clinical Sciences, The Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
| | - G Ter Haar
- Department of Veterinary Clinical Sciences, The Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
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Oudelaar AM, Hanssen LL, Hardison RC, Kassouf MT, Hughes JR, Higgs DR. Between form and function: the complexity of genome folding. Hum Mol Genet 2017; 26:R208-R215. [PMID: 28977451 PMCID: PMC5886466 DOI: 10.1093/hmg/ddx306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 01/24/2023] Open
Abstract
It has been known for over a century that chromatin is not randomly distributed within the nucleus. However, the question of how DNA is folded and the influence of such folding on nuclear processes remain topics of intensive current research. A longstanding, unanswered question is whether nuclear organization is simply a reflection of nuclear processes such as transcription and replication, or whether chromatin is folded by independent mechanisms and this per se encodes function? Evidence is emerging that both may be true. Here, using the α-globin gene cluster as an illustrative model, we provide an overview of the most recent insights into the layers of genome organization across different scales and how this relates to gene activity.
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Affiliation(s)
- A. Marieke Oudelaar
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Lars L.P. Hanssen
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mira T. Kassouf
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Douglas R. Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
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Huang P, Keller CA, Giardine B, Grevet JD, Davies JOJ, Hughes JR, Kurita R, Nakamura Y, Hardison RC, Blobel GA. Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. Genes Dev 2017; 31:1704-1713. [PMID: 28916711 PMCID: PMC5647940 DOI: 10.1101/gad.303461.117] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/21/2017] [Indexed: 01/04/2023]
Abstract
In this study, Huang et al. compared the chromosomal architectures of fetal and adult human erythroblasts and found that, globally, chromatin structures and compartments A/B are highly similar at both developmental stages. Their results uncover a new critical regulatory region as a potential target for therapeutic genome editing for hemoglobinopathies and highlight the power of chromosome conformation analysis in discovering new cis control elements. Chromatin structure is tightly intertwined with transcription regulation. Here we compared the chromosomal architectures of fetal and adult human erythroblasts and found that, globally, chromatin structures and compartments A/B are highly similar at both developmental stages. At a finer scale, we detected distinct folding patterns at the developmentally controlled β-globin locus. Specifically, new fetal stage-specific contacts were uncovered between a region separating the fetal (γ) and adult (δ and β) globin genes (encompassing the HBBP1 and BGLT3 noncoding genes) and two distal chromosomal sites (HS5 and 3′HS1) that flank the locus. In contrast, in adult cells, the HBBP1–BGLT3 region contacts the embryonic ε-globin gene, physically separating the fetal globin genes from the enhancer (locus control region [LCR]). Deletion of the HBBP1 region in adult cells alters contact landscapes in ways more closely resembling those of fetal cells, including increased LCR–γ-globin contacts. These changes are accompanied by strong increases in γ-globin transcription. Notably, the effects of HBBP1 removal on chromatin architecture and gene expression closely mimic those of deleting the fetal globin repressor BCL11A, implicating BCL11A in the function of the HBBP1 region. Our results uncover a new critical regulatory region as a potential target for therapeutic genome editing for hemoglobinopathies and highlight the power of chromosome conformation analysis in discovering new cis control elements.
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Affiliation(s)
- Peng Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Jeremy D Grevet
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - James O J Davies
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Jim R Hughes
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Koto-ku, Tokyo 135-8521, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Schwessinger R, Suciu MC, McGowan SJ, Telenius J, Taylor S, Higgs DR, Hughes JR. Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints. Genome Res 2017; 27:1730-1742. [PMID: 28904015 PMCID: PMC5630036 DOI: 10.1101/gr.220202.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/07/2017] [Indexed: 12/22/2022]
Abstract
In the era of genome-wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory SNPs depend on inadequate knowledge of cell-specific DNA binding motifs. Here, we present Sasquatch, a new computational approach that uses DNase footprint data to estimate and visualize the effects of noncoding variants on transcription factor binding. Sasquatch performs a comprehensive k-mer-based analysis of DNase footprints to determine any k-mer's potential for protein binding in a specific cell type and how this may be changed by sequence variants. Therefore, Sasquatch uses an unbiased approach, independent of known transcription factor binding sites and motifs. Sasquatch only requires a single DNase-seq data set per cell type, from any genotype, and produces consistent predictions from data generated by different experimental procedures and at different sequence depths. Here we demonstrate the effectiveness of Sasquatch using previously validated functional SNPs and benchmark its performance against existing approaches. Sasquatch is available as a versatile webtool incorporating publicly available data, including the human ENCODE collection. Thus, Sasquatch provides a powerful tool and repository for prioritizing likely regulatory SNPs in the noncoding genome.
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Affiliation(s)
- Ron Schwessinger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Maria C Suciu
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Simon J McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Jelena Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Stephen Taylor
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Doug R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
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Yao X, Tan J, Lim KJ, Koh J, Ooi WF, Li Z, Huang D, Xing M, Chan YS, Qu JZ, Tay ST, Wijaya G, Lam YN, Hong JH, Lee-Lim AP, Guan P, Ng MSW, He CZ, Lin JS, Nandi T, Qamra A, Xu C, Myint SS, Davies JOJ, Goh JY, Loh G, Tan BC, Rozen SG, Yu Q, Tan IBH, Cheng CWS, Li S, Chang KTE, Tan PH, Silver DL, Lezhava A, Steger G, Hughes JR, Teh BT, Tan P. VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma. Cancer Discov 2017; 7:1284-1305. [DOI: 10.1158/2159-8290.cd-17-0375] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 07/19/2017] [Accepted: 08/25/2017] [Indexed: 11/16/2022]
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Jeziorska DM, Murray RJS, De Gobbi M, Gaentzsch R, Garrick D, Ayyub H, Chen T, Li E, Telenius J, Lynch M, Graham B, Smith AJH, Lund JN, Hughes JR, Higgs DR, Tufarelli C. DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease. Proc Natl Acad Sci U S A 2017; 114:E7526-E7535. [PMID: 28827334 PMCID: PMC5594649 DOI: 10.1073/pnas.1703087114] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human genome contains ∼30,000 CpG islands (CGIs). While CGIs associated with promoters nearly always remain unmethylated, many of the ∼9,000 CGIs lying within gene bodies become methylated during development and differentiation. Both promoter and intragenic CGIs may also become abnormally methylated as a result of genome rearrangements and in malignancy. The epigenetic mechanisms by which some CGIs become methylated but others, in the same cell, remain unmethylated in these situations are poorly understood. Analyzing specific loci and using a genome-wide analysis, we show that transcription running across CGIs, associated with specific chromatin modifications, is required for DNA methyltransferase 3B (DNMT3B)-mediated DNA methylation of many naturally occurring intragenic CGIs. Importantly, we also show that a subgroup of intragenic CGIs is not sensitive to this process of transcription-mediated methylation and that this correlates with their individual intrinsic capacity to initiate transcription in vivo. We propose a general model of how transcription could act as a primary determinant of the patterns of CGI methylation in normal development and differentiation, and in human disease.
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Affiliation(s)
- Danuta M Jeziorska
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Robert J S Murray
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
- Division of Medical Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, United Kingdom
| | - Marco De Gobbi
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Ricarda Gaentzsch
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - David Garrick
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Helena Ayyub
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, Division of Basic Science Research, The University of Texas M. D. Anderson Cancer Center, Smithville, TX 78957
| | - En Li
- China Novartis Institutes for BioMedical Research, Shanghai 201203, China
| | - Jelena Telenius
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Magnus Lynch
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Bryony Graham
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Andrew J H Smith
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
- Medical Research Council Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh EH16 4UU, United Kingdom
| | - Jonathan N Lund
- Division of Medical Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, United Kingdom
| | - Jim R Hughes
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom
| | - Douglas R Higgs
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford OX3 9DS, United Kingdom;
| | - Cristina Tufarelli
- Division of Medical Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, United Kingdom;
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Pasricha SR, Lim PJ, Duarte TL, Casu C, Oosterhuis D, Mleczko-Sanecka K, Suciu M, Da Silva AR, Al-Hourani K, Arezes J, McHugh K, Gooding S, Frost JN, Wray K, Santos A, Porto G, Repapi E, Gray N, Draper SJ, Ashley N, Soilleux E, Olinga P, Muckenthaler MU, Hughes JR, Rivella S, Milne TA, Armitage AE, Drakesmith H. Hepcidin is regulated by promoter-associated histone acetylation and HDAC3. Nat Commun 2017; 8:403. [PMID: 28864822 PMCID: PMC5581335 DOI: 10.1038/s41467-017-00500-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/04/2017] [Indexed: 12/21/2022] Open
Abstract
Hepcidin regulates systemic iron homeostasis. Suppression of hepcidin expression occurs physiologically in iron deficiency and increased erythropoiesis but is pathologic in thalassemia and hemochromatosis. Here we show that epigenetic events govern hepcidin expression. Erythropoiesis and iron deficiency suppress hepcidin via erythroferrone-dependent and -independent mechanisms, respectively, in vivo, but both involve reversible loss of H3K9ac and H3K4me3 at the hepcidin locus. In vitro, pan-histone deacetylase inhibition elevates hepcidin expression, and in vivo maintains H3K9ac at hepcidin-associated chromatin and abrogates hepcidin suppression by erythropoietin, iron deficiency, thalassemia, and hemochromatosis. Histone deacetylase 3 and its cofactor NCOR1 regulate hepcidin; histone deacetylase 3 binds chromatin at the hepcidin locus, and histone deacetylase 3 knockdown counteracts hepcidin suppression induced either by erythroferrone or by inhibiting bone morphogenetic protein signaling. In iron deficient mice, the histone deacetylase 3 inhibitor RGFP966 increases hepcidin, and RNA sequencing confirms hepcidin is one of the genes most differentially regulated by this drug in vivo. We conclude that suppression of hepcidin expression involves epigenetic regulation by histone deacetylase 3.Hepcidin controls systemic iron levels by inhibiting intestinal iron absorption and iron recycling. Here, Pasricha et al. demonstrate that the hepcidin-chromatin locus displays HDAC3-mediated reversible epigenetic modifications during both erythropoiesis and iron deficiency.
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Affiliation(s)
- Sant-Rayn Pasricha
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Department of Medicine, The Royal Melbourne Hospital, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, 3010, Australia.
| | - Pei Jin Lim
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Tiago L Duarte
- Instituto de Investigação e Inovação em Saúde and IBMC-Instituto de Biologia Molecular e Celular, University of Porto, 4200-135, Porto, Portugal
| | - Carla Casu
- Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Dorenda Oosterhuis
- Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, 9700-AD, Groningen, The Netherlands
| | - Katarzyna Mleczko-Sanecka
- Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg; and Molecular Medicine Partnership Unit, Heidelberg, 69117, Germany
- International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
| | - Maria Suciu
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana Rita Da Silva
- Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg; and Molecular Medicine Partnership Unit, Heidelberg, 69117, Germany
| | - Kinda Al-Hourani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - João Arezes
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Kirsty McHugh
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Sarah Gooding
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joe N Frost
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Katherine Wray
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana Santos
- Instituto de Investigação e Inovação em Saúde and IBMC-Instituto de Biologia Molecular e Celular, University of Porto, 4200-135, Porto, Portugal
| | - Graça Porto
- Instituto de Investigação e Inovação em Saúde and IBMC-Instituto de Biologia Molecular e Celular, University of Porto, 4200-135, Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, University of Porto Portugal, 4050-313, Porto, Portugal
| | - Emmanouela Repapi
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Nicki Gray
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Simon J Draper
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Neil Ashley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Elizabeth Soilleux
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DU, UK
- Division of Cellular and Molecular Pathology, Department of Pathology, Cambridge University, Cambridge, CB2 0QQ, UK
| | - Peter Olinga
- Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, 9700-AD, Groningen, The Netherlands
| | - Martina U Muckenthaler
- Department of Pediatric Hematology, Oncology and Immunology, University of Heidelberg; and Molecular Medicine Partnership Unit, Heidelberg, 69117, Germany
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Stefano Rivella
- Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Andrew E Armitage
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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44
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Hanssen LLP, Kassouf MT, Oudelaar AM, Biggs D, Preece C, Downes DJ, Gosden M, Sharpe JA, Sloane-Stanley JA, Hughes JR, Davies B, Higgs DR. Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nat Cell Biol 2017; 19:952-961. [PMID: 28737770 PMCID: PMC5540176 DOI: 10.1038/ncb3573] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/15/2017] [Indexed: 12/16/2022]
Abstract
The genome is organized via CTCF-cohesin-binding sites, which partition chromosomes into 1-5 megabase (Mb) topologically associated domains (TADs), and further into smaller sub-domains (sub-TADs). Here we examined in vivo an ∼80 kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ∼1 Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF-cohesin sites that are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. Whereas the α-globin regulatory elements normally act solely on promoters downstream of the enhancers, removal of a conserved upstream CTCF-cohesin boundary extends the sub-TAD to adjacent upstream CTCF-cohesin-binding sites. The α-globin enhancers now interact with the flanking chromatin, upregulating expression of genes within this extended sub-TAD. Rather than acting solely as a barrier to chromatin modification, CTCF-cohesin boundaries in this sub-TAD delimit the region of chromatin to which enhancers have access and within which they interact with receptive promoters.
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Affiliation(s)
- Lars L P Hanssen
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Mira T Kassouf
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Daniel Biggs
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Chris Preece
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Matthew Gosden
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Jacqueline A Sharpe
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | | | - Jim R Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Benjamin Davies
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
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45
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Simon CS, Downes DJ, Gosden ME, Telenius J, Higgs DR, Hughes JR, Costello I, Bikoff EK, Robertson EJ. Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo. Development 2017; 144:1249-1260. [PMID: 28174238 PMCID: PMC5399628 DOI: 10.1242/dev.147322] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/25/2017] [Indexed: 12/28/2022]
Abstract
The T-box transcription factor (TF) Eomes is a key regulator of cell fate decisions during early mouse development. The cis-acting regulatory elements that direct expression in the anterior visceral endoderm (AVE), primitive streak (PS) and definitive endoderm (DE) have yet to be defined. Here, we identified three gene-proximal enhancer-like sequences (PSE_a, PSE_b and VPE) that faithfully activate tissue-specific expression in transgenic embryos. However, targeted deletion experiments demonstrate that PSE_a and PSE_b are dispensable, and only VPE is required for optimal Eomes expression in vivo. Embryos lacking this enhancer display variably penetrant defects in anterior-posterior axis orientation and DE formation. Chromosome conformation capture experiments reveal VPE-promoter interactions in embryonic stem cells (ESCs), prior to gene activation. The locus resides in a large (500 kb) pre-formed compartment in ESCs and activation during DE differentiation occurs in the absence of 3D structural changes. ATAC-seq analysis reveals that VPE, PSE_a and four additional putative enhancers display increased chromatin accessibility in DE that is associated with Smad2/3 binding coincident with transcriptional activation. By contrast, activation of the Eomes target genes Foxa2 and Lhx1 is associated with higher order chromatin reorganisation. Thus, diverse regulatory mechanisms govern activation of lineage specifying TFs during early development. Summary: Expression of the mouse T-box factor Eomes is controlled by a key gene-proximal enhancer-like element, with changes in chromatin accessibility influencing its activity in definitive endoderm.
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Affiliation(s)
- Claire S Simon
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Matthew E Gosden
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Ita Costello
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Elizabeth K Bikoff
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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46
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Davies JOJ, Oudelaar AM, Higgs DR, Hughes JR. How best to identify chromosomal interactions: a comparison of approaches. Nat Methods 2017; 14:125-134. [PMID: 28139673 DOI: 10.1038/nmeth.4146] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/20/2016] [Indexed: 12/28/2022]
Abstract
Chromosome conformation capture (3C) methods are central to understanding the link between nuclear structure and function, and the physical interactions between distal regulatory elements and promoters. However, no one method is appropriate to address all biological questions, as each variant differs markedly in resolution, reproducibility, throughput and biases. A thorough appreciation of the strengths and weaknesses of each technique is critical when choosing the correct method for a specific application or for gauging how best to interpret different sources of data. In addition, the analysis method must be carefully considered, as this choice can profoundly affect the output. In this Review, we describe and compare the different available 3C-based approaches, with a focus on the analysis of mammalian genomes.
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Affiliation(s)
- James O J Davies
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - A Marieke Oudelaar
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - Douglas R Higgs
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | - Jim R Hughes
- Medical Research Council (MRC) Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
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47
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Oudelaar AM, Downes DJ, Davies JOJ, Hughes JR. Low-input Capture-C: A Chromosome Conformation Capture Assay to Analyze Chromatin Architecture in Small Numbers of Cells. Bio Protoc 2017; 7:e2645. [PMID: 29270442 DOI: 10.21769/bioprotoc.2645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This protocol describes two new low-input Capture-C approaches that can generate high-quality 3C interaction profiles from 10,000-20,000 cells, depending on the resolution used for analysis.
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Affiliation(s)
- A Marieke Oudelaar
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Damien J Downes
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - James O J Davies
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Jim R Hughes
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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48
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Godfrey L, Kerry J, Thorne R, Repapi E, Davies JOJ, Tapia M, Ballabio E, Hughes JR, Geng H, Konopleva M, Milne TA. MLL-AF4 binds directly to a BCL-2 specific enhancer and modulates H3K27 acetylation. Exp Hematol 2016; 47:64-75. [PMID: 27856324 PMCID: PMC5333536 DOI: 10.1016/j.exphem.2016.11.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/21/2016] [Accepted: 11/02/2016] [Indexed: 11/15/2022]
Abstract
Survival rates for children and adults carrying mutations in the Mixed Lineage Leukemia (MLL) gene continue to have a very poor prognosis. The most common MLL mutation in acute lymphoblastic leukemia is the t(4;11)(q21;q23) chromosome translocation that fuses MLL in-frame with the AF4 gene producing MLL-AF4 and AF4-MLL fusion proteins. Previously, we found that MLL-AF4 binds to the BCL-2 gene and directly activates it through DOT1L recruitment and increased H3K79me2/3 levels. In the study described here, we performed a detailed analysis of MLL-AF4 regulation of the entire BCL-2 family. By measuring nascent RNA production in MLL-AF4 knockdowns, we found that of all the BCL-2 family genes, MLL-AF4 directly controls the active transcription of both BCL-2 and MCL-1 and also represses BIM via binding of the polycomb group repressor 1 (PRC1) complex component CBX8. We further analyzed MLL-AF4 activation of the BCL-2 gene using Capture-C and identified a BCL-2-specific enhancer, consisting of two clusters of H3K27Ac at the 3' end of the gene. Loss of MLL-AF4 activity results in a reduction of H3K79me3 levels in the gene body and H3K27Ac levels at the 3' BCL-2 enhancer, revealing a novel regulatory link between these two histone marks and MLL-AF4-mediated activation of BCL-2.
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Affiliation(s)
- Laura Godfrey
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Jon Kerry
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Ross Thorne
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Emmanouela Repapi
- Weatherall Institute of Molecular Medicine, Computational Biology Research Group, University of Oxford, Headington, Oxford, UK
| | - James O J Davies
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Marta Tapia
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Erica Ballabio
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Jim R Hughes
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK
| | - Huimin Geng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
| | - Marina Konopleva
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Thomas A Milne
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, Headington, Oxford, UK.
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49
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Platt JL, Salama R, Smythies J, Choudhry H, Davies JO, Hughes JR, Ratcliffe PJ, Mole DR. Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters. EMBO Rep 2016; 17:1410-1421. [PMID: 27506891 PMCID: PMC5048371 DOI: 10.15252/embr.201642198] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 06/20/2016] [Accepted: 07/15/2016] [Indexed: 01/22/2023] Open
Abstract
Hypoxia-inducible factor (HIF) directs an extensive transcriptional cascade that transduces numerous adaptive responses to hypoxia. Pan-genomic analyses, using chromatin immunoprecipitation and transcript profiling, have revealed large numbers of HIF-binding sites that are generally associated with hypoxia-inducible transcripts, even over long chromosomal distances. However, these studies do not define the specific targets of HIF-binding sites and do not reveal how induction of HIF affects chromatin conformation over distantly connected functional elements. To address these questions, we deployed a recently developed chromosome conformation assay that enables simultaneous high-resolution analyses from multiple viewpoints. These assays defined specific long-range interactions between intergenic HIF-binding regions and one or more promoters of hypoxia-inducible genes, revealing the existence of multiple enhancer-promoter, promoter-enhancer, and enhancer-enhancer interactions. However, neither short-term activation of HIF by hypoxia, nor long-term stabilization of HIF in von Hippel-Lindau (VHL)-defective cells greatly alters these interactions, indicating that at least under these conditions, HIF can operate on preexisting patterns of chromatin-chromatin interactions that define potential transcriptional targets and permit rapid gene activation by hypoxic stress.
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Affiliation(s)
- James L Platt
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, UK
| | - Rafik Salama
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, UK
| | - James Smythies
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, UK
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Center of Innovation in Personalized Medicine King Fahd Center for Medical Research King Abdulaziz University, Jeddah, Saudi Arabia
| | - James Oj Davies
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine University of Oxford, Oxford, UK
| | - Jim R Hughes
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine University of Oxford, Oxford, UK
| | | | - David R Mole
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, UK
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50
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Hay D, Hughes JR, Babbs C, Davies JO, Graham BJ, Hanssen L, Kassouf MT, Marieke Oudelaar AM, Sharpe JA, Suciu MC, Telenius J, Williams R, Rode C, Li PS, Pennacchio LA, Sloane-Stanley JA, Ayyub H, Butler S, Sauka-Spengler T, Gibbons RJ, Smith AJ, Wood WG, Higgs DR. Genetic dissection of the α-globin super-enhancer in vivo. Nat Genet 2016; 48:895-903. [PMID: 27376235 PMCID: PMC5058437 DOI: 10.1038/ng.3605] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/01/2016] [Indexed: 12/18/2022]
Abstract
Many genes determining cell identity are regulated by clusters of Mediator-bound enhancer elements collectively referred to as super-enhancers. These super-enhancers have been proposed to manifest higher-order properties important in development and disease. Here we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer individually and in informative combinations, we demonstrate that each constituent enhancer seems to act independently and in an additive fashion with respect to hematological phenotype, gene expression, chromatin structure and chromosome conformation, without clear evidence of synergistic or higher-order effects. Our study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation.
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Affiliation(s)
- Deborah Hay
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - James O.J. Davies
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Bryony J. Graham
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Lars Hanssen
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Mira T. Kassouf
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | | | - Jacqueline A Sharpe
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Maria C. Suciu
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Ruth Williams
- Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Pik-Shan Li
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Len A. Pennacchio
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California
| | | | - Helena Ayyub
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Sue Butler
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | | | - Richard J. Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Andrew J.H. Smith
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - William G. Wood
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Douglas R. Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
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