1
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Payne S, Neal A, De Val S. Transcription factors regulating vasculogenesis and angiogenesis. Dev Dyn 2024; 253:28-58. [PMID: 36795082 PMCID: PMC10952167 DOI: 10.1002/dvdy.575] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Transcription factors (TFs) play a crucial role in regulating the dynamic and precise patterns of gene expression required for the initial specification of endothelial cells (ECs), and during endothelial growth and differentiation. While sharing many core features, ECs can be highly heterogeneous. Differential gene expression between ECs is essential to pattern the hierarchical vascular network into arteries, veins and capillaries, to drive angiogenic growth of new vessels, and to direct specialization in response to local signals. Unlike many other cell types, ECs have no single master regulator, instead relying on differing combinations of a necessarily limited repertoire of TFs to achieve tight spatial and temporal activation and repression of gene expression. Here, we will discuss the cohort of TFs known to be involved in directing gene expression during different stages of mammalian vasculogenesis and angiogenesis, with a primary focus on development.
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Affiliation(s)
- Sophie Payne
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Alice Neal
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Sarah De Val
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
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2
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Deleuze V, Garcia L, Rouaisnel B, Salma M, Kinoo A, Andrieu-Soler C, Soler E. Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions. iScience 2023; 26:107641. [PMID: 37670779 PMCID: PMC10475484 DOI: 10.1016/j.isci.2023.107641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/09/2023] [Accepted: 08/11/2023] [Indexed: 09/07/2023] Open
Abstract
Targeted genome editing holds great promise in biology. However, efficient genome modification, including gene knock-in (KI), remains an unattained goal in multiple cell types and loci due to poor transfection efficiencies and low target genes expression, impeding the positive selection of recombined cells. Here, we describe a genome editing approach to achieve efficient gene targeting using hard to transfect erythroid cell lines. We demonstrate robust fluorescent protein KI efficiency in low expressed transcription factor (TF) genes (e.g., Myb or Zeb1). We further show the ability to target two independent loci in individual cells, exemplified by MYB-GFP and NuMA-Cherry double KI, allowing multicolor labeling of regulatory factors at physiological endogenous levels. Our KI tagging approach allowed us to perform genome-wide TF analysis at increased signal-to-noise ratios, and highlighted previously unidentified MYB target genes and pathways. Overall, we establish a versatile CRISPR-Cas9-based platform, offering attractive opportunities for the dissection of the erythroid differentiation process.
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Affiliation(s)
| | - Leonor Garcia
- IGMM, University Montpellier, CNRS, Montpellier, France
| | | | - Mohammad Salma
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
| | - Alexia Kinoo
- IGMM, University Montpellier, CNRS, Montpellier, France
| | - Charlotte Andrieu-Soler
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
| | - Eric Soler
- IGMM, University Montpellier, CNRS, Montpellier, France
- Laboratory of Excellence GR-Ex, Université de Paris, Paris, France
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3
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Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L, Guerrero JA, Kaptoge S, Knight JC, Meacham S, Sambrook J, Seyres D, Stegle O, Verboon JM, Walter K, Watkins NA, Danesh J, Roberts DJ, Di Angelantonio E, Sankaran VG, Frontini M, Burgess S, Kuijpers T, Peters JE, Butterworth AS, Ouwehand WH, Soranzo N, Astle WJ. A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology. Nat Commun 2023; 14:5023. [PMID: 37596262 PMCID: PMC10439125 DOI: 10.1038/s41467-023-40679-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/07/2023] [Indexed: 08/20/2023] Open
Abstract
Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and α-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.
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Affiliation(s)
- Parsa Akbari
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
- Medical Research Council Biostatistics Unit, University of Cambridge, East Forvie Building, Cambridge Biomedical Campus, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
| | - Dragana Vuckovic
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Luca Stefanucci
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Tao Jiang
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
| | - Kousik Kundu
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Roman Kreuzhuber
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, 1 Blackfan Circle, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, 77 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Janine H Collins
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- Department of Haematology, Barts Health National Health Service Trust, London, E1 1BB, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Luigi Grassi
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Institute for Health and Care Research Cambridge BioResource, Box 229, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Jose A Guerrero
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Stephen Kaptoge
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Stuart Meacham
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jennifer Sambrook
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Institute for Health and Care Research Cambridge BioResource, Box 229, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Denis Seyres
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Institute for Health and Care Research Cambridge BioResource, Box 229, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, 1 Blackfan Circle, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Klaudia Walter
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Nicholas A Watkins
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - David J Roberts
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Headley Way, Headington, Oxford, OX3 9DU, UK
- National Institute for Health Research Oxford Biomedical Research Centre-Haematology Theme, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
- National Health Service Blood and Transplant, Oxford Centre, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
- Health Data Science Research Centre, Fondazione Human Technopole, Viale Rita Levi Montalcini 1, Milan, 20157, Italy
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, 1 Blackfan Circle, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, RILD Building, Barrack Road, Exeter, EX2 5DW, UK
| | - Stephen Burgess
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK
- Medical Research Council Biostatistics Unit, University of Cambridge, East Forvie Building, Cambridge Biomedical Campus, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK
| | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Disease, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, CB2 0PT, UK
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Sanquin, University of Amsterdam, Amsterdam, Netherlands
| | - James E Peters
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Immunology and Inflammation, Imperial College London, Commonwealth Building, The Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK.
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, CB2 0BB, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.
- Department of Haematology, University College London Hospitals, WC1E 6AS, London, UK.
| | - Nicole Soranzo
- Department of Human Genetics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK.
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Genomics Research Centre, Fondazione Human Technopole, Viale Rita Levi Montalcini 1, Milan, 20157, Italy.
| | - William J Astle
- Medical Research Council Biostatistics Unit, University of Cambridge, East Forvie Building, Cambridge Biomedical Campus, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK.
- The National Institute for Health and Care Research Blood and Transplant Unit in Donor Health and Genomics, Strangeways Research Laboratory, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge, CB1 8RN, UK.
- National Health Service Blood and Transplant, Cambridge Centre, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.
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4
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Sharma A, Mistriel-Zerbib S, Najar RA, Engal E, Bentata M, Taqatqa N, Dahan S, Cohen K, Jaffe-Herman S, Geminder O, Baker M, Nevo Y, Plaschkes I, Kay G, Drier Y, Berger M, Salton M. Isoforms of the TAL1 transcription factor have different roles in hematopoiesis and cell growth. PLoS Biol 2023; 21:e3002175. [PMID: 37379322 DOI: 10.1371/journal.pbio.3002175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/30/2023] [Indexed: 06/30/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) protein 1 (TAL1) is a central transcription factor in hematopoiesis. The timing and level of TAL1 expression orchestrate the differentiation to specialized blood cells and its overexpression is a common cause of T-ALL. Here, we studied the 2 protein isoforms of TAL1, short and long, which are generated by the use of alternative promoters as well as by alternative splicing. We analyzed the expression of each isoform by deleting an enhancer or insulator, or by opening chromatin at the enhancer location. Our results show that each enhancer promotes expression from a specific TAL1 promoter. Expression from a specific promoter gives rise to a unique 5' UTR with differential regulation of translation. Moreover, our study suggests that the enhancers regulate TAL1 exon 3 alternative splicing by inducing changes in the chromatin at the splice site, which we demonstrate is mediated by KMT2B. Furthermore, our results indicate that TAL1-short binds more strongly to TAL1 E-protein partners and functions as a stronger transcription factor than TAL1-long. Specifically TAL1-short has a unique transcription signature promoting apoptosis. Finally, when we expressed both isoforms in mice bone marrow, we found that while overexpression of both isoforms prevents lymphoid differentiation, expression of TAL-short alone leads to hematopoietic stem cell exhaustion. Furthermore, we found that TAL1-short promoted erythropoiesis and reduced cell survival in the CML cell line K562. While TAL1 and its partners are considered promising therapeutic targets in the treatment of T-ALL, our results show that TAL1-short could act as a tumor suppressor and suggest that altering TAL1 isoform's ratio could be a preferred therapeutic approach.
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Affiliation(s)
- Aveksha Sharma
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shani Mistriel-Zerbib
- Faculty of Medicine, The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rauf Ahmad Najar
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eden Engal
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mercedes Bentata
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nadeen Taqatqa
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sara Dahan
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Klil Cohen
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Jaffe-Herman
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ophir Geminder
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mai Baker
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gillian Kay
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yotam Drier
- Faculty of Medicine, The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael Berger
- Faculty of Medicine, The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maayan Salton
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
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5
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Garcia-Segura ME, Durainayagam BR, Liggi S, Graça G, Jimenez B, Dehghan A, Tzoulaki I, Karaman I, Elliott P, Griffin JL. Pathway-based integration of multi-omics data reveals lipidomics alterations validated in an Alzheimer's disease mouse model and risk loci carriers. J Neurochem 2023; 164:57-76. [PMID: 36326588 PMCID: PMC10107183 DOI: 10.1111/jnc.15719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
Alzheimer's disease (AD) is a highly prevalent neurodegenerative disorder. Despite increasing evidence of the importance of metabolic dysregulation in AD, the underlying metabolic changes that may impact amyloid plaque formation are not understood, particularly for late-onset AD. This study analyzed genome-wide association studies (GWAS), transcriptomics, and proteomics data obtained from several data repositories to obtain differentially expressed (DE) multi-omics elements in mouse models of AD. We characterized the metabolic modulation in these data sets using gene ontology, transcription factor, pathway, and cell-type enrichment analyses. A predicted lipid signature was extracted from genome-scale metabolic networks (GSMN) and subsequently validated in a lipidomic data set derived from cortical tissue of ABCA-7 null mice, a mouse model of one of the genes associated with late-onset AD. Moreover, a metabolome-wide association study (MWAS) was performed to further characterize the association between dysregulated lipid metabolism in human blood serum and genes associated with AD risk. We found 203 DE transcripts, 164 DE proteins, and 58 DE GWAS-derived mouse orthologs associated with significantly enriched metabolic biological processes. Lipid and bioenergetic metabolic pathways were significantly over-represented across the AD multi-omics data sets. Microglia and astrocytes were significantly enriched in the lipid-predominant AD-metabolic transcriptome. We also extracted a predicted lipid signature that was validated and robustly modeled class separation in the ABCA7 mice cortical lipidome, with 11 of these lipid species exhibiting statistically significant modulations. MWAS revealed 298 AD single nucleotide polymorphisms-metabolite associations, of which 70% corresponded to lipid classes. These results support the importance of lipid metabolism dysregulation in AD and highlight the suitability of mapping AD multi-omics data into GSMNs to identify metabolic alterations.
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Affiliation(s)
- Monica Emili Garcia-Segura
- Department of Brain Sciences, Imperial College London, London, UK.,Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Brenan R Durainayagam
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.,UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
| | - Sonia Liggi
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Gonçalo Graça
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Beatriz Jimenez
- Section of Bioanalytical Chemistry and the National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Abbas Dehghan
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,MRC Centre for Environment and Health, Imperial College London, London, UK
| | - Ioanna Tzoulaki
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,National Institute for Health Research Imperial Biomedical Research Centre, Imperial College London, UK.,Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Ibrahim Karaman
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Paul Elliott
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,MRC Centre for Environment and Health, Imperial College London, London, UK.,National Institute for Health Research Imperial Biomedical Research Centre, Imperial College London, UK
| | - Julian L Griffin
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.,UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK.,Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,The Rowett Institute, University of Aberdeen, Aberdeen, Scotland
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6
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Garcia-Segura ME, Durainayagam BR, Liggi S, Graça G, Jimenez B, Dehghan A, Tzoulaki I, Karaman I, Elliott P, Griffin JL. Pathway-based integration of multi-omics data reveals lipidomics alterations validated in an Alzheimer's disease mouse model and risk loci carriers. J Neurochem 2023. [PMID: 36326588 DOI: 10.1101/2021.05.10.21255052v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Alzheimer's disease (AD) is a highly prevalent neurodegenerative disorder. Despite increasing evidence of the importance of metabolic dysregulation in AD, the underlying metabolic changes that may impact amyloid plaque formation are not understood, particularly for late-onset AD. This study analyzed genome-wide association studies (GWAS), transcriptomics, and proteomics data obtained from several data repositories to obtain differentially expressed (DE) multi-omics elements in mouse models of AD. We characterized the metabolic modulation in these data sets using gene ontology, transcription factor, pathway, and cell-type enrichment analyses. A predicted lipid signature was extracted from genome-scale metabolic networks (GSMN) and subsequently validated in a lipidomic data set derived from cortical tissue of ABCA-7 null mice, a mouse model of one of the genes associated with late-onset AD. Moreover, a metabolome-wide association study (MWAS) was performed to further characterize the association between dysregulated lipid metabolism in human blood serum and genes associated with AD risk. We found 203 DE transcripts, 164 DE proteins, and 58 DE GWAS-derived mouse orthologs associated with significantly enriched metabolic biological processes. Lipid and bioenergetic metabolic pathways were significantly over-represented across the AD multi-omics data sets. Microglia and astrocytes were significantly enriched in the lipid-predominant AD-metabolic transcriptome. We also extracted a predicted lipid signature that was validated and robustly modeled class separation in the ABCA7 mice cortical lipidome, with 11 of these lipid species exhibiting statistically significant modulations. MWAS revealed 298 AD single nucleotide polymorphisms-metabolite associations, of which 70% corresponded to lipid classes. These results support the importance of lipid metabolism dysregulation in AD and highlight the suitability of mapping AD multi-omics data into GSMNs to identify metabolic alterations.
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Affiliation(s)
- Monica Emili Garcia-Segura
- Department of Brain Sciences, Imperial College London, London, UK
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Brenan R Durainayagam
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
| | - Sonia Liggi
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Gonçalo Graça
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Beatriz Jimenez
- Section of Bioanalytical Chemistry and the National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Abbas Dehghan
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- MRC Centre for Environment and Health, Imperial College London, London, UK
| | - Ioanna Tzoulaki
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, Imperial College London, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Ibrahim Karaman
- Section of Bioinformatics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Paul Elliott
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- MRC Centre for Environment and Health, Imperial College London, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, Imperial College London, UK
| | - Julian L Griffin
- Section of Biomolecular Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- UK-Dementia Research Institute (UK-DRI) at Imperial College London, London, UK
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- The Rowett Institute, University of Aberdeen, Aberdeen, Scotland
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7
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Cell landscape of larval and adult Xenopus laevis at single-cell resolution. Nat Commun 2022; 13:4306. [PMID: 35879314 PMCID: PMC9314398 DOI: 10.1038/s41467-022-31949-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
The rapid development of high-throughput single-cell RNA sequencing technology offers a good opportunity to dissect cell heterogeneity of animals. A large number of organism-wide single-cell atlases have been constructed for vertebrates such as Homo sapiens, Macaca fascicularis, Mus musculus and Danio rerio. However, an intermediate taxon that links mammals to vertebrates of more ancient origin is still lacking. Here, we construct the first Xenopus cell landscape to date, including larval and adult organs. Common cell lineage-specific transcription factors have been identified in vertebrates, including fish, amphibians and mammals. The comparison of larval and adult erythrocytes identifies stage-specific hemoglobin subtypes, as well as a common type of cluster containing both larval and adult hemoglobin, mainly at NF59. In addition, cell lineages originating from all three layers exhibits both antigen processing and presentation during metamorphosis, indicating a common regulatory mechanism during metamorphosis. Overall, our study provides a large-scale resource for research on Xenopus metamorphosis and adult organs.
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8
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Differential Etv2 threshold requirement for endothelial and erythropoietic development. Cell Rep 2022; 39:110881. [PMID: 35649376 PMCID: PMC9203129 DOI: 10.1016/j.celrep.2022.110881] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 02/23/2022] [Accepted: 05/06/2022] [Indexed: 11/21/2022] Open
Abstract
Endothelial and erythropoietic lineages arise from a common developmental progenitor. Etv2 is a master transcriptional regulator required for the development of both lineages. However, the mechanisms through which Etv2 initiates the gene-regulatory networks (GRNs) for endothelial and erythropoietic specification and how the two GRNs diverge downstream of Etv2 remain incompletely understood. Here, by analyzing a hypomorphic Etv2 mutant, we demonstrate different threshold requirements for initiation of the downstream GRNs for endothelial and erythropoietic development. We show that Etv2 functions directly in a coherent feedforward transcriptional network for vascular endothelial development, and a low level of Etv2 expression is sufficient to induce and sustain the endothelial GRN. In contrast, Etv2 induces the erythropoietic GRN indirectly via activation of Tal1, which requires a significantly higher threshold of Etv2 to initiate and sustain erythropoietic development. These results provide important mechanistic insight into the divergence of the endothelial and erythropoietic lineages.
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9
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Wells M, Steiner L. Epigenetic and Transcriptional Control of Erythropoiesis. Front Genet 2022; 13:805265. [PMID: 35330735 PMCID: PMC8940284 DOI: 10.3389/fgene.2022.805265] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/16/2022] [Indexed: 12/21/2022] Open
Abstract
Erythropoiesis is a process of enormous magnitude, with the average person generating two to three million red cells every second. Erythroid progenitors start as large cells with large nuclei, and over the course of three to four cell divisions they undergo a dramatic decrease in cell size accompanied by profound nuclear condensation, which culminates in enucleation. As maturing erythroblasts are undergoing these dramatic phenotypic changes, they accumulate hemoglobin and express high levels of other erythroid-specific genes, while silencing much of the non-erythroid transcriptome. These phenotypic and gene expression changes are associated with distinct changes in the chromatin landscape, and require close coordination between transcription factors and epigenetic regulators, as well as precise regulation of RNA polymerase II activity. Disruption of these processes are associated with inherited anemias and myelodysplastic syndromes. Here, we review the epigenetic mechanisms that govern terminal erythroid maturation, and their role in human disease.
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Affiliation(s)
- Maeve Wells
- Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Laurie Steiner
- Department of Pediatrics, University of Rochester, Rochester, NY, United States
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10
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Dey S, Lee J, Noguchi CT. Erythropoietin Non-hematopoietic Tissue Response and Regulation of Metabolism During Diet Induced Obesity. Front Pharmacol 2021; 12:725734. [PMID: 34603036 PMCID: PMC8479821 DOI: 10.3389/fphar.2021.725734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022] Open
Abstract
Erythropoietin (EPO) receptor (EPOR) determines EPO response. High level EPOR on erythroid progenitor cells gives rise to EPO regulated production of red blood cells. Animal models provide evidence for EPO activity in non-hematopoietic tissue mediated by EPOR expression. Beyond erythropoiesis, EPO activity includes neuroprotection in brain ischemia and trauma, endothelial nitric oxide production and cardioprotection, skeletal muscle wound healing, and context dependent bone remodeling affecting bone repair or bone loss. This review highlights examples of EPO protective activity in select non-hematopoietic tissue with emphasis on metabolic response mediated by EPOR expression in fat and brain and sex-specific regulation of fat mass and inflammation associated with diet induced obesity. Endogenous EPO maintains glucose and insulin tolerance and protects against fat mass accumulation and inflammation. Accompanying the increase in erythropoiesis with EPO treatment is improved glucose tolerance and insulin response. During high fat diet feeding, EPO also decreases fat mass accumulation in male mice. The increased white adipose tissue inflammation and macrophage infiltration associated with diet induced obesity are also reduced with EPO treatment with a shift toward an anti-inflammatory state and decreased inflammatory cytokine production. In female mice the protective effect of estrogen against obesity supersedes EPO regulation of fat mass and inflammation, and requires estrogen receptor alpha activity. In brain, EPOR expression in the hypothalamus localizes to proopiomelanocortin neurons in the arcuate nucleus that promotes a lean phenotype. EPO stimulation of proopiomelanocortin neurons increases STAT3 signaling and production of proopiomelanocortin. Cerebral EPO contributes to metabolic response, and elevated brain EPO reduces fat mass and hypothalamus inflammation during diet induced obesity in male mice without affecting EPO stimulated erythropoiesis. Ovariectomy abrogates the sex-specific metabolic response of brain EPO. The sex-dimorphic EPO metabolic response associated with fat mass accumulation and inflammation during diet induced obesity provide evidence for crosstalk between estrogen and EPO in their anti-obesity potential in female mice mediated in part via tissue specific response in brain and white adipose tissue. Endogenous and exogenous EPO response in non-hematopoietic tissue demonstrated in animal models suggests additional activity by which EPO treatment may affect human health beyond increased erythropoiesis.
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Affiliation(s)
- Soumyadeep Dey
- Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jeeyoung Lee
- Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Constance T Noguchi
- Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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11
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Mechanisms of Binding Specificity among bHLH Transcription Factors. Int J Mol Sci 2021; 22:ijms22179150. [PMID: 34502060 PMCID: PMC8431614 DOI: 10.3390/ijms22179150] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
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12
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Ullah F, Ben-Hur A. A self-attention model for inferring cooperativity between regulatory features. Nucleic Acids Res 2021; 49:e77. [PMID: 33950192 PMCID: PMC8287919 DOI: 10.1093/nar/gkab349] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 11/14/2022] Open
Abstract
Deep learning has demonstrated its predictive power in modeling complex biological phenomena such as gene expression. The value of these models hinges not only on their accuracy, but also on the ability to extract biologically relevant information from the trained models. While there has been much recent work on developing feature attribution methods that discover the most important features for a given sequence, inferring cooperativity between regulatory elements, which is the hallmark of phenomena such as gene expression, remains an open problem. We present SATORI, a Self-ATtentiOn based model to detect Regulatory element Interactions. Our approach combines convolutional layers with a self-attention mechanism that helps us capture a global view of the landscape of interactions between regulatory elements in a sequence. A comprehensive evaluation demonstrates the ability of SATORI to identify numerous statistically significant TF-TF interactions, many of which have been previously reported. Our method is able to detect higher numbers of experimentally verified TF-TF interactions than existing methods, and has the advantage of not requiring a computationally expensive post-processing step. Finally, SATORI can be used for detection of any type of feature interaction in models that use a similar attention mechanism, and is not limited to the detection of TF-TF interactions.
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Affiliation(s)
- Fahad Ullah
- Department of Computer Science, Colorado State University, Fort Collins, CO 80523, USA
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, CO 80523, USA
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13
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A Positive Regulatory Feedback Loop between EKLF/KLF1 and TAL1/SCL Sustaining the Erythropoiesis. Int J Mol Sci 2021; 22:ijms22158024. [PMID: 34360789 PMCID: PMC8347936 DOI: 10.3390/ijms22158024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/25/2022] Open
Abstract
The erythroid Krüppel-like factor EKLF/KLF1 is a hematopoietic transcription factor binding to the CACCC DNA motif and participating in the regulation of erythroid differentiation. With combined use of microarray-based gene expression profiling and the promoter-based ChIP-chip assay of E14.5 fetal liver cells from wild type (WT) and EKLF-knockout (Eklf−/−) mouse embryos, we identified the pathways and direct target genes activated or repressed by EKLF. This genome-wide study together with the molecular/cellular analysis of the mouse erythroleukemic cells (MEL) indicate that among the downstream direct target genes of EKLF is Tal1/Scl. Tal1/Scl encodes another DNA-binding hematopoietic transcription factor TAL1/SCL, known to be an Eklf activator and essential for definitive erythroid differentiation. Further identification of the authentic Tal gene promoter in combination with the in vivo genomic footprinting approach and DNA reporter assay demonstrate that EKLF activates the Tal gene through binding to a specific CACCC motif located in its promoter. These data establish the existence of a previously unknow positive regulatory feedback loop between two DNA-binding hematopoietic transcription factors, which sustains mammalian erythropoiesis.
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14
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A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker. Nat Commun 2021; 12:3806. [PMID: 34155213 PMCID: PMC8217497 DOI: 10.1038/s41467-021-23980-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/19/2021] [Indexed: 02/08/2023] Open
Abstract
Many single nucleotide variants (SNVs) associated with human traits and genetic diseases are thought to alter the activity of existing regulatory elements. Some SNVs may also create entirely new regulatory elements which change gene expression, but the mechanism by which they do so is largely unknown. Here we show that a single base change in an otherwise unremarkable region of the human α-globin cluster creates an entirely new promoter and an associated unidirectional transcript. This SNV downregulates α-globin expression causing α-thalassaemia. Of note, the new promoter lying between the α-globin genes and their associated super-enhancer disrupts their interaction in an orientation-dependent manner. Together these observations show how both the order and orientation of the fundamental elements of the genome determine patterns of gene expression and support the concept that active genes may act to disrupt enhancer-promoter interactions in mammals as in Drosophila. Finally, these findings should prompt others to fully evaluate SNVs lying outside of known regulatory elements as causing changes in gene expression by creating new regulatory elements. The role of promoters as potential insulator elements has been largely unexplored in mammals. Here the authors show that a single nucleotide variant in the α-globin locus forms a new promoter and acts as an orientation-dependent enhancer-blocking insulator element.
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15
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Ranzoni AM, Tangherloni A, Berest I, Riva SG, Myers B, Strzelecka PM, Xu J, Panada E, Mohorianu I, Zaugg JB, Cvejic A. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell Stem Cell 2021; 28:472-487.e7. [PMID: 33352111 PMCID: PMC7939551 DOI: 10.1016/j.stem.2020.11.015] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/18/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023]
Abstract
Regulation of hematopoiesis during human development remains poorly defined. Here we applied single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to over 8,000 human immunophenotypic blood cells from fetal liver and bone marrow. We inferred their differentiation trajectory and identified three highly proliferative oligopotent progenitor populations downstream of hematopoietic stem cells (HSCs)/multipotent progenitors (MPPs). Along this trajectory, we observed opposing patterns of chromatin accessibility and differentiation that coincided with dynamic changes in the activity of distinct lineage-specific transcription factors. Integrative analysis of chromatin accessibility and gene expression revealed extensive epigenetic but not transcriptional priming of HSCs/MPPs prior to their lineage commitment. Finally, we refined and functionally validated the sorting strategy for the HSCs/MPPs and achieved around 90% enrichment. Our study provides a useful framework for future investigation of human developmental hematopoiesis in the context of blood pathologies and regenerative medicine.
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Affiliation(s)
- Anna Maria Ranzoni
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Andrea Tangherloni
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Ivan Berest
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany
| | - Simone Giovanni Riva
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Brynelle Myers
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Paulina M Strzelecka
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Jiarui Xu
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Elisa Panada
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Irina Mohorianu
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany
| | - Ana Cvejic
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
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16
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Edginton-White B, Bonifer C. The transcriptional regulation of normal and malignant blood cell development. FEBS J 2021; 289:1240-1255. [PMID: 33511785 DOI: 10.1111/febs.15735] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 01/26/2021] [Indexed: 11/27/2022]
Abstract
Development of multicellular organisms requires the differential usage of our genetic information to change one cell fate into another. This process drives the appearance of different cell types that come together to form specialized tissues sustaining a healthy organism. In the last decade, by moving away from studying single genes toward a global view of gene expression control, a revolution has taken place in our understanding of how genes work together and how cells communicate to translate the information encoded in the genome into a body plan. The development of hematopoietic cells has long served as a paradigm of development in general. In this review, we highlight how transcription factors and chromatin components work together to shape the gene regulatory networks controlling gene expression in the hematopoietic system and to drive blood cell differentiation. In addition, we outline how this process goes astray in blood cancers. We also touch upon emerging concepts that place these processes firmly into their associated subnuclear structures adding another layer of the control of differential gene expression.
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Affiliation(s)
- Benjamin Edginton-White
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
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17
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Gene Expression Analysis of Mevalonate Kinase Deficiency Affected Children Identifies Molecular Signatures Related to Hematopoiesis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18031170. [PMID: 33525735 PMCID: PMC7908123 DOI: 10.3390/ijerph18031170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/21/2021] [Accepted: 01/23/2021] [Indexed: 12/12/2022]
Abstract
Mevalonate kinase deficiency (MKD) is a rare autoinflammatory genetic disorder characterized by recurrent fever attacks and systemic inflammation with potentially severe complications. Although it is recognized that the lack of protein prenylation consequent to mevalonate pathway blockade drives IL1β hypersecretion, and hence autoinflammation, MKD pathogenesis and the molecular mechanisms underlaying most of its clinical manifestations are still largely unknown. In this study, we performed a comprehensive bioinformatic analysis of a microarray dataset of MKD patients, using gene ontology and Ingenuity Pathway Analysis (IPA) tools, in order to identify the most significant differentially expressed genes and infer their predicted relationships into biological processes, pathways, and networks. We found that hematopoiesis linked biological functions and pathways are predominant in the gene ontology of differentially expressed genes in MKD, in line with the observed clinical feature of anemia. We also provided novel information about the molecular mechanisms at the basis of the hematological abnormalities observed, that are linked to the chronic inflammation and to defective prenylation. Considering the broad and unspecific spectrum of MKD clinical manifestations and the difficulty in its diagnosis, a better understanding of MKD molecular bases could be translated to the clinical level to facilitate diagnosis, and improve management and therapy.
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18
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Meyer A, Herkt S, Kunze-Schumacher H, Kohrs N, Ringleb J, Schneider L, Kuvardina ON, Oellerich T, Häupl B, Krueger A, Seifried E, Bonig H, Lausen J. The transcription factor TAL1 and miR-17-92 create a regulatory loop in hematopoiesis. Sci Rep 2020; 10:21438. [PMID: 33293632 PMCID: PMC7722897 DOI: 10.1038/s41598-020-78629-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
A network of gene regulatory factors such as transcription factors and microRNAs establish and maintain gene expression patterns during hematopoiesis. In this network, transcription factors regulate each other and are involved in regulatory loops with microRNAs. The microRNA cluster miR-17-92 is located within the MIR17HG gene and encodes six mature microRNAs. It is important for hematopoietic differentiation and plays a central role in malignant disease. However, the transcription factors downstream of miR-17-92 are largely elusive and the transcriptional regulation of miR-17-92 is not fully understood. Here we show that miR-17-92 forms a regulatory loop with the transcription factor TAL1. The miR-17-92 cluster inhibits expression of TAL1 and indirectly leads to decreased stability of the TAL1 transcriptional complex. We found that TAL1 and its heterodimerization partner E47 regulate miR-17-92 transcriptionally. Furthermore, miR-17-92 negatively influences erythroid differentiation, a process that depends on gene activation by the TAL1 complex. Our data give example of how transcription factor activity is fine-tuned during normal hematopoiesis. We postulate that disturbance of the regulatory loop between TAL1 and the miR-17-92 cluster could be an important step in cancer development and progression.
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Affiliation(s)
- Annekarin Meyer
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Stefanie Herkt
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Heike Kunze-Schumacher
- Institute for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Nicole Kohrs
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Strasse 42-44, 60596, Frankfurt am Main, Germany
| | - Julia Ringleb
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Strasse 42-44, 60596, Frankfurt am Main, Germany
| | - Lucas Schneider
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Olga N Kuvardina
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Frankfurt Cancer Institute, Goethe University, 60596, Frankfurt, Germany
| | - Björn Häupl
- Department of Medicine II, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Frankfurt Cancer Institute, Goethe University, 60596, Frankfurt, Germany
| | - Andreas Krueger
- Institute for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Erhard Seifried
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany.,Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, 98195, USA
| | - Joern Lausen
- Institute for Transfusion Medicine and Immunohematology, and German Red Cross Blood Service BaWüHe, Goethe University, Sandhofstraße 1, 60528, Frankfurt, Germany. .,Department of Eukaryotic Genetics, Institute of Industrial Genetics, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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19
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Noguchi CT. Erythropoietin regulates metabolic response in mice via receptor expression in adipose tissue, brain, and bone. Exp Hematol 2020; 92:32-42. [PMID: 32950599 DOI: 10.1016/j.exphem.2020.09.190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022]
Abstract
Erythropoietin (EPO) acts by binding to erythroid progenitor cells to regulate red blood cell production. While EPO receptor (Epor) expression is highest on erythroid tissue, animal models exhibit EPO activity in nonhematopoietic tissues, mediated, in part, by tissue-specific Epor expression. This review describes the metabolic response in mice to endogenous EPO and EPO treatment associated with glucose metabolism, fat mass accumulation, and inflammation in white adipose tissue and brain during diet-induced obesity and with bone marrow fat and bone remodeling. During high-fat diet-induced obesity, EPO treatment improves glucose tolerance, decreases fat mass accumulation, and shifts white adipose tissue from a pro-inflammatory to an anti-inflammatory state. Fat mass regulation by EPO is sex dimorphic, apparent in males and abrogated by estrogen in females. Cerebral EPO also regulates fat mass and hypothalamus inflammation associated with diet-induced obesity in males and ovariectomized female mice. In bone, EPO contributes to the balance between adipogenesis and osteogenesis in both male and female mice. EPO treatment promotes bone loss mediated via Epor in osteoblasts and reduces bone marrow adipocytes before and independent of change in white adipose tissue fat mass. EPO regulation of bone loss and fat mass is independent of EPO-stimulated erythropoiesis. EPO nonhematopoietic tissue response may relate to the long-term consequences of EPO treatment of anemia in chronic kidney disease and to the alternative treatment of oral hypoxia-inducible factor prolyl hydroxylase inhibitors that increase endogenous EPO production.
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Affiliation(s)
- Constance Tom Noguchi
- Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.
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20
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A Unique Epigenomic Landscape Defines Human Erythropoiesis. Cell Rep 2020; 28:2996-3009.e7. [PMID: 31509757 PMCID: PMC6863094 DOI: 10.1016/j.celrep.2019.08.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/28/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022] Open
Abstract
Mammalian erythropoiesis yields a highly specialized cell type, the mature erythrocyte, evolved to meet the organismal needs of increased oxygen-carrying capacity. To better understand the regulation of erythropoiesis, we performed genome-wide studies of chromatin accessibility, DNA methylation, and transcriptomics using a recently developed strategy to obtain highly purified populations of primary human erythroid cells. The integration of gene expression, DNA methylation, and chromatin state dynamics reveals that stage-specific gene regulation during erythropoiesis is a stepwise and hierarchical process involving many cis-regulatory elements. Erythroid-specific, nonpromoter sites of chromatin accessibility are linked to erythroid cell phenotypic variation and inherited disease. Comparative analyses of stage-specific chromatin accessibility indicate that there is limited early chromatin priming of erythroid genes during hematopoiesis. The epigenome of terminally differentiating erythroid cells defines a distinct subset of highly specialized cells that are vastly dissimilar from other hematopoietic and nonhematopoietic cell types. These epigenomic and transcriptome data are powerful tools to study human erythropoiesis. Schulz et al. use genome-wide studies of chromatin accessibility, DNA methylation, and transcriptomes in primary human erythroid cells to reveal important characteristics of erythropoiesis. Chromatin accessibility of terminal erythroid differentiation is markedly dissimilar from other hematopoietic cell types. Epigenomic changes are linked to erythroid cell traits and disease genes.
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21
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Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biol 2020; 21:59. [PMID: 32138752 PMCID: PMC7059722 DOI: 10.1186/s13059-020-01973-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/23/2020] [Indexed: 12/11/2022] Open
Abstract
The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinylated dCas9, endogenous biotin ligases, and pooled sgRNAs, we describe the dCas9-based CAPTURE method for multiplexed analysis of locus-specific chromatin interactions. The redesigned system allows for quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling comparisons across CREs within and between gene clusters. Multiplexed analyses of the spatiotemporal configuration of erythroid super-enhancers and promoter-centric interactions reveal organizational principles of genome structure and function.
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22
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Suresh S, Rajvanshi PK, Noguchi CT. The Many Facets of Erythropoietin Physiologic and Metabolic Response. Front Physiol 2020; 10:1534. [PMID: 32038269 PMCID: PMC6984352 DOI: 10.3389/fphys.2019.01534] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/05/2019] [Indexed: 12/30/2022] Open
Abstract
In mammals, erythropoietin (EPO), produced in the kidney, is essential for bone marrow erythropoiesis, and hypoxia induction of EPO production provides for the important erythropoietic response to ischemic stress, such as during blood loss and at high altitude. Erythropoietin acts by binding to its cell surface receptor which is expressed at the highest level on erythroid progenitor cells to promote cell survival, proliferation, and differentiation in production of mature red blood cells. In addition to bone marrow erythropoiesis, EPO causes multi-tissue responses associated with erythropoietin receptor (EPOR) expression in non-erythroid cells such neural cells, endothelial cells, and skeletal muscle myoblasts. Animal and cell models of ischemic stress have been useful in elucidating the potential benefit of EPO affecting maintenance and repair of several non-hematopoietic organs including brain, heart and skeletal muscle. Metabolic and glucose homeostasis are affected by endogenous EPO and erythropoietin administration affect, in part via EPOR expression in white adipose tissue. In diet-induced obese mice, EPO is protective for white adipose tissue inflammation and gives rise to a gender specific response in weight control associated with white fat mass accumulation. Erythropoietin regulation of fat mass is masked in female mice due to estrogen production. EPOR is also expressed in bone marrow stromal cells (BMSC) and EPO administration in mice results in reduced bone independent of the increase in hematocrit. Concomitant reduction in bone marrow adipocytes and bone morphogenic protein suggests that high EPO inhibits adipogenesis and osteogenesis. These multi-tissue responses underscore the pleiotropic potential of the EPO response and may contribute to various physiological manifestations accompanying anemia or ischemic response and pharmacological uses of EPO.
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Affiliation(s)
- Sukanya Suresh
- Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Praveen Kumar Rajvanshi
- Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Constance T Noguchi
- Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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23
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Gutiérrez L, Caballero N, Fernández-Calleja L, Karkoulia E, Strouboulis J. Regulation of GATA1 levels in erythropoiesis. IUBMB Life 2019; 72:89-105. [PMID: 31769197 DOI: 10.1002/iub.2192] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/14/2019] [Indexed: 12/15/2022]
Abstract
GATA1 is considered as the "master" transcription factor in erythropoiesis. It regulates at the transcriptional level all aspects of erythroid maturation and function, as revealed by gene knockout studies in mice and by genome-wide occupancies in erythroid cells. The GATA1 protein contains two zinc finger domains and an N-terminal transactivation domain. GATA1 translation results in the production of the full-length protein and of a shorter variant (GATA1s) lacking the N-terminal transactivation domain, which is functionally deficient in supporting erythropoiesis. GATA1 protein abundance is highly regulated in erythroid cells at different levels, including transcription, mRNA translation, posttranslational modifications, and protein degradation, in a differentiation-stage-specific manner. Maintaining high GATA1 protein levels is essential in the early stages of erythroid maturation, whereas downregulating GATA1 protein levels is a necessary step in terminal erythroid differentiation. The importance of maintaining proper GATA1 protein homeostasis in erythropoiesis is demonstrated by the fact that both GATA1 loss and its overexpression result in lethal anemia. Importantly, alterations in any of those GATA1 regulatory checkpoints have been recognized as an important cause of hematological disorders such as dyserythropoiesis (with or without thrombocytopenia), β-thalassemia, Diamond-Blackfan anemia, myelodysplasia, or leukemia. In this review, we provide an overview of the multilevel regulation of GATA1 protein homeostasis in erythropoiesis and of its deregulation in hematological disease.
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Affiliation(s)
- Laura Gutiérrez
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Medicine, Universidad de Oviedo, Oviedo, Spain
| | - Noemí Caballero
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luis Fernández-Calleja
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Elena Karkoulia
- Institute of Molecular Biology and Biotechnology, Foundation of Research & Technology Hellas, Heraklion, Crete, Greece
| | - John Strouboulis
- Cancer Comprehensive Center, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
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24
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Romano O, Miccio A. GATA factor transcriptional activity: Insights from genome-wide binding profiles. IUBMB Life 2019; 72:10-26. [PMID: 31574210 DOI: 10.1002/iub.2169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/05/2019] [Indexed: 01/07/2023]
Abstract
The members of the GATA family of transcription factors have homologous zinc fingers and bind to similar sequence motifs. Recent advances in genome-wide technologies and the integration of bioinformatics data have led to a better understanding of how GATA factors regulate gene expression; GATA-factor-induced transcriptional and epigenetic changes have now been analyzed at unprecedented levels of detail. Here, we review the results of genome-wide studies of GATA factor occupancy in human and murine cell lines and primary cells (as determined by chromatin immunoprecipitation sequencing), and then discuss the molecular mechanisms underlying the mediation of transcriptional and epigenetic regulation by GATA factors.
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Laboratory of chromatin and gene regulation during development, Imagine Institute, INSERM UMR, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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25
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Greenside P, Shimko T, Fordyce P, Kundaje A. Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. Bioinformatics 2019; 34:i629-i637. [PMID: 30423062 PMCID: PMC6129272 DOI: 10.1093/bioinformatics/bty575] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Motivation Transcription factors bind regulatory DNA sequences in a combinatorial manner to modulate gene expression. Deep neural networks (DNNs) can learn the cis-regulatory grammars encoded in regulatory DNA sequences associated with transcription factor binding and chromatin accessibility. Several feature attribution methods have been developed for estimating the predictive importance of individual features (nucleotides or motifs) in any input DNA sequence to its associated output prediction from a DNN model. However, these methods do not reveal higher-order feature interactions encoded by the models. Results We present a new method called Deep Feature Interaction Maps (DFIM) to efficiently estimate interactions between all pairs of features in any input DNA sequence. DFIM accurately identifies ground truth motif interactions embedded in simulated regulatory DNA sequences. DFIM identifies synergistic interactions between GATA1 and TAL1 motifs from in vivo TF binding models. DFIM reveals epistatic interactions involving nucleotides flanking the core motif of the Cbf1 TF in yeast from in vitro TF binding models. We also apply DFIM to regulatory sequence models of in vivo chromatin accessibility to reveal interactions between regulatory genetic variants and proximal motifs of target TFs as validated by TF binding quantitative trait loci. Our approach makes significant strides in improving the interpretability of deep learning models for genomics. Availability and implementation Code is available at: https://github.com/kundajelab/dfim. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Peyton Greenside
- Biomedical Informatics Training Program, Stanford University, Stanford, CA
| | | | - Polly Fordyce
- Genetics, Stanford University, Stanford, CA.,Bioengineering, Stanford University, Stanford, CA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Chem-H Institute, Stanford University, Stanford, CA, USA
| | - Anshul Kundaje
- Genetics, Stanford University, Stanford, CA.,Computer Science, Stanford University, Stanford, CA, USA
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26
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Zhu Q, Liu N, Orkin SH, Yuan GC. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol 2019; 20:192. [PMID: 31500663 PMCID: PMC6734249 DOI: 10.1186/s13059-019-1802-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/26/2019] [Indexed: 01/20/2023] Open
Abstract
We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&RUNTools extracts endonuclease cut site information from sequences of short-read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&RUN. CUT&RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/ .
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Affiliation(s)
- Qian Zhu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard Chan School of Public Health, Boston, MA, USA
| | - Nan Liu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard Chan School of Public Health, Boston, MA, USA.
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27
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Vatikioti A, Karkoulia E, Ioannou M, Strouboulis J. Translational regulation and deregulation in erythropoiesis. Exp Hematol 2019; 75:11-20. [PMID: 31154069 DOI: 10.1016/j.exphem.2019.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 02/02/2023]
Abstract
Translational regulation plays a critical role in erythropoiesis, as it reflects the translational needs of enucleated mature erythroid cells in the absence of transcription and the large translational demands of balanced globin chain synthesis during erythroid maturation. In addition, red blood cells need to respond quickly to changes in their environment and the demands of the organism. Translational regulation occurs at several levels in erythroid cells, including the differential utilization of upstream open reading frames during differentiation and in response to signaling and the employment of RNA-binding proteins in an erythroid cell-specific fashion. Translation initiation is a critical juncture for translational regulation in response to environmental signals such as heme and iron availability, whereas regulatory mechanisms for ribosome recycling are consistent with recent observations highlighting the importance of maintaining adequate ribosome levels in differentiating erythroid cells. Translational deregulation in erythroid cells leads to disease associated with ineffective erythropoiesis, further highlighting the pivotal role translational regulation in erythropoiesis plays in human physiology and homeostasis. Overall, erythropoiesis has served as a unique model that has provided invaluable insight into translational regulation.
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Affiliation(s)
- Alexandra Vatikioti
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece; Graduate Program in Molecular Biology and Biomedicine, Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Elena Karkoulia
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece
| | - Marina Ioannou
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece
| | - John Strouboulis
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece.
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28
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Enhancer long-range contacts: The multi-adaptor protein LDB1 is the tie that binds. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:625-633. [DOI: 10.1016/j.bbagrm.2019.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/20/2022]
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29
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SCL/TAL1 cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells. Nat Commun 2018; 9:5375. [PMID: 30560907 PMCID: PMC6299140 DOI: 10.1038/s41467-018-07787-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 11/23/2018] [Indexed: 01/03/2023] Open
Abstract
During development, it is unclear if lineage-fated cells derive from multilineage-primed progenitors and whether active mechanisms operate to restrict cell fate. Here we investigate how mesoderm specifies into blood-fated cells. We document temporally restricted co-expression of blood (Scl/Tal1), cardiac (Mesp1) and paraxial (Tbx6) lineage-affiliated transcription factors in single cells, at the onset of blood specification, supporting the existence of common progenitors. At the same time-restricted stage, absence of SCL results in expansion of cardiac/paraxial cell populations and increased cardiac/paraxial gene expression, suggesting active suppression of alternative fates. Indeed, SCL normally activates expression of co-repressor ETO2 and Polycomb-PRC1 subunits (RYBP, PCGF5) and maintains levels of Polycomb-associated histone marks (H2AK119ub/H3K27me3). Genome-wide analyses reveal ETO2 and RYBP co-occupy most SCL target genes, including cardiac/paraxial loci. Reduction of Eto2 or Rybp expression mimics Scl-null cardiac phenotype. Therefore, SCL-mediated transcriptional repression prevents mis-specification of blood-fated cells, establishing active repression as central to fate determination processes. Mechanisms that operate during embryonic development to restrict cell fate are currently under investigation. Here the authors characterise the role of SCL/TAL1 at the onset of blood specification in embryonic development using mouse EB differentiation culture as a model system.
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30
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Chiu SK, Saw J, Huang Y, Sonderegger SE, Wong NC, Powell DR, Beck D, Pimanda JE, Tremblay CS, Curtis DJ. A novel role for Lyl1 in primitive erythropoiesis. Development 2018; 145:dev.162990. [PMID: 30185409 DOI: 10.1242/dev.162990] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023]
Abstract
Stem cell leukemia (Scl or Tal1) and lymphoblastic leukemia 1 (Lyl1) encode highly related members of the basic helix-loop-helix family of transcription factors that are co-expressed in the erythroid lineage. Previous studies have suggested that Scl is essential for primitive erythropoiesis. However, analysis of single-cell RNA-seq data of early embryos showed that primitive erythroid cells express both Scl and Lyl1 Therefore, to determine whether Lyl1 can function in primitive erythropoiesis, we crossed conditional Scl knockout mice with mice expressing a Cre recombinase under the control of the Epo receptor, active in erythroid progenitors. Embryos with 20% expression of Scl from E9.5 survived to adulthood. However, mice with reduced expression of Scl and absence of Lyl1 (double knockout; DKO) died at E10.5 because of progressive loss of erythropoiesis. Gene expression profiling of DKO yolk sacs revealed loss of Gata1 and many of the known target genes of the SCL-GATA1 complex. ChIP-seq analyses in a human erythroleukemia cell line showed that LYL1 exclusively bound a small subset of SCL targets including GATA1. Together, these data show for the first time that Lyl1 can maintain primitive erythropoiesis.
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Affiliation(s)
- Sung K Chiu
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Jesslyn Saw
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Yizhou Huang
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia.,Centre for Health Technologies, School of Biomedical Engineering and the School of Software, University of Technology, Sydney, NSW 2007, Australia
| | - Stefan E Sonderegger
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Nicholas C Wong
- Central Clinical School, Monash University, Melbourne, VIC 3004, Australia.,Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia
| | - Dominic Beck
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia.,Centre for Health Technologies, School of Biomedical Engineering and the School of Software, University of Technology, Sydney, NSW 2007, Australia
| | - John E Pimanda
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia.,Department of Haematology, Prince of Wales Hospital, Sydney, NSW 2031, Australia.,Department of Pathology, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Cedric S Tremblay
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - David J Curtis
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia .,Department of Clinical Haematology, The Alfred Hospital, Melbourne, VIC 3004, Australia
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31
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In 't Hout FEM, van Duren J, Monteferrario D, Brinkhuis E, Mariani N, Westers TM, Chitu D, Nikoloski G, van de Loosdrecht AA, van der Reijden BA, Jansen JH, Huls G. TCF4 promotes erythroid development. Exp Hematol 2018; 69:17-21.e1. [PMID: 30315825 DOI: 10.1016/j.exphem.2018.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/27/2018] [Accepted: 10/05/2018] [Indexed: 12/27/2022]
Abstract
Transcription factor 4 (TCF4) is implicated in lymphoid cell differentiation and its expression predicts outcome in acute myeloid leukemia. Here, we investigated the role of TCF4 in myelopoiesis. Overexpression of TCF4 (TCF4OE) in umbilical cord blood (UCB) cells resulted in a twofold increase in erythroid colony forming units (CFU-Es), whereas knock-down (KD) of TCF4 (TCF4KD) caused a dramatic decrease in the number of erythroid colonies. In megakaryocyte CFUs (CFU-MKs), both TCF4KD and TCF4OE inhibited MK colony formation. TCF4 did not have an impact on granulocyte, macrophage, or granulocyte-macrophage colonies or on the proportion of MK-erythrocyte progenitors (MEPs) in culture. Because TCF4 affects erythroid/MK development and these lineages are affected in myelodysplastic syndrome (MDS), we studied the impact of TCF4 expression in this disease. MDS patients with high (≥median) TCF4 mRNA expression had higher hemoglobin (Hb) levels than MDS patients with low TCF4 expression (mean 9.0 vs. 8.55 g/dL, p = 0.02). Overall, TCF4 mRNA expression was lower in hematopoietic stem cells, common myeloid progenitors, and MEPs from MDS patients, but not in granulocyte-macrophage progenitors, compared with healthy controls. Therefore, in cell fractions with erythroid lineage potential, TCF4 is expressed less in MDS patients than in healthy controls. This correlates with the low overall Hb levels seen in MDS patients compared with healthy individuals and is consistent with the positive impact of TCF4 on erythroid development while not having impact on white colonies. These results indicate a role for TCF4 as a novel factor in erythroid-megakaryocytic differentiation.
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Affiliation(s)
- Florentien E M In 't Hout
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jolanda van Duren
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Davide Monteferrario
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Emma Brinkhuis
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Niccolo Mariani
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Theresia M Westers
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Hematology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Dana Chitu
- HOVON Data Center, Erasmus University Medical Center-Daniel den Hoed, Rotterdam, The Netherlands
| | - Gorica Nikoloski
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Arjan A van de Loosdrecht
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Hematology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Centre, Nijmegen, The Netherlands.
| | - Gerwin Huls
- Department of Hematology, University Medical Centre Groningen, Groningen, The Netherlands
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32
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Tan TK, Zhang C, Sanda T. Oncogenic transcriptional program driven by TAL1 in T-cell acute lymphoblastic leukemia. Int J Hematol 2018; 109:5-17. [PMID: 30145780 DOI: 10.1007/s12185-018-2518-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/21/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
TAL1/SCL is a prime example of an oncogenic transcription factor that is abnormally expressed in acute leukemia due to the replacement of regulator elements. This gene has also been recognized as an essential regulator of hematopoiesis. TAL1 expression is strictly regulated in a lineage- and stage-specific manner. Such precise control is crucial for the switching of the transcriptional program. The misexpression of TAL1 in immature thymocytes leads to a widespread series of orchestrated downstream events that affect several different cellular machineries, resulting in a lethal consequence, namely T-cell acute lymphoblastic leukemia (T-ALL). In this article, we will discuss the transcriptional regulatory network and downstream target genes, including protein-coding genes and non-coding RNAs, controlled by TAL1 in normal hematopoiesis and T-cell leukemogenesis.
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Affiliation(s)
- Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Chujing Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, 14 Medical Drive, #12-01, Singapore, 117599, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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33
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Chen J, Gálvez-Peralta M, Zhang X, Deng J, Liu Z, Nebert DW. In utero gene expression in the Slc39a8(neo/neo) knockdown mouse. Sci Rep 2018; 8:10703. [PMID: 30013175 PMCID: PMC6048144 DOI: 10.1038/s41598-018-29109-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
Slc39a8 encodes ZIP8, a divalent cation/bicarbonate symporter expressed in pluripotent mouse embryonic stem cells, and therefore ubiquitous in adult tissues; ZIP8 influxes Zn2+, Mn2+ and Fe2+. Slc39a8(neo/neo) knockdown mice exhibit 10-15% of wild-type ZIP8 mRNA and protein levels, and show pleiotropic phenotype of stunted growth, neonatal lethality, multi-organ dysmorphogenesis, and dysregulated hematopoiesis manifested as severe anemia. Herein we performed RNA-seq analysis of gestational day (GD)13.5 yolk sac and placenta, and GD16.5 liver, kidney, lung, heart and cerebellum, comparing Slc39a8(neo/neo) with Slc39a8(+/+) wild-type. Meta-data analysis of differentially-expressed genes revealed 29 unique genes from all tissues - having enriched GO categories associated with hematopoiesis and hypoxia and KEGG categories of complement, response to infection, and coagulation cascade - consistent with dysregulated hematopoietic stem cell fate. Based on transcription factor (TF) profiles in the JASPAR database, and searching for TF-binding sites enriched by Pscan, we identified numerous genes encoding zinc-finger and other TFs associated with hematopoietic stem cell functions. We conclude that, in this mouse model, deficient ZIP8-mediated divalent cation transport affects zinc-finger (e.g. GATA proteins) and other TFs interacting with GATA proteins (e.g. TAL1), predominantly in yolk sac. These data strongly support the phenotype of dysmorphogenesis and anemia seen in Slc39a8(neo/neo) mice in utero.
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Affiliation(s)
- Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Marina Gálvez-Peralta
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA.,Department of Pharmaceutical Sciences, West Virginia University Medical Center, Morgantown, WV, 26506, USA
| | - Xiang Zhang
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA
| | - Jingyuan Deng
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA.,Amazon.com, Inc., Seattle, WA, 98101, USA
| | - Zijuan Liu
- Department of Biological Sciences, Oakland University, Rochester, MI, 48309, USA
| | - Daniel W Nebert
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA.
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Philipsen S, Hardison RC. Evolution of hemoglobin loci and their regulatory elements. Blood Cells Mol Dis 2018; 70:2-12. [PMID: 28811072 PMCID: PMC5807248 DOI: 10.1016/j.bcmd.2017.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/13/2017] [Accepted: 08/03/2017] [Indexed: 11/21/2022]
Abstract
Across the expanse of vertebrate evolution, each species produces multiple forms of hemoglobin in erythroid cells at appropriate times and in the proper amounts. The multiple hemoglobins are encoded in two globin gene clusters in almost all species. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. This preservation of synteny may reflect the presence of a powerful enhancer of globin gene expression in the NPRL3 gene. Despite substantial divergence in noncoding DNA sequences among mammals, several epigenetic features of the globin gene regulatory regions are preserved across vertebrates. The preserved features include multiple DNase hypersensitive sites, at least one of which is an enhancer, and binding by key lineage-restricted transcription factors such as GATA1 and TAL1, which in turn recruit coactivators such as P300 that catalyze acetylation of histones. The maps of epigenetic features are strongly correlated with activity in gene regulation, and resources for accessing and visualizing such maps are readily available to the community of researchers and students.
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Affiliation(s)
- Sjaak Philipsen
- Department of Cell Biology Ee1071b, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Huck Institute for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.
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35
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Abstract
Lineage-specific transcription factors are critical for long-range enhancer interactions, but direct or indirect contributions of architectural proteins such as CCCTC-binding factor (CTCF) to enhancer function remain less clear. The LDB1 complex mediates enhancer-gene interactions at the β-globin locus through LDB1 self-interaction. We find that an LDB1-bound enhancer upstream of carbonic anhydrase 2 (Car2) activates its expression by interacting directly with CTCF at the gene promoter. Both LDB1 and CTCF are required for enhancer-Car2 looping, and the domain of LDB1 contacted by CTCF is necessary to rescue Car2 transcription in LDB1-deficient cells. Genome-wide studies and CRISPR/Cas9 genome editing indicate that LDB1-CTCF enhancer looping underlies activation of a substantial fraction of erythroid genes. Our results provide a mechanism by which long-range interactions of architectural protein CTCF can be tailored to achieve a tissue-restricted pattern of chromatin loops and gene expression.
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36
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Yang J, Ma J, Xiong Y, Wang Y, Jin K, Xia W, Chen Q, Huang J, Zhang J, Jiang N, Jiang S, Ma D. Epigenetic regulation of megakaryocytic and erythroid differentiation by PHF2 histone demethylase. J Cell Physiol 2018; 233:6841-6852. [PMID: 29336484 DOI: 10.1002/jcp.26438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 01/05/2018] [Indexed: 12/16/2022]
Abstract
Plant homeodomain finger 2 (PHF2) is a JmjC family histone demethylase that demethylates H3K9me2, a repressive gene marker. PHF2 was found to play a role in the differentiation of several tissue types such as osteoblast and adipocyte differentiation. We report here that PHF2 plays a role in the epigenetic regulation of megakaryocytic (MK) and erythroid differentiation. We investigated PHF2 expression during MK and erythroid differentiation in K562 and human CD34+ progenitor (hCD34+ ) cells. Our data demonstrate that PHF2 expression is down-regulated during megakaryopoiesis and erythropoiesis. PHF2 has a negative role in MK and erythroid differentiation of K562 cells; knockdown of PHF2 promotes MK and erythroid differentiation of hCD34+ cells. Similarly, we found that p53 expression is also down-regulated during MK and erythroid differentiation, which parallels PHF2 expression. PHF2 binds to the p53 promoter and regulates the expression of p53 by demethylating H3K9me2 in the promoter region of p53. Taken together, our data show that PHF2 is a negative epigenetic regulator of MK and erythroid differentiation, and that one of the pathways through which PHF2 affects MK and erythroid differentiation is via regulation of p53 expression.
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Affiliation(s)
- Jichun Yang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yu Xiong
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity & Child Health Hospital of China Welfare Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaiyue Jin
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wenjun Xia
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qing Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jianbo Huang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Nan Jiang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shayi Jiang
- Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Duan Ma
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China
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37
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Wang Z, Zhang Q, Zhang W, Lin JR, Cai Y, Mitra J, Zhang ZD. HEDD: Human Enhancer Disease Database. Nucleic Acids Res 2018; 46:D113-D120. [PMID: 29077884 PMCID: PMC5753236 DOI: 10.1093/nar/gkx988] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 12/26/2022] Open
Abstract
Enhancers, as specialized genomic cis-regulatory elements, activate transcription of their target genes and play an important role in pathogenesis of many human complex diseases. Despite recent systematic identification of them in the human genome, currently there is an urgent need for comprehensive annotation databases of human enhancers with a focus on their disease connections. In response, we built the Human Enhancer Disease Database (HEDD) to facilitate studies of enhancers and their potential roles in human complex diseases. HEDD currently provides comprehensive genomic information for ∼2.8 million human enhancers identified by ENCODE, FANTOM5 and RoadMap with disease association scores based on enhancer-gene and gene-disease connections. It also provides Web-based analytical tools to visualize enhancer networks and score enhancers given a set of selected genes in a specific gene network. HEDD is freely accessible at http://zdzlab.einstein.yu.edu/1/hedd.php.
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Affiliation(s)
- Zhen Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Wen Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ying Cai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joydeep Mitra
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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Vagapova ER, Spirin PV, Lebedev TD, Prassolov VS. The Role of TAL1 in Hematopoiesis and Leukemogenesis. Acta Naturae 2018; 10:15-23. [PMID: 29713515 PMCID: PMC5916730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
TAL1 (SCL/TAL1, T-cell acute leukemia protein 1) is a transcription factor that is involved in the process of hematopoiesis and leukemogenesis. It participates in blood cell formation, forms mesoderm in early embryogenesis, and regulates hematopoiesis in adult organisms. TAL1 is essential in maintaining the multipotency of hematopoietic stem cells (HSC) and keeping them in quiescence (stage G0). TAL1 forms complexes with various transcription factors, regulating hematopoiesis (E2A/HEB, GATA1-3, LMO1-2, Ldb1, ETO2, RUNX1, ERG, FLI1). In these complexes, TAL1 regulates normal myeloid differentiation, controls the proliferation of erythroid progenitors, and determines the choice of the direction of HSC differentiation. The transcription factors TAL1, E2A, GATA1 (or GATA2), LMO2, and Ldb1 are the major components of the SCL complex. In addition to normal hematopoiesis, this complex may also be involved in the process of blood cell malignant transformation. Upregulation of C-KIT expression is one of the main roles played by the SCL complex. Today, TAL1 and its partners are considered promising therapeutic targets in the treatment of T-cell acute lymphoblastic leukemia.
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Affiliation(s)
- E. R. Vagapova
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - P. V. Spirin
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - T. D. Lebedev
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
| | - V. S. Prassolov
- The Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow,119991, Russia
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39
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Maqueda M, Roca E, Brotons D, Soria JM, Perera A. Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches. PLoS One 2017; 12:e0180322. [PMID: 29028836 PMCID: PMC5640184 DOI: 10.1371/journal.pone.0180322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/14/2017] [Indexed: 12/18/2022] Open
Abstract
Gene expression (GE) analyses on blood samples from marathon and half-marathon runners have reported significant impacts on the immune and inflammatory systems. An ultra-marathon trail (UMT) represents a greater effort due to its more testing conditions. For the first time, we report the genome-wide GE profiling in a group of 16 runners participating in an 82 km UMT competition. We quantified their differential GE profile before and after the race using HuGene2.0st microarrays (Affymetrix Inc., California, US). The results obtained were decomposed by means of an independent component analysis (ICA) targeting independent expression modes. We observed significant differences in the expression levels of 5,084 protein coding genes resulting in an overrepresentation of 14% of the human biological pathways from the Kyoto Encyclopedia of Genes and Genomes database. These were mainly clustered on terms related with protein synthesis repression, altered immune system and infectious diseases related mechanisms. In a second analysis, 27 out of the 196 transcriptional regulators (TRs) included in the Open Regulatory Annotation database were overrepresented. Among these TRs, we identified transcription factors from the hypoxia-inducible factors (HIF) family EPAS1 (p< 0.01) and HIF1A (p<0.001), and others jointly described in the gluconeogenesis program such as HNF4 (p< 0.001), EGR1 (p<0.001), CEBPA (p< 0.001) and a highly specific TR, YY1 (p<0.01). The five independent components, obtained from ICA, further revealed a down-regulation of 10 genes distributed in the complex I, III and V from the electron transport chain. This mitochondrial activity reduction is compatible with HIF-1 system activation. The vascular endothelial growth factor (VEGF) pathway, known to be regulated by HIF, also emerged (p<0.05). Additionally, and related to the brain rewarding circuit, the endocannabinoid signalling pathway was overrepresented (p<0.05).
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Affiliation(s)
- Maria Maqueda
- Department of ESAII, Center for Biomedical Engineering Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Catalonia, Spain
- * E-mail:
| | - Emma Roca
- Summit 2014 S.L., Centelles, Barcelona, Catalonia Spain
- Department of Electronic Engineering, Center for Biomedical Engineering Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia, Spain
| | | | - Jose Manuel Soria
- Unit of Genomics of Complex Diseases, Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Barcelona, Catalonia, Spain
| | - Alexandre Perera
- Department of ESAII, Center for Biomedical Engineering Research, Universitat Politècnica de Catalunya, Barcelona, Catalonia, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Catalonia, Spain
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40
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Varrault A, Dantec C, Le Digarcher A, Chotard L, Bilanges B, Parrinello H, Dubois E, Rialle S, Severac D, Bouschet T, Journot L. Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network. Nucleic Acids Res 2017; 45:10466-10480. [PMID: 28985358 PMCID: PMC5737700 DOI: 10.1093/nar/gkx672] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 06/29/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023] Open
Abstract
PLAGL1/ZAC1 undergoes parental genomic imprinting, is paternally expressed, and is a member of the imprinted gene network (IGN). It encodes a zinc finger transcription factor with anti-proliferative activity and is a candidate tumor suppressor gene on 6q24 whose expression is frequently lost in various neoplasms. Conversely, gain of PLAGL1 function is responsible for transient neonatal diabetes mellitus, a rare genetic disease that results from defective pancreas development. In the present work, we showed that Plagl1 up-regulation was not associated with DNA damage-induced cell cycle arrest. It was rather associated with physiological cell cycle exit that occurred with contact inhibition, growth factor withdrawal, or cell differentiation. To gain insights into Plagl1 mechanism of action, we identified Plagl1 target genes by combining chromatin immunoprecipitation and genome-wide transcriptomics in transfected cell lines. Plagl1-elicited gene regulation correlated with multiple binding to the proximal promoter region through a GC-rich motif. Plagl1 target genes included numerous genes involved in signaling, cell adhesion, and extracellular matrix composition, including collagens. Plagl1 targets also included 22% of the 409 genes that make up the IGN. Altogether, this work identified Plagl1 as a transcription factor that coordinated the regulation of a subset of IGN genes and controlled extracellular matrix composition.
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Affiliation(s)
- Annie Varrault
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Christelle Dantec
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Laëtitia Chotard
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Benoit Bilanges
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Hugues Parrinello
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Emeric Dubois
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Stéphanie Rialle
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Dany Severac
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
- Montpellier GenomiX, MGX, BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, F-34094 Montpellier, France
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41
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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] [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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42
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Sanda T, Leong WZ. TAL1 as a master oncogenic transcription factor in T-cell acute lymphoblastic leukemia. Exp Hematol 2017; 53:7-15. [PMID: 28652130 DOI: 10.1016/j.exphem.2017.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/11/2017] [Indexed: 11/29/2022]
Abstract
In hematopoietic cell development, the transcriptional program is strictly regulated in a lineage- and stage-specific manner that requires a number of transcription factors to work in a cascade or in a loop, in addition to interactions with nonhematopoietic cells in the microenvironment. Disruption of the transcriptional program alters the cellular state and may predispose cells to the acquisition of genetic abnormalities. Early studies have shown that proteins that promote cell differentiation often serve as tumor suppressors, whereas inhibitors of those proteins act as oncogenes in the context of acute leukemia. A prime example is T-cell acute lymphoblastic leukemia (T-ALL), a malignant disorder characterized by clonal proliferation of immature stage thymocytes. Although a relatively small number of genetic abnormalities are observed in T-ALL, these abnormalities are crucial for leukemogenesis. Many oncogenes and tumor suppressors in T-ALL are transcription factors that are required for normal hematopoiesis. The transformation process in T-ALL is efficient and orchestrated; the oncogene disrupts the transcriptional program directing T-cell differentiation and also uses its native ability as a master transcription factor in hematopoiesis. This imbalance in the transcriptional program is a primary determinant underlying the molecular pathogenesis of T-ALL. In this review, we focus on the oncogenic transcription factor TAL1 and the tumor-suppressor E-proteins and discuss the malignant cell state, the transcriptional circuit, and the consequence of molecular abnormalities in T-ALL.
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Affiliation(s)
- Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Wei Zhong Leong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
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43
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Suske G. NF-Y and SP transcription factors — New insights in a long-standing liaison. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:590-597. [DOI: 10.1016/j.bbagrm.2016.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/18/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022]
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44
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Kuvardina ON, Herkt S, Meyer A, Schneider L, Yillah J, Kohrs N, Bonig H, Seifried E, Müller-Tidow C, Lausen J. Hematopoietic transcription factors and differential cofactor binding regulate PRKACB isoform expression. Oncotarget 2017; 8:71685-71698. [PMID: 29069738 PMCID: PMC5641081 DOI: 10.18632/oncotarget.17386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/27/2017] [Indexed: 01/05/2023] Open
Abstract
Hematopoietic differentiation is controlled by key transcription factors, which regulate stem cell functions and differentiation. TAL1 is a central transcription factor for hematopoietic stem cell development in the embryo and for gene regulation during erythroid/megakaryocytic differentiation. Knowledge of the target genes controlled by a given transcription factor is important to understand its contribution to normal development and disease. To uncover direct target genes of TAL1 we used high affinity streptavidin/biotin-based chromatin precipitation (Strep-CP) followed by Strep-CP on ChIP analysis using ChIP promoter arrays. We identified 451 TAL1 target genes in K562 cells. Furthermore, we analysed the regulation of one of these genes, the catalytic subunit beta of protein kinase A (PRKACB), during megakaryopoiesis of K562 and primary human CD34+ stem cell/progenitor cells. We found that TAL1 together with hematopoietic transcription factors RUNX1 and GATA1 binds to the promoter of the isoform 3 of PRKACB (Cβ3). During megakaryocytic differentiation a coactivator complex on the Cβ3 promoter, which includes WDR5 and p300, is replaced with a corepressor complex. In this manner, activating chromatin modifications are removed and expression of the PRKACB-Cβ3 isoform during megakaryocytic differentiation is reduced. Our data uncover a role of the TAL1 complex in controlling differential isoform expression of PRKACB. These results reveal a novel function of TAL1, RUNX1 and GATA1 in the transcriptional control of protein kinase A activity, with implications for cellular signalling control during differentiation and disease.
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Affiliation(s)
- Olga N Kuvardina
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Stefanie Herkt
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Annekarin Meyer
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Lucas Schneider
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Jasmin Yillah
- Georg-Speyer-Haus, Institute for Tumorbiology and experimental Therapy, Frankfurt, Germany
| | - Nicole Kohrs
- Georg-Speyer-Haus, Institute for Tumorbiology and experimental Therapy, Frankfurt, Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Erhard Seifried
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Jörn Lausen
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
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45
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SCL/TAL1: a multifaceted regulator from blood development to disease. Blood 2017; 129:2051-2060. [DOI: 10.1182/blood-2016-12-754051] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/17/2017] [Indexed: 12/12/2022] Open
Abstract
Abstract
SCL/TAL1 (stem cell leukemia/T-cell acute lymphoblastic leukemia [T-ALL] 1) is an essential transcription factor in normal and malignant hematopoiesis. It is required for specification of the blood program during development, adult hematopoietic stem cell survival and quiescence, and terminal maturation of select blood lineages. Following ectopic expression, SCL contributes to oncogenesis in T-ALL. Remarkably, SCL’s activities are all mediated through nucleation of a core quaternary protein complex (SCL:E-protein:LMO1/2 [LIM domain only 1 or 2]:LDB1 [LIM domain-binding protein 1]) and dynamic recruitment of conserved combinatorial associations of additional regulators in a lineage- and stage-specific context. The finely tuned control of SCL’s regulatory functions (lineage priming, activation, and repression of gene expression programs) provides insight into fundamental developmental and transcriptional mechanisms, and highlights mechanistic parallels between normal and oncogenic processes. Importantly, recent discoveries are paving the way to the development of innovative therapeutic opportunities in SCL+ T-ALL.
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46
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Waardenberg AJ, Homan B, Mohamed S, Harvey RP, Bouveret R. Prediction and validation of protein-protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. Open Biol 2016; 6:rsob.160183. [PMID: 27683156 PMCID: PMC5043580 DOI: 10.1098/rsob.160183] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/05/2016] [Indexed: 01/14/2023] Open
Abstract
The ability to accurately predict the DNA targets and interacting cofactors of transcriptional regulators from genome-wide data can significantly advance our understanding of gene regulatory networks. NKX2-5 is a homeodomain transcription factor that sits high in the cardiac gene regulatory network and is essential for normal heart development. We previously identified genomic targets for NKX2-5 in mouse HL-1 atrial cardiomyocytes using DNA-adenine methyltransferase identification (DamID). Here, we apply machine learning algorithms and propose a knowledge-based feature selection method for predicting NKX2-5 protein : protein interactions based on motif grammar in genome-wide DNA-binding data. We assessed model performance using leave-one-out cross-validation and a completely independent DamID experiment performed with replicates. In addition to identifying previously described NKX2-5-interacting proteins, including GATA, HAND and TBX family members, a number of novel interactors were identified, with direct protein : protein interactions between NKX2-5 and retinoid X receptor (RXR), paired-related homeobox (PRRX) and Ikaros zinc fingers (IKZF) validated using the yeast two-hybrid assay. We also found that the interaction of RXRα with NKX2-5 mutations found in congenital heart disease (Q187H, R189G and R190H) was altered. These findings highlight an intuitive approach to accessing protein-protein interaction information of transcription factors in DNA-binding experiments.
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Affiliation(s)
- Ashley J Waardenberg
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia Children's Medical Research Institute, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Bernou Homan
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Stephanie Mohamed
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia St Vincent's Clinical School, University of Sydney, Westmead, New South Wales 2145, Australia School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Romaric Bouveret
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia St Vincent's Clinical School, University of Sydney, Westmead, New South Wales 2145, Australia
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47
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Obier N, Bonifer C. Chromatin programming by developmentally regulated transcription factors: lessons from the study of haematopoietic stem cell specification and differentiation. FEBS Lett 2016; 590:4105-4115. [PMID: 27497427 DOI: 10.1002/1873-3468.12343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/26/2016] [Accepted: 07/31/2016] [Indexed: 01/08/2023]
Abstract
Although the body plan of individuals is encoded in their genomes, each cell type expresses a different gene expression programme and therefore has access to only a subset of this information. Alterations to gene expression programmes are the underlying basis for the differentiation of multiple cell types and are driven by tissue-specific transcription factors (TFs) that interact with the epigenetic regulatory machinery to programme the chromatin landscape into transcriptionally active and inactive states. The haematopoietic system has long served as a paradigm for studying the molecular principles that regulate gene expression in development. In this review article, we summarize the current knowledge on the mechanism of action of TFs regulating haematopoietic stem cell specification and differentiation, and place this information into the context of general principles governing development.
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Affiliation(s)
- Nadine Obier
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, UK
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48
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Gautier EF, Ducamp S, Leduc M, Salnot V, Guillonneau F, Dussiot M, Hale J, Giarratana MC, Raimbault A, Douay L, Lacombe C, Mohandas N, Verdier F, Zermati Y, Mayeux P. Comprehensive Proteomic Analysis of Human Erythropoiesis. Cell Rep 2016; 16:1470-1484. [PMID: 27452463 PMCID: PMC5274717 DOI: 10.1016/j.celrep.2016.06.085] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/16/2016] [Accepted: 06/22/2016] [Indexed: 01/13/2023] Open
Abstract
Mass spectrometry-based proteomics now enables the absolute quantification of thousands of proteins in individual cell types. We used this technology to analyze the dynamic proteome changes occurring during human erythropoiesis. We quantified the absolute expression of 6,130 proteins during erythroid differentiation from late burst-forming units-erythroid (BFU-Es) to orthochromatic erythroblasts. A modest correlation between mRNA and protein expression was observed. We identified several proteins with unexpected expression patterns in erythroid cells, highlighting a breakpoint in the erythroid differentiation process at the basophilic stage. We also quantified the distribution of proteins between reticulocytes and pyrenocytes after enucleation. These analyses identified proteins that are actively sorted either with the reticulocyte or the pyrenocyte. Our study provides the absolute quantification of protein expression during a complex cellular differentiation process in humans, and it establishes a framework for future studies of disordered erythropoiesis.
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Affiliation(s)
- Emilie-Fleur Gautier
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France
| | - Sarah Ducamp
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France
| | - Marjorie Leduc
- Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Plateforme de Protéomique de l'Université Paris Descartes (3P5), 75014 Paris, France
| | - Virginie Salnot
- Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Plateforme de Protéomique de l'Université Paris Descartes (3P5), 75014 Paris, France
| | - François Guillonneau
- Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Plateforme de Protéomique de l'Université Paris Descartes (3P5), 75014 Paris, France
| | | | - John Hale
- New York Blood Center, New York, NY 10065, USA
| | - Marie-Catherine Giarratana
- Laboratory of Excellence GReX, 75015 Paris, France; UPMC University Paris 06, UMR_S938 CDR Saint-Antoine, INSERM, Prolifération et Différenciation des Cellules Souches, 75012 Paris, France
| | - Anna Raimbault
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France
| | - Luc Douay
- Laboratory of Excellence GReX, 75015 Paris, France; UPMC University Paris 06, UMR_S938 CDR Saint-Antoine, INSERM, Prolifération et Différenciation des Cellules Souches, 75012 Paris, France
| | - Catherine Lacombe
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France; Ligue Nationale Contre le Cancer, Equipe Labellisée, 75014 Paris, France
| | | | - Frédérique Verdier
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France; Ligue Nationale Contre le Cancer, Equipe Labellisée, 75014 Paris, France
| | - Yael Zermati
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France; Ligue Nationale Contre le Cancer, Equipe Labellisée, 75014 Paris, France
| | - Patrick Mayeux
- INSERM U1016, Institut Cochin, 75014 Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR8104, 75014 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France; Laboratory of Excellence GReX, 75015 Paris, France; Plateforme de Protéomique de l'Université Paris Descartes (3P5), 75014 Paris, France; Ligue Nationale Contre le Cancer, Equipe Labellisée, 75014 Paris, France.
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The proto-oncogenic protein TAL1 controls TGF-β1 signaling through interaction with SMAD3. BIOCHIMIE OPEN 2016; 2:69-78. [PMID: 29632840 PMCID: PMC5889486 DOI: 10.1016/j.biopen.2016.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/07/2016] [Indexed: 01/13/2023]
Abstract
TGF-β1 is involved in many aspects of tissue development and homeostasis including hematopoiesis. The TAL1 transcription factor is also an important player of this latter process and is expressed very early in the myeloid and erythroid lineages. We previously established a link between TGF-β1 signaling and TAL1 by showing that the cytokine was able to induce its proteolytic degradation by the ubiquitin proteasome pathway. In this manuscript we show that TAL1 interacts with SMAD3 that acts in the pathway downstream of TGF-β1 association with its receptor. TAL1 expression strengthens the positive or negative effect of SMAD3 on various genes. Both transcription factors activate the inhibitory SMAD7 factor through the E box motif present in its transcriptional promoter. DNA precipitation assays showed that TAL1 present in Jurkat or K562 cells binds to this SMAD binding element in a SMAD3 dependent manner. SMAD3 and TAL1 also inhibit several genes including ID1, hTERT and TGF-β1 itself. In this latter case TAL1 and SMAD3 can impair the positive effect exerted by E47. Our results indicate that TAL1 expression can modulate TGF-β1 signaling by interacting with SMAD3 and by increasing its transcriptional properties. They also suggest the existence of a negative feedback loop between TAL1 expression and TGF-β1 signaling.
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50
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Insight into GATA1 transcriptional activity through interrogation of cis elements disrupted in human erythroid disorders. Proc Natl Acad Sci U S A 2016; 113:4434-9. [PMID: 27044088 DOI: 10.1073/pnas.1521754113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Whole-exome sequencing has been incredibly successful in identifying causal genetic variants and has revealed a number of novel genes associated with blood and other diseases. One limitation of this approach is that it overlooks mutations in noncoding regulatory elements. Furthermore, the mechanisms by which mutations in transcriptionalcis-regulatory elements result in disease remain poorly understood. Here we used CRISPR/Cas9 genome editing to interrogate three such elements harboring mutations in human erythroid disorders, which in all cases are predicted to disrupt a canonical binding motif for the hematopoietic transcription factor GATA1. Deletions of as few as two to four nucleotides resulted in a substantial decrease (>80%) in target gene expression. Isolated deletions of the canonical GATA1 binding motif completely abrogated binding of the cofactor TAL1, which binds to a separate motif. Having verified the functionality of these three GATA1 motifs, we demonstrate strong evolutionary conservation of GATA1 motifs in regulatory elements proximal to other genes implicated in erythroid disorders, and show that targeted disruption of such elements results in altered gene expression. By modeling transcription factor binding patterns, we show that multiple transcription factors are associated with erythroid gene expression, and have created predictive maps modeling putative disruptions of their binding sites at key regulatory elements. Our study provides insight into GATA1 transcriptional activity and may prove a useful resource for investigating the pathogenicity of noncoding variants in human erythroid disorders.
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