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Ling Z, Li J, Jiang T, Zhang Z, Zhu Y, Zhou Z, Yang J, Tong X, Yang B, Huang L. Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits. Commun Biol 2024; 7:381. [PMID: 38553586 PMCID: PMC10980749 DOI: 10.1038/s42003-024-06050-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
Genetic variants can influence complex traits by altering gene expression through changes to regulatory elements. However, the genetic variants that affect the activity of regulatory elements in pigs are largely unknown, and the extent to which these variants influence gene expression and contribute to the understanding of complex phenotypes remains unclear. Here, we annotate 90,991 high-quality regulatory elements using acetylation of histone H3 on lysine 27 (H3K27ac) ChIP-seq of 292 pig livers. Combined with genome resequencing and RNA-seq data, we identify 28,425 H3K27ac quantitative trait loci (acQTLs) and 12,250 expression quantitative trait loci (eQTLs). Through the allelic imbalance analysis, we validate two causative acQTL variants in independent datasets. We observe substantial sharing of genetic controls between gene expression and H3K27ac, particularly within promoters. We infer that 46% of H3K27ac exhibit a concomitant rather than causative relationship with gene expression. By integrating GWAS, eQTLs, acQTLs, and transcription factor binding prediction, we further demonstrate their application, through metabolites dulcitol, phosphatidylcholine (PC) (16:0/16:0) and published phenotypes, in identifying likely causal variants and genes, and discovering sub-threshold GWAS loci. We provide insight into the relationship between regulatory elements and gene expression, and the genetic foundation for dissecting the molecular mechanism of phenotypes.
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Affiliation(s)
- Ziqi Ling
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
| | - Jing Li
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Tao Jiang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Zhen Zhang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Yaling Zhu
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Zhimin Zhou
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Jiawen Yang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Xinkai Tong
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China
| | - Bin Yang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
| | - Lusheng Huang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, P.R. China.
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2
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Cheung WA, Johnson AF, Rowell WJ, Farrow E, Hall R, Cohen ASA, Means JC, Zion TN, Portik DM, Saunders CT, Koseva B, Bi C, Truong TK, Schwendinger-Schreck C, Yoo B, Johnston JJ, Gibson M, Evrony G, Rizzo WB, Thiffault I, Younger ST, Curran T, Wenger AM, Grundberg E, Pastinen T. Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort. Nat Commun 2023; 14:3090. [PMID: 37248219 DOI: 10.1038/s41467-023-38782-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
Long-read HiFi genome sequencing allows for accurate detection and direct phasing of single nucleotide variants, indels, and structural variants. Recent algorithmic development enables simultaneous detection of CpG methylation for analysis of regulatory element activity directly in HiFi reads. We present a comprehensive haplotype resolved 5-base HiFi genome sequencing dataset from a rare disease cohort of 276 samples in 152 families to identify rare (~0.5%) hypermethylation events. We find that 80% of these events are allele-specific and predicted to cause loss of regulatory element activity. We demonstrate heritability of extreme hypermethylation including rare cis variants associated with short (~200 bp) and large hypermethylation events (>1 kb), respectively. We identify repeat expansions in proximal promoters predicting allelic gene silencing via hypermethylation and demonstrate allelic transcriptional events downstream. On average 30-40 rare hypermethylation tiles overlap rare disease genes per patient, providing indications for variation prioritization including a previously undiagnosed pathogenic allele in DIP2B causing global developmental delay. We propose that use of HiFi genome sequencing in unsolved rare disease cases will allow detection of unconventional diseases alleles due to loss of regulatory element activity.
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Affiliation(s)
- Warren A Cheung
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Adam F Johnson
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | | | - Emily Farrow
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | | | - Ana S A Cohen
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - John C Means
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Tricia N Zion
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | | | | | - Boryana Koseva
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Chengpeng Bi
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Tina K Truong
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Carl Schwendinger-Schreck
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Byunggil Yoo
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Jeffrey J Johnston
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Margaret Gibson
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Gilad Evrony
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
| | - William B Rizzo
- Child Health Research Institute, Department of Pediatrics, Nebraska Medical Center, Omaha, NE, USA
| | - Isabelle Thiffault
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Scott T Younger
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Tom Curran
- Children's Mercy Research Institute, Kansas City, MO, USA
| | | | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA.
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA.
| | - Tomi Pastinen
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA.
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA.
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3
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Cao T, Li A, Huang Y. pandasGWAS: a Python package for easy retrieval of GWAS catalog data. BMC Genomics 2023; 24:238. [PMID: 37142970 PMCID: PMC10161511 DOI: 10.1186/s12864-023-09340-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/26/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Since the NHGRI-EBI Catalog of human genome-wide association studies was established by NHGRI in 2008, research on it has attracted more and more researchers as the amount of data has grown rapidly. Easy-to-use, open-source, general-purpose programs for accessing the NHGRI-EBI Catalog of human genome-wide association studies are in great demand for current Python data analysis pipeline. RESULTS In this work we present pandasGWAS, a Python package that provides programmatic access to the NHGRI-EBI Catalog of human genome-wide association studies. Instead of downloading all data locally, pandasGWAS queries data based on input criteria and handles paginated data gracefully. The data is then transformed into multiple associated pandas.DataFrame objects according to its hierarchical relationships, which makes it easy to integrate into current Python-based data analysis toolkits. CONCLUSIONS pandasGWAS is an open-source Python package that provides the first Python client interface to the GWAS Catalog REST API. Compared with existing tools, the data structure of pandasGWAS is more consistent with the design specification of GWAS Catalog REST API, and provides many easy-to-use mathematical symbol operations.
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Affiliation(s)
- Tianze Cao
- School of Mathematics, Hangzhou Normal University, Hangzhou, 311121, China
| | - Anshui Li
- Department of Statistics, Shaoxing University, Shaoxing, 312000, China
| | - Yuexia Huang
- School of Mathematics, Hangzhou Normal University, Hangzhou, 311121, China.
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4
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Liang Y, Li L, Xin T, Li B, Zhang D. Superenhancer-transcription factor regulatory network in malignant tumors. Open Med (Wars) 2021; 16:1564-1582. [PMID: 34722892 PMCID: PMC8525661 DOI: 10.1515/med-2021-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 06/02/2021] [Accepted: 06/16/2021] [Indexed: 11/15/2022] Open
Abstract
Objective This study aims to identify superenhancer (SE)-transcriptional factor (TF) regulatory network related to eight common malignant tumors based on ChIP-seq data modified by histone H3K27ac in the enhancer region of the SRA database. Methods H3K27ac ChIP-seq data of eight common malignant tumor samples were downloaded from the SRA database and subjected to comparison with the human reference genome hg19. TFs regulated by SEs were screened with HOMER software. Core regulatory circuitry (CRC) in malignant tumor samples was defined through CRCmapper software and validated by RNA-seq data in TCGA. The findings were substantiated in bladder cancer cell experiments. Results Different malignant tumors could be distinguished through the H3K27ac signal. After SE identification in eight common malignant tumor samples, 35 SE-regulated genes were defined as malignant tumor-specific. SE-regulated specific TFs effectively distinguished the types of malignant tumors. Finally, we obtained 60 CRC TFs, and SMAD3 exhibited a strong H3K27ac signal in eight common malignant tumor samples. In vitro experimental data verified the presence of a SE-TF regulatory network in bladder cancer, and SE-TF regulatory network enhanced the malignant phenotype of bladder cancer cells. Conclusion The SE-TF regulatory network with SMAD3 as the core TF may participate in the carcinogenesis of malignant tumors.
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Affiliation(s)
- Yuan Liang
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Linlin Li
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Tian Xin
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Binru Li
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Dalin Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, No. 155, Nanjing North Street, Shenyang 110001, Liaoning Province, People's Republic of China
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5
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Tian L, Khan A, Ning Z, Yuan K, Zhang C, Lou H, Yuan Y, Xu S. Genome-wide comparison of allele-specific gene expression between African and European populations. Hum Mol Genet 2018; 27:1067-1077. [DOI: 10.1093/hmg/ddy027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/05/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Lei Tian
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Asifullah Khan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200 KP, Pakistan
| | - Zhilin Ning
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Yuan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyi Lou
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Yuan Yuan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Shuhua Xu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China
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6
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Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, Watt S, Datta A, Clarke L, Flicek P, Mead D, Paul DS, Beck S, Bourque G, Lathrop M, Tchernof A, Vohl MC, Demenais F, Pin I, Downes K, Stunnenberg HG, Soranzo N, Pastinen T, Grundberg E. Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome. Genome Biol 2017; 18:50. [PMID: 28283040 PMCID: PMC5346261 DOI: 10.1186/s13059-017-1173-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023] Open
Abstract
Background The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have only been carried out in a limited set of samples. Results We describe a large-scale coordinated study of allelic and non-allelic effects on DNA methylation, histone mark deposition, and gene expression, detecting the interrelations between epigenetic and functional features at unprecedented resolution. We use information from whole genome and targeted bisulfite sequencing from 910 samples to perform genotype-dependent analyses of allele-specific methylation (ASM) and non-allelic methylation (mQTL). In addition, we introduce a novel genotype-independent test to detect methylation imbalance between chromosomes. Of the ~2.2 million CpGs tested for ASM, mQTL, and genotype-independent effects, we identify ~32% as being genetically regulated (ASM or mQTL) and ~14% as being putatively epigenetically regulated. We also show that epigenetically driven effects are strongly enriched in repressed regions and near transcription start sites, whereas the genetically regulated CpGs are enriched in enhancers. Known imprinted regions are enriched among epigenetically regulated loci, but we also observe several novel genomic regions (e.g., HOX genes) as being epigenetically regulated. Finally, we use our ASM datasets for functional interpretation of disease-associated loci and show the advantage of utilizing naïve T cells for understanding autoimmune diseases. Conclusions Our rich catalogue of haploid methylomes across multiple tissues will allow validation of epigenome association studies and exploration of new biological models for allelic exclusion in the human genome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1173-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Warren A Cheung
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Andréanne Morin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Valérie Siroux
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Inserm U1209, CNRS, University Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Dylan Aïssi
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Inserm U1209, CNRS, University Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Lu Chen
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Louella Vasquez
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Fiona Allum
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, G1V 0A6, Canada
| | - Emmanuelle Bouzigon
- Genetic Variation and Human Diseases Unit, UMR-946, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | | | - Elodie Boulier
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Adriana Redensek
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Stephen Watt
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Avik Datta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Daniel Mead
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Dirk S Paul
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.,Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, CB1 8RN, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - André Tchernof
- Québec Heart and Lung Institute, Laval University, Québec, QC, G1V 4G5, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, G1V 0A6, Canada
| | - Florence Demenais
- Genetic Variation and Human Diseases Unit, UMR-946, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Isabelle Pin
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Inserm U1209, CNRS, University Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France.,Pédiatrie, Centre Hospitalier Universitaire (CHU) Grenoble Alpes, Grenoble, France
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.,National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Hendrick G Stunnenberg
- Faculty of Science, Department of Molecular Biology, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Nicole Soranzo
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.,The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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7
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Role of DNA methylation in expression control of the IKZF3-GSDMA region in human epithelial cells. PLoS One 2017; 12:e0172707. [PMID: 28241063 PMCID: PMC5328393 DOI: 10.1371/journal.pone.0172707] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 02/08/2017] [Indexed: 12/29/2022] Open
Abstract
Chromosomal region 17q12-q21 is associated with asthma and harbors regulatory polymorphisms that influence expression levels of all five protein-coding genes in the region: IKAROS family zinc finger 3 (Aiolos) (IKZF3), zona pellucida binding protein 2 (ZPBP2), ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3), and gasdermins A and B (GSDMA, GSDMB). Furthermore, DNA methylation in this region has been implicated as a potential modifier of the genetic risk of asthma development. To further characterize the effect of DNA methylation, we examined the impact of treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza-dC) that causes DNA demethylation, on expression and promoter methylation of the five 17q12-q21 genes in the human airway epithelium cell line NuLi-1, embryonic kidney epithelium cell line 293T and human adenocarcinoma cell line MCF-7. 5-aza-dC treatment led to upregulation of expression of GSDMA in all three cell lines. ZPBP2 was upregulated in NuLi-1, but remained repressed in 293T and MCF-7 cells, whereas ORMDL3 was upregulated in 293T and MCF-7 cells, but not NuLi-1. Upregulation of ZPBP2 and GSDMA was accompanied by a decrease in promoter methylation. Moreover, 5-aza-dC treatment modified allelic expression of ZPBP2 and ORMDL3 suggesting that different alleles may respond differently to treatment. We also identified a polymorphic CTCF-binding site in intron 1 of ORMDL3 carrying a CG SNP rs4065275 and determined its methylation level. The site’s methylation was unaffected by 5-aza-dC treatment in NuLi-1 cells. We conclude that modest changes (8–13%) in promoter methylation levels of ZPBP2 and GSDMA may cause substantial changes in RNA levels and that allelic expression of ZPBP2 and ORMDL3 is mediated by DNA methylation.
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8
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Adoue V, Schiavi A, Light N, Almlöf JC, Lundmark P, Ge B, Kwan T, Caron M, Rönnblom L, Wang C, Chen SH, Goodall AH, Cambien F, Deloukas P, Ouwehand WH, Syvänen AC, Pastinen T. Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs. Mol Syst Biol 2014; 10:754. [PMID: 25326100 PMCID: PMC4299376 DOI: 10.15252/msb.20145114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Most complex disease-associated genetic variants are located in non-coding regions and are
therefore thought to be regulatory in nature. Association mapping of differential allelic expression
(AE) is a powerful method to identify SNPs with direct cis-regulatory impact
(cis-rSNPs). We used AE mapping to identify cis-rSNPs regulating
gene expression in 55 and 63 HapMap lymphoblastoid cell lines from a Caucasian and an African
population, respectively, 70 fibroblast cell lines, and 188 purified monocyte samples and found
40–60% of these cis-rSNPs to be shared across cell types. We uncover
a new class of cis-rSNPs, which disrupt footprint-derived de novo
motifs that are predominantly bound by repressive factors and are implicated in disease
susceptibility through overlaps with GWAS SNPs. Finally, we provide the proof-of-principle for a new
approach for genome-wide functional validation of transcription factor–SNP interactions. By
perturbing NFκB action in lymphoblasts, we identified 489 cis-regulated
transcripts with altered AE after NFκB perturbation. Altogether, we perform a comprehensive
analysis of cis-variation in four cell populations and provide new tools for the
identification of functional variants associated to complex diseases.
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Affiliation(s)
- Veronique Adoue
- Institute National de la Santé et de la Recherche Médicale (INSERM), U1043, Toulouse, France
| | - Alicia Schiavi
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Nicholas Light
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Jonas Carlsson Almlöf
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Lundmark
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bing Ge
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Lars Rönnblom
- Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Chuan Wang
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Shu-Huang Chen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Alison H Goodall
- Department of Cardiovascular Science, University of Leicester, Leicester, UK Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, UK Cardiogenics Consortium
| | - Francois Cambien
- Cardiogenics Consortium INSERM UMRS 937 Pierre and Marie Curie University and Medical School, Paris, France
| | - Panos Deloukas
- Cardiogenics Consortium Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Willem H Ouwehand
- Cardiogenics Consortium Department of Haematology, University of Cambridge, Cambridge, UK National Health Service Blood and Transplant, Cambridge Centre, Cambridge, UK
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
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