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McCaw ZR, O'Dushlaine C, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. An allelic-series rare-variant association test for candidate-gene discovery. Am J Hum Genet 2023; 110:1330-1342. [PMID: 37494930 PMCID: PMC10432147 DOI: 10.1016/j.ajhg.2023.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/28/2023] Open
Abstract
Allelic series are of candidate therapeutic interest because of the existence of a dose-response relationship between the functionality of a gene and the degree or severity of a phenotype. We define an allelic series as a collection of variants in which increasingly deleterious mutations lead to increasingly large phenotypic effects, and we have developed a gene-based rare-variant association test specifically targeted to identifying genes containing allelic series. Building on the well-known burden test and sequence kernel association test (SKAT), we specify a variety of association models covering different genetic architectures and integrate these into a Coding-Variant Allelic-Series Test (COAST). Through extensive simulations, we confirm that COAST maintains the type I error and improves the power when the pattern of coding-variant effect sizes increases monotonically with mutational severity. We applied COAST to identify allelic-series genes for four circulating-lipid traits and five cell-count traits among 145,735 subjects with available whole-exome sequencing data from the UK Biobank. Compared with optimal SKAT (SKAT-O), COAST identified 29% more Bonferroni-significant associations with circulating-lipid traits, on average, and 82% more with cell-count traits. All of the gene-trait associations identified by COAST have corroborating evidence either from rare-variant associations in the full cohort (Genebass, n = 400,000) or from common-variant associations in the GWAS Catalog. In addition to detecting many gene-trait associations present in Genebass by using only a fraction (36.9%) of the sample, COAST detects associations, such as that between ANGPTL4 and triglycerides, that are absent from Genebass but that have clear common-variant support.
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Affiliation(s)
| | | | | | | | | | | | - Francesco Paolo Casale
- Institute of AI for Health, Helmholtz Munich, Neuherberg, Germany; Helmholtz Pioneer Campus, Helmholtz Munich, Neuherberg, Germany; School of Computation, Information and Technology, Technical University of Munich, Munich, Germany
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Baud A, Casale FP, Barkley-Levenson AM, Farhadi N, Montillot C, Yalcin B, Nicod J, Palmer AA, Stegle O. Dissecting indirect genetic effects from peers in laboratory mice. Genome Biol 2021; 22:216. [PMID: 34311762 PMCID: PMC8311926 DOI: 10.1186/s13059-021-02415-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The phenotype of an individual can be affected not only by the individual's own genotypes, known as direct genetic effects (DGE), but also by genotypes of interacting partners, indirect genetic effects (IGE). IGE have been detected using polygenic models in multiple species, including laboratory mice and humans. However, the underlying mechanisms remain largely unknown. Genome-wide association studies of IGE (igeGWAS) can point to IGE genes, but have not yet been applied to non-familial IGE arising from "peers" and affecting biomedical phenotypes. In addition, the extent to which igeGWAS will identify loci not identified by dgeGWAS remains an open question. Finally, findings from igeGWAS have not been confirmed by experimental manipulation. RESULTS We leverage a dataset of 170 behavioral, physiological, and morphological phenotypes measured in 1812 genetically heterogeneous laboratory mice to study IGE arising between same-sex, adult, unrelated mice housed in the same cage. We develop and apply methods for igeGWAS in this context and identify 24 significant IGE loci for 17 phenotypes (FDR < 10%). We observe no overlap between IGE loci and DGE loci for the same phenotype, which is consistent with the moderate genetic correlations between DGE and IGE for the same phenotype estimated using polygenic models. Finally, we fine-map seven significant IGE loci to individual genes and find supportive evidence in an experiment with a knockout model that Epha4 gives rise to IGE on stress-coping strategy and wound healing. CONCLUSIONS Our results demonstrate the potential for igeGWAS to identify IGE genes and shed light into the mechanisms of peer influence.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
- Current Address: Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- Microsoft Research New England, Cambridge, MA USA
| | | | - Nilgoun Farhadi
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
| | - Charlotte Montillot
- INSERM U1231 GAD Laboratory, University Bourgogne Franche-Comté, 21070 Dijon, France
| | - Binnaz Yalcin
- INSERM U1231 GAD Laboratory, University Bourgogne Franche-Comté, 21070 Dijon, France
| | - Jerome Nicod
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Current Address: The Francis Crick Institute, London, UK
| | - Abraham A. Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, 69120 Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, UK
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3
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Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Interactions between genetic variation and cellular environment in skeletal muscle gene expression. PLoS One 2018; 13:e0195788. [PMID: 29659628 PMCID: PMC5901994 DOI: 10.1371/journal.pone.0195788] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 03/29/2018] [Indexed: 12/18/2022] Open
Abstract
From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis-acting genotype-environment interactions (GxE)—genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate environmental response expression quantitative trait loci (reQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.
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Affiliation(s)
- D. Leland Taylor
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - David A. Knowles
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea H. Ramirez
- Department of Medicine, Vanderbilt University Medical Center, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Brooke N. Wolford
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Li Guan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ricardo D’Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephen C. J. Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Peter S. Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Michael R. Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Ryan P. Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leena Kinnunen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Jouko Saramies
- South Karelia Social and Health Care District, Lappeenranta, Finland
| | - Jouko Sundvall
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Timo A. Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Jaakko Tuomilehto
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Neurosciences and Preventive Medicine, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Dasman Diabetes Institute, Dasman, Kuwait
| | - Heikki A. Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine and Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, Haartmaninkatu 4, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, Finland
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- * E-mail: (EB); (FSC)
| | - Francis S. Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- * E-mail: (EB); (FSC)
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4
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Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 2017; 546:370-375. [PMID: 28489815 PMCID: PMC5524171 DOI: 10.1038/nature22403] [Citation(s) in RCA: 344] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 04/27/2017] [Indexed: 02/07/2023]
Abstract
Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells.
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Affiliation(s)
- Helena Kilpinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Angela Goncalves
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Andreas Leha
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Vackar Afzal
- Centre for Gene Regulation &Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Kaur Alasoo
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sofie Ashford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Sendu Bala
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Dalila Bensaddek
- Centre for Gene Regulation &Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Oliver J Culley
- Centre for Stem Cells &Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Petr Danecek
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Adam Faulconbridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Annie Kathuria
- Centre for Stem Cells &Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Davis McCarthy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- St Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia
| | - Shane A McCarthy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ruta Meleckyte
- Centre for Stem Cells &Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Yasin Memari
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nathalie Moens
- Centre for Stem Cells &Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Filipa Soares
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Biomedical Research Centre, Anne McLaren Laboratory, Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Alice Mann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chukwuma A Agu
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alex Alderton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rachel Nelson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah Harper
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Minal Patel
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alistair White
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sharad R Patel
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Reena Halai
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Christopher M Kirton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anja Kolb-Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Philip Beales
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Davide Danovi
- Centre for Stem Cells &Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Angus I Lamond
- Centre for Gene Regulation &Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Willem H Ouwehand
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Ludovic Vallier
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Wellcome Trust and MRC Cambridge Stem Cell Institute and Biomedical Research Centre, Anne McLaren Laboratory, Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Fiona M Watt
- Centre for Stem Cells &Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel J Gaffney
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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5
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Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs. Nature 2017; 546:686. [PMID: 28614302 DOI: 10.1038/nature23012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This corrects the article DOI: 10.1038/nature22403.
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6
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Casale FP, Horta D, Rakitsch B, Stegle O. Joint genetic analysis using variant sets reveals polygenic gene-context interactions. PLoS Genet 2017; 13:e1006693. [PMID: 28426829 PMCID: PMC5398484 DOI: 10.1371/journal.pgen.1006693] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 03/15/2017] [Indexed: 01/28/2023] Open
Abstract
Joint genetic models for multiple traits have helped to enhance association analyses. Most existing multi-trait models have been designed to increase power for detecting associations, whereas the analysis of interactions has received considerably less attention. Here, we propose iSet, a method based on linear mixed models to test for interactions between sets of variants and environmental states or other contexts. Our model generalizes previous interaction tests and in particular provides a test for local differences in the genetic architecture between contexts. We first use simulations to validate iSet before applying the model to the analysis of genotype-environment interactions in an eQTL study. Our model retrieves a larger number of interactions than alternative methods and reveals that up to 20% of cases show context-specific configurations of causal variants. Finally, we apply iSet to test for sub-group specific genetic effects in human lipid levels in a large human cohort, where we identify a gene-sex interaction for C-reactive protein that is missed by alternative methods. Genetic effects on phenotypes can depend on external contexts, including environment. Statistical tests for identifying such interactions are important to understand how individual genetic variants may act in different contexts. Interaction effects can either be studied using measurements of a given phenotype in different contexts, under the same genetic backgrounds, or by stratifying a population into subgroups. Here, we derive a method based on linear mixed models that can be applied to both of these designs. iSet enables testing for interactions between context and sets of variants, and accounts for polygenic effects. We validate our model using simulations, before applying it to the genetic analysis of gene expression studies and genome-wide association studies of human blood lipid levels. We find that modeling interactions with variant sets offers increased power, thereby uncovering interactions that cannot be detected by alternative methods.
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Affiliation(s)
- Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, United Kingdom
- * E-mail: (FPC); (OS)
| | - Danilo Horta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, United Kingdom
| | - Barbara Rakitsch
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, United Kingdom
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, United Kingdom
- * E-mail: (FPC); (OS)
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7
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Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell 2017; 167:1398-1414.e24. [PMID: 27863251 PMCID: PMC5119954 DOI: 10.1016/j.cell.2016.10.026] [Citation(s) in RCA: 389] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 08/19/2016] [Accepted: 10/14/2016] [Indexed: 12/20/2022]
Abstract
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14+ monocytes, CD16+ neutrophils, and naive CD4+ T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk. Genome, transcriptome, and epigenome reference panel in three human immune cell types Identified 4,418 genes associated with epigenetic changes independent of genetics Described genome-epigenome coordination defining cell-type-specific regulatory events Functionally mapped disease mechanisms at 345 unique autoimmune disease loci
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Affiliation(s)
- 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
| | - Bing Ge
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Louella Vasquez
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Tony Kwan
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Diego Garrido-Martín
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader, 88, Barcelona 8003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10- 12, Barcelona 8002, Spain
| | - Stephen Watt
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Ying Yan
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Kousik Kundu
- 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
| | - Simone Ecker
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain; UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Avik Datta
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Richardson
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Frances Burden
- 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
| | - Daniel Mead
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Alice L Mann
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Jose Maria Fernandez
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain
| | - Sophia Rowlston
- 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
| | - Steven P Wilder
- Genome Analysis, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Samantha Farrow
- 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
| | - Xiaojian Shao
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - John J Lambourne
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada; 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
| | - Adriana Redensek
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Cornelis A Albers
- Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, P.O. Box 9101, Nijmegen 6500 HB, the Netherlands; Molecular Developmental Biology, Radboud Institute for Life Sciences, Radboud University, P.O. Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Vyacheslav Amstislavskiy
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Sofie Ashford
- 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
| | - Kim Berentsen
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Lorenzo Bomba
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Guillaume Bourque
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - David Bujold
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Stephan Busche
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Maxime Caron
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Shu-Huang Chen
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Warren Cheung
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Oliver Delaneau
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, Geneva 1211, Switzerland
| | - Emmanouil T Dermitzakis
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, Geneva 1211, Switzerland
| | - Heather Elding
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Irina Colgiu
- Human Genetics Informatics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Frederik O Bagger
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Paul Flicek
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Valentina Iotchkova
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eva Janssen-Megens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Bowon Kim
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Ernesto Lowy
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amit Mandoli
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Filomena Matarese
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Matthew T Maurano
- Institute for Systems Genetics, New York University Langone Medical Center, ACLS West, Room 511, 430 East 29(th) Street, New York, NY 10016, USA
| | - John A Morris
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Vera Pancaldi
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain
| | - Farzin Pourfarzad
- Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Plesmanlaan 125, Amsterdam 1066CX, the Netherlands
| | - Karola Rehnstrom
- 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
| | - Augusto Rendon
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; Bioinformatics, Genomics England, Charterhouse Square, London EC1M 6BQ, UK
| | - Thomas Risch
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Nilofar Sharifi
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Marie-Michelle Simon
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Marc Sultan
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain
| | - Klaudia Walter
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Shuang-Yin Wang
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Mattia Frontini
- 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; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Stylianos E Antonarakis
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, Geneva 1211, Switzerland
| | - Laura Clarke
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Roderic Guigo
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader, 88, Barcelona 8003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10- 12, Barcelona 8002, Spain; Computational Genomics, Institut Hospital del Mar d'Investigacions Mediques (IMIM), Carrer del Dr. Aiguader, 88, Barcelona 8003, Spain
| | - Daniel Rico
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain; Institute of Cellular Medicine, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Willem H Ouwehand
- 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; National Health Service (NHS) Blood and Transplant, 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 at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK
| | - Taco W Kuijpers
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Plesmanlaan 125, Amsterdam 1066CX, the Netherlands; Emma Children's Hospital, Academic Medical Center (AMC), University of Amsterdam, Location H7-230, Meibergdreef 9, Amsterdam 1105AZ, the Netherlands
| | - 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, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - 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
| | - Tomi Pastinen
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada.
| | - 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 at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK.
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8
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Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS. Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. Genome Biol 2017; 18:18. [PMID: 28126036 PMCID: PMC5270224 DOI: 10.1186/s13059-017-1156-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/17/2017] [Indexed: 12/11/2022] Open
Abstract
Background A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. Results We apply a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14+CD16− monocytes, CD66b+CD16+ neutrophils, and CD4+CD45RA+ naïve T cells from the same 125 healthy individuals. We discover substantially increased variability in neutrophils compared to monocytes and T cells. In neutrophils, genes with hypervariable expression are found to be implicated in key immune pathways and are associated with cellular properties and environmental exposure. We also observe increased sex-specific gene expression differences in neutrophils. Neutrophil-specific DNA methylation hypervariable sites are enriched at dynamic chromatin regions and active enhancers. Conclusions Our data highlight the importance of transcriptional and epigenetic variability for the key role of neutrophils as the first responders to inflammatory stimuli. We provide a resource to enable further functional studies into the plasticity of immune cells, which can be accessed from: http://blueprint-dev.bioinfo.cnio.es/WP10/hypervariability. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1156-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simone Ecker
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain. .,UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Lu Chen
- Department of Human Genetics, 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, Hinxton, UK
| | - Vera Pancaldi
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Frederik O Bagger
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, Hinxton, UK.,National Health Service (NHS) Blood and Transplant, 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
| | - José María Fernández
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Enrique Carrillo de Santa Pau
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - David Juan
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Alice L Mann
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Stephen Watt
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Nikos Sidiropoulos
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Angelika Merkel
- National Center for Genomic Analysis (CNAG), Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer Baldiri i Reixac 4, 08028, Barcelona, Spain
| | | | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, Hinxton, UK.,National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.,British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, Hinxton, UK.,National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Dr. Penfield, Montreal, H3A 0G1, Canada
| | - Taco W Kuijpers
- Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Plesmanlaan 125, Amsterdam, 1066CX, The Netherlands.,Emma Children's Hospital, Academic Medical Center (AMC), University of Amsterdam, Location H7-230, Meibergdreef 9, Amsterdam, 1105AX, The Netherlands
| | - Daniel Rico
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Nicole Soranzo
- Department of Human Genetics, 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, Hinxton, 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, Wort's Causeway, Cambridge, CB1 8RN, UK.
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9
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Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O. Genetic Variation in the Social Environment Contributes to Health and Disease. PLoS Genet 2017; 13:e1006498. [PMID: 28121987 PMCID: PMC5266220 DOI: 10.1371/journal.pgen.1006498] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 11/21/2016] [Indexed: 11/29/2022] Open
Abstract
Assessing the impact of the social environment on health and disease is challenging. As social effects are in part determined by the genetic makeup of social partners, they can be studied from associations between genotypes of one individual and phenotype of another (social genetic effects, SGE, also called indirect genetic effects). For the first time we quantified the contribution of SGE to more than 100 organismal phenotypes and genome-wide gene expression measured in laboratory mice. We find that genetic variation in cage mates (i.e. SGE) contributes to variation in organismal and molecular measures related to anxiety, wound healing, immune function, and body weight. Social genetic effects explained up to 29% of phenotypic variance, and for several traits their contribution exceeded that of direct genetic effects (effects of an individual's genotypes on its own phenotype). Importantly, we show that ignoring SGE can severely bias estimates of direct genetic effects (heritability). Thus SGE may be an important source of "missing heritability" in studies of complex traits in human populations. In summary, our study uncovers an important contribution of the social environment to phenotypic variation, sets the basis for using SGE to dissect social effects, and identifies an opportunity to improve studies of direct genetic effects.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Megan K. Mulligan
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jesse F. Ingels
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Casey J. Bohl
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Jacques Callebert
- AP-HP, Hôpital Lariboisière, Department of Biochemistry, INSERM U942, Paris, France
| | - Jean-Marie Launay
- AP-HP, Hôpital Lariboisière, Department of Biochemistry, INSERM U942, Paris, France
| | - Jon Krohn
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | | | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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10
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Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature 2015; 526:75-81. [PMID: 26432246 PMCID: PMC4617611 DOI: 10.1038/nature15394] [Citation(s) in RCA: 1364] [Impact Index Per Article: 151.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 08/20/2015] [Indexed: 12/11/2022]
Abstract
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.
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Affiliation(s)
- Peter H. Sudmant
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Eugene J. Gardner
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W Baltimore Street, Baltimore, 21201 Maryland USA
| | - Robert E. Handsaker
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, Boston, 02115 Massachusetts USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, 55905 Minnesota USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
- Howard Hughes Medical Institute, University of Washington, Seattle, 98195 Washington USA
| | - Yan Zhang
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
| | - Kai Ye
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Genetics, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
| | - Goo Jun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, 48109 Michigan USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler St., Houston, 77030 Texas USA
| | - Markus Hsi-Yang Fritz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Miriam K. Konkel
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, 70803 Louisiana USA
| | - Ankit Malhotra
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
| | - Adrian M. Stütz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Xinghua Shi
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, 28223 North Carolina USA
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Jieming Chen
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, 06520 Connecticut USA
| | - Fereydoun Hormozdiari
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Gargi Dayama
- Department of Computational Medicine & Bioinformatics, University of Michigan, 500 S. State Street, Ann Arbor, 48109 Michigan USA
| | - Ken Chen
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
| | - Maika Malig
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Mark J. P. Chaisson
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Klaudia Walter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - Sascha Meiers
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Seva Kashin
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, Boston, 02115 Massachusetts USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
| | - Erik Garrison
- Department of Biology, Boston College, 355 Higgins Hall, 140 Commonwealth Avenue, Chestnut Hill, 02467 Massachusetts USA
| | - Adam Auton
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, 10461 New York USA
| | - Hugo Y. K. Lam
- Bina Technologies, Roche Sequencing, 555 Twin Dolphin Drive, Redwood City, 94065 California USA
| | - Xinmeng Jasmine Mu
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, 06800 Turkey
| | - Danny Antaki
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
| | - Taejeong Bae
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, 55905 Minnesota USA
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
| | - Peter Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland USA
| | - Zechen Chong
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Elif Dal
- Department of Computer Engineering, Bilkent University, Ankara, 06800 Turkey
| | - Li Ding
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Genetics, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Medicine, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Siteman Cancer Center, 660 South Euclid Avenue, St Louis, 63110 Missouri USA
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, 1241 Catherine Street, Ann Arbor, 48109 Michigan USA
| | - Xian Fan
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
| | - Madhusudan Gujral
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
| | - Fatma Kahveci
- Department of Computer Engineering, Bilkent University, Ankara, 06800 Turkey
| | - Jeffrey M. Kidd
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, 48109 Michigan USA
- Department of Human Genetics, University of Michigan, 1241 Catherine Street, Ann Arbor, 48109 Michigan USA
| | - Yu Kong
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, 10461 New York USA
| | - Eric-Wubbo Lameijer
- Molecular Epidemiology, Leiden University Medical Center, Leiden, 2300RA The Netherlands
| | - Shane McCarthy
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Richard A. Gibbs
- Baylor College of Medicine, 1 Baylor Plaza, Houston, 77030 Texas USA
| | - Gabor Marth
- Department of Biology, Boston College, 355 Higgins Hall, 140 Commonwealth Avenue, Chestnut Hill, 02467 Massachusetts USA
| | - Christopher E. Mason
- The Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 1305 York Avenue, Weill Cornell Medical College, New York, 10065 New York USA
- The Feil Family Brain and Mind Research Institute, 413 East 69th St, Weill Cornell Medical College, New York, 10065 New York USA
| | - Androniki Menelaou
- University of Oxford, 1 South Parks Road, Oxford, OX3 9DS UK
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, 3584 CG The Netherlands
| | - Donna M. Muzny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Bradley J. Nelson
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
| | - Amina Noor
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
| | - Nicholas F. Parrish
- Institute for Virus Research, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, 606-8507 Kyoto Japan
| | - Matthew Pendleton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Andrew Quitadamo
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, 28223 North Carolina USA
| | - Benjamin Raeder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Mallory Romanovitch
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
| | - Andreas Schlattl
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Andrey A. Shabalin
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Richmond, 23298-0581 Virginia USA
| | - Andreas Untergasser
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
- Zentrum für Molekulare Biologie, University of Heidelberg, Im Neuenheimer Feld 282, Heidelberg, 69120 Germany
| | - Jerilyn A. Walker
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, 70803 Louisiana USA
| | - Min Wang
- Baylor College of Medicine, 1 Baylor Plaza, Houston, 77030 Texas USA
| | - Fuli Yu
- Baylor College of Medicine, 1 Baylor Plaza, Houston, 77030 Texas USA
| | - Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
| | - Jing Zhang
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
| | - Xiangqun Zheng-Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Wanding Zhou
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
| | - Thomas Zichner
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
| | - Jonathan Sebat
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, 70803 Louisiana USA
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, Boston, 02115 Massachusetts USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
| | - The 1000 Genomes Project Consortium
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W Baltimore Street, Baltimore, 21201 Maryland USA
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, Boston, 02115 Massachusetts USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, 55905 Minnesota USA
- Howard Hughes Medical Institute, University of Washington, Seattle, 98195 Washington USA
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Genetics, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, 48109 Michigan USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler St., Houston, 77030 Texas USA
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, 70803 Louisiana USA
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, 28223 North Carolina USA
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, 06520 Connecticut USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, 500 S. State Street, Ann Arbor, 48109 Michigan USA
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, 77030 Texas USA
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
- Department of Biology, Boston College, 355 Higgins Hall, 140 Commonwealth Avenue, Chestnut Hill, 02467 Massachusetts USA
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, 10461 New York USA
- Bina Technologies, Roche Sequencing, 555 Twin Dolphin Drive, Redwood City, 94065 California USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142 Massachusetts USA
- Department of Computer Engineering, Bilkent University, Ankara, 06800 Turkey
- University of California San Diego (UCSD), 9500 Gilman Drive, La Jolla, 92093 California USA
- National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892 Maryland USA
- Department of Medicine, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, 63108 Missouri USA
- Siteman Cancer Center, 660 South Euclid Avenue, St Louis, 63110 Missouri USA
- Department of Human Genetics, University of Michigan, 1241 Catherine Street, Ann Arbor, 48109 Michigan USA
- Molecular Epidemiology, Leiden University Medical Center, Leiden, 2300RA The Netherlands
- Baylor College of Medicine, 1 Baylor Plaza, Houston, 77030 Texas USA
- The Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 1305 York Avenue, Weill Cornell Medical College, New York, 10065 New York USA
- The Feil Family Brain and Mind Research Institute, 413 East 69th St, Weill Cornell Medical College, New York, 10065 New York USA
- University of Oxford, 1 South Parks Road, Oxford, OX3 9DS UK
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, 3584 CG The Netherlands
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
- Institute for Virus Research, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, 606-8507 Kyoto Japan
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, 1112 East Clay Street, McGuire Hall, Richmond, 23298-0581 Virginia USA
- Zentrum für Molekulare Biologie, University of Heidelberg, Im Neuenheimer Feld 282, Heidelberg, 69120 Germany
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, 06511 Connecticut USA
- Department of Graduate Studies – Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, 120-750 Seoul South Korea
| | - Ryan E. Mills
- Department of Computational Medicine & Bioinformatics, University of Michigan, 500 S. State Street, Ann Arbor, 48109 Michigan USA
- Department of Human Genetics, University of Michigan, 1241 Catherine Street, Ann Arbor, 48109 Michigan USA
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 & 437, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, 266 Whitney Avenue, New Haven, 06520 Connecticut USA
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, 06511 Connecticut USA
| | - Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York School of Natural Sciences, 1428 Madison Avenue, New York, 10029 New York USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
| | - Scott E. Devine
- Institute for Genome Sciences, University of Maryland School of Medicine, 801 W Baltimore Street, Baltimore, 21201 Maryland USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery 263 Farmington Avenue, Farmington, 06030 Connecticut USA
- Department of Graduate Studies – Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, 120-750 Seoul South Korea
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195-5065 Washington USA
- Howard Hughes Medical Institute, University of Washington, Seattle, 98195 Washington USA
| | - Jan O. Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117 Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge UK
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11
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Casale FP, Rakitsch B, Lippert C, Stegle O. Efficient set tests for the genetic analysis of correlated traits. Nat Methods 2015; 12:755-8. [PMID: 26076425 DOI: 10.1038/nmeth.3439] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 05/18/2015] [Indexed: 01/17/2023]
Abstract
Set tests are a powerful approach for genome-wide association testing between groups of genetic variants and quantitative traits. We describe mtSet (http://github.com/PMBio/limix), a mixed-model approach that enables joint analysis across multiple correlated traits while accounting for population structure and relatedness. mtSet effectively combines the benefits of set tests with multi-trait modeling and is computationally efficient, enabling genetic analysis of large cohorts (up to 500,000 individuals) and multiple traits.
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Affiliation(s)
- Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Barbara Rakitsch
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Christoph Lippert
- 1] Microsoft Research, Los Angeles, California, USA. [2] Human Longevity, Inc., Mountain View, California, USA
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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12
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Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife 2015; 4:e05255. [PMID: 25939354 DOI: 10.7554/elife.05255.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 03/26/2015] [Indexed: 05/20/2023] Open
Abstract
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation.
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Affiliation(s)
- Manu J Dubin
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Pei Zhang
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Dazhe Meng
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | | | - Edward J Osborne
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Philipp Drewe
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - André Kahles
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Geraldine Jean
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Bjarni Vilhjálmsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Joanna Jagoda
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Selen Irez
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Viktor Voronin
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Qiang Song
- Molecular and Computational Biology, University of Southern California, Los Angeles, United States
| | - Quan Long
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Gunnar Rätsch
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Richard M Clark
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
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13
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Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife 2015; 4:e05255. [PMID: 25939354 PMCID: PMC4413256 DOI: 10.7554/elife.05255] [Citation(s) in RCA: 313] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 03/26/2015] [Indexed: 01/21/2023] Open
Abstract
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation. DOI:http://dx.doi.org/10.7554/eLife.05255.001 Organisms need to adapt quickly to changes in their environment. Mutations in the DNA sequence of genes can lead to new adaptations, but this can take many generations. Instead, altering how genes are switched on by changing how the DNA is packaged in cells can allow organisms to adapt within and between generations. One way that genes are controlled in organisms is by a process known as DNA methylation, where ‘methyl’ tags are added to DNA and act as markers for other proteins involved in activating genes. DNA is made of four different molecules called ‘nucleotides’ that are arranged in different orders to produce a vast variety of DNA sequences. One type of DNA methylation can happen at sites where a nucleotide called cytosine is followed by two other non-cytosine nucleotides. Another type of methylation can take place at sites where a cytosine is followed by a guanine nucleotide. However, it is not clear how big a role DNA methylation plays in allowing organisms to adapt to their changing environment. Here, Dubin, Zhang, Meng, Remigereau et al. studied DNA methylation in a plant called Arabidopsis thaliana. Several different varieties of A. thaliana plants from Sweden were grown at two different temperatures. The experiments showed that the A. thaliana plants grown at higher temperatures were more likely to have methyl tags attached to sections of DNA called transposons, which are able to move around the genome. There was a lot of variety in the levels of this DNA methylation in the different plants, and some of it was shown to be associated with variation in a gene that is involved in DNA methylation. However, not all of the DNA methylation in these plants was sensitive to the temperature the plants were grown in. Dubin, Zhang, Meng, Remigereau et al. show that the pattern of a type of DNA methylation that is found within genes depends on how far north in Sweden the plants' ancestors came from rather than the temperature the plants were grown in. Plants that originated from colder regions, farther north, had more DNA methylation within many genes and these genes were more active. These findings suggest that genetic differences in these plants strongly influence the levels of DNA methylation, and they provide the first direct link between DNA methylation and adaption to the environment. Future studies should reveal how DNA methylation is regulated in these plants, and whether it plays a key role in adaptation, or merely reflects other changes in the genome. DOI:http://dx.doi.org/10.7554/eLife.05255.002
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Affiliation(s)
- Manu J Dubin
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Pei Zhang
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Dazhe Meng
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | | | - Edward J Osborne
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Philipp Drewe
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - André Kahles
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Geraldine Jean
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Bjarni Vilhjálmsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Joanna Jagoda
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Selen Irez
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Viktor Voronin
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Qiang Song
- Molecular and Computational Biology, University of Southern California, Los Angeles, United States
| | - Quan Long
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Gunnar Rätsch
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Richard M Clark
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
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14
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Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. eLife 2015; 4:e05255. [PMID: 25939354 DOI: 10.7554/elife.05255.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 03/26/2015] [Indexed: 05/23/2023] Open
Abstract
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and between generations. However, neither the extent to which this occurs, nor the mechanisms involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis thaliana accessions grown at two different temperatures. Environmental effects were limited to transposons, where CHH methylation was found to increase with temperature. Genome-wide association studies (GWAS) revealed that the extensive CHH methylation variation was strongly associated with genetic variants in both cis and trans, including a major trans-association close to the DNA methyltransferase CMT2. Unlike CHH methylation, CpG gene body methylation (GBM) was not affected by growth temperature, but was instead correlated with the latitude of origin. Accessions from colder regions had higher levels of GBM for a significant fraction of the genome, and this was associated with increased transcription for the genes affected. GWAS revealed that this effect was largely due to trans-acting loci, many of which showed evidence of local adaptation.
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Affiliation(s)
- Manu J Dubin
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Pei Zhang
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Dazhe Meng
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | | | - Edward J Osborne
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Philipp Drewe
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - André Kahles
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Geraldine Jean
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Bjarni Vilhjálmsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Joanna Jagoda
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Selen Irez
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Viktor Voronin
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Qiang Song
- Molecular and Computational Biology, University of Southern California, Los Angeles, United States
| | - Quan Long
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Gunnar Rätsch
- Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Richard M Clark
- Department of Biology, University of Utah, Salt Lake City, United States
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
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