Journal Article
. 2013 Jun; 2:e00523.
doi: 10.7554/eLife.00523.

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

Maria Gutierrez-Arcelus 1 Tuuli Lappalainen  Stephen B Montgomery  Alfonso Buil  Halit Ongen  Alisa Yurovsky  Julien Bryois  Thomas Giger  Luciana Romano  Alexandra Planchon  Emilie Falconnet  Deborah Bielser  Maryline Gagnebin  Ismael Padioleau  Christelle Borel  Audrey Letourneau  Periklis Makrythanasis  Michel Guipponi  Corinne Gehrig  Stylianos E Antonarakis  Emmanouil T Dermitzakis  
Affiliations
  • PMID: 23755361
  •     56 References
  •     195 citations

Abstract

DNA methylation is an essential epigenetic mark whose role in gene regulation and its dependency on genomic sequence and environment are not fully understood. In this study we provide novel insights into the mechanistic relationships between genetic variation, DNA methylation and transcriptome sequencing data in three different cell-types of the GenCord human population cohort. We find that the association between DNA methylation and gene expression variation among individuals are likely due to different mechanisms from those establishing methylation-expression patterns during differentiation. Furthermore, cell-type differential DNA methylation may delineate a platform in which local inter-individual changes may respond to or act in gene regulation. We show that unlike genetic regulatory variation, DNA methylation alone does not significantly drive allele specific expression. Finally, inferred mechanistic relationships using genetic variation as well as correlations with TF abundance reveal both a passive and active role of DNA methylation to regulatory interactions influencing gene expression. DOI:http://dx.doi.org/10.7554/eLife.00523.001.

Keywords: Human; epigenetics; gene regulation; genome variation; methylation.

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Epigenetics, 2015 Oct 29; 11(1). PMID: 26507253    Free PMC article.
The epigenomic landscape of African rainforest hunter-gatherers and farmers.
Maud Fagny, Etienne Patin, +17 authors, Lluis Quintana-Murci.
Nat Commun, 2015 Dec 01; 6. PMID: 26616214    Free PMC article.
Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci.
Eilis Hannon, Helen Spiers, +9 authors, Jonathan Mill.
Nat Neurosci, 2015 Dec 01; 19(1). PMID: 26619357    Free PMC article.
Highly Cited.
Stress and glucocorticoid receptor transcriptional programming in time and space: Implications for the brain-gut axis.
J W Wiley, G A Higgins, B D Athey.
Neurogastroenterol Motil, 2015 Dec 23; 28(1). PMID: 26690871    Free PMC article.
Review.
Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome.
Yu Gyoung Tak, Peggy J Farnham.
Epigenetics Chromatin, 2016 Jan 01; 8. PMID: 26719772    Free PMC article.
Highly Cited. Review.
Principles Governing DNA Methylation during Neuronal Lineage and Subtype Specification.
Ali Sharma, Shifra S Klein, +2 authors, Miklos Toth.
J Neurosci, 2016 Feb 05; 36(5). PMID: 26843651    Free PMC article.
Autoimmune diseases - connecting risk alleles with molecular traits of the immune system.
Maria Gutierrez-Arcelus, Stephen S Rich, Soumya Raychaudhuri.
Nat Rev Genet, 2016 Feb 26; 17(3). PMID: 26907721    Free PMC article.
Highly Cited. Review.
Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases.
Yan V Sun, Yi-Juan Hu.
Adv Genet, 2016 Feb 27; 93. PMID: 26915271    Free PMC article.
Highly Cited. Review.
The heritability and patterns of DNA methylation in normal human colorectum.
Amy Rowlatt, Gustavo Hernández-Suárez, +8 authors, Albert Tenesa.
Hum Mol Genet, 2016 Mar 05; 25(12). PMID: 26936820    Free PMC article.
Leveraging gene-environment interactions and endotypes for asthma gene discovery.
Klaus Bønnelykke, Carole Ober.
J Allergy Clin Immunol, 2016 Mar 08; 137(3). PMID: 26947980    Free PMC article.
Review.
Environment-induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children.
Tobias Bauer, Saskia Trump, +30 authors, Irina Lehmann.
Mol Syst Biol, 2016 Mar 26; 12(3). PMID: 27013061    Free PMC article.
DNA Methylation in Osteoarthritis.
Wouter den Hollander, Ingrid Meulenbelt.
Curr Genomics, 2016 Mar 29; 16(6). PMID: 27019616    Free PMC article.
Transcript Isoform Variation Associated with Cytosine Modification in Human Lymphoblastoid Cell Lines.
Xu Zhang, Wei Zhang.
Genetics, 2016 Apr 01; 203(2). PMID: 27029734    Free PMC article.
Shared genetic control of expression and methylation in peripheral blood.
Konstantin Shakhbazov, Joseph E Powell, +5 authors, Allan F McRae.
BMC Genomics, 2016 Apr 07; 17. PMID: 27048375    Free PMC article.
Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.
Javier Quilez, Audrey Guilmatre, +6 authors, Andrew J Sharp.
Nucleic Acids Res, 2016 Apr 10; 44(8). PMID: 27060133    Free PMC article.
Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk.
Ashley K Tehranchi, Marsha Myrthil, +3 authors, Hunter B Fraser.
Cell, 2016 Apr 19; 165(3). PMID: 27087447    Free PMC article.
Genetic sources of population epigenomic variation.
Aaron Taudt, Maria Colomé-Tatché, Frank Johannes.
Nat Rev Genet, 2016 May 10; 17(6). PMID: 27156976
Review.
Zebrafish Discoveries in Cancer Epigenetics.
Yelena Chernyavskaya, Brandon Kent, Kirsten C Sadler.
Adv Exp Med Biol, 2016 May 12; 916. PMID: 27165354    Free PMC article.
Review.
DNA Methylation Signatures of Early Childhood Malnutrition Associated With Impairments in Attention and Cognition.
Cyril J Peter, Laura K Fischer, +17 authors, Schahram Akbarian.
Biol Psychiatry, 2016 Oct 22; 80(10). PMID: 27184921    Free PMC article.
Epigenetic Inheritance and Its Role in Evolutionary Biology: Re-Evaluation and New Perspectives.
Warren Burggren.
Biology (Basel), 2016 May 28; 5(2). PMID: 27231949    Free PMC article.
CACNA1C hypermethylation is associated with bipolar disorder.
A Starnawska, D Demontis, +11 authors, M Nyegaard.
Transl Psychiatry, 2016 Jun 09; 6(6). PMID: 27271857    Free PMC article.
Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation.
Saskia Trump, Matthias Bieg, +22 authors, Roland Eils.
Sci Rep, 2016 Jun 29; 6. PMID: 27349968    Free PMC article.
DNA methylation signature of human fetal alcohol spectrum disorder.
Elodie Portales-Casamar, Alexandre A Lussier, +12 authors, Michael S Kobor.
Epigenetics Chromatin, 2016 Jul 01; 9. PMID: 27358653    Free PMC article.
Highly Cited.
Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.
Dazhe Meng, Manu Dubin, +4 authors, Magnus Nordborg.
PLoS Genet, 2016 Jul 12; 12(7). PMID: 27398721    Free PMC article.
Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates.
Semira Gonseth, Adam J de Smith, +8 authors, Joseph L Wiemels.
Epigenetics, 2016 Jul 13; 11(9). PMID: 27403598    Free PMC article.
Epigenetic regulation of OAS2 shows disease-specific DNA methylation profiles at individual CpG sites.
Xiaolian Gu, Linda Boldrup, +7 authors, Karin Nylander.
Sci Rep, 2016 Aug 31; 6. PMID: 27572959    Free PMC article.
Discover the network underlying the connections between aging and age-related diseases.
Jialiang Yang, Tao Huang, +7 authors, Zhidong Tu.
Sci Rep, 2016 Sep 02; 6. PMID: 27582315    Free PMC article.
Genetics and Genomics of Coronary Artery Disease.
Milos Pjanic, Clint L Miller, +3 authors, Thomas Quertermous.
Curr Cardiol Rep, 2016 Sep 03; 18(10). PMID: 27586139    Free PMC article.
Review.
DNA methylation mediates genetic variation for adaptive transgenerational plasticity.
Jacob J Herman, Sonia E Sultan.
Proc Biol Sci, 2016 Sep 16; 283(1838). PMID: 27629032    Free PMC article.
Heritable DNA Methylation in CD4+ Cells among Complex Families Displays Genetic and Non-Genetic Effects.
Kenneth Day, Lindsay L Waite, +10 authors, Devin M Absher.
PLoS One, 2016 Oct 30; 11(10). PMID: 27792787    Free PMC article.
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
Lu Chen, Bing Ge, +73 authors, Nicole Soranzo.
Cell, 2016 Nov 20; 167(5). PMID: 27863251    Free PMC article.
Highly Cited.
The Future is The Past: Methylation QTLs in Schizophrenia.
Anke Hoffmann, Michael Ziller, Dietmar Spengler.
Genes (Basel), 2016 Nov 26; 7(12). PMID: 27886132    Free PMC article.
Review.
Mendelian inheritance of trimodal CpG methylation sites suggests distal cis-acting genetic effects.
Shaza B Zaghlool, Mashael Al-Shafai, +5 authors, Karsten Suhre.
Clin Epigenetics, 2016 Nov 30; 8. PMID: 27895808    Free PMC article.
Disease variants alter transcription factor levels and methylation of their binding sites.
Marc Jan Bonder, René Luijk, +53 authors, Bastiaan T Heijmans.
Nat Genet, 2016 Dec 06; 49(1). PMID: 27918535
Highly Cited.
Tobacco smoking and smoking-related DNA methylation are associated with the development of frailty among older adults.
Xu Gao, Yan Zhang, +3 authors, Hermann Brenner.
Epigenetics, 2016 Dec 22; 12(2). PMID: 28001461    Free PMC article.
Down syndrome and the complexity of genome dosage imbalance.
Stylianos E Antonarakis.
Nat Rev Genet, 2016 Dec 29; 18(3). PMID: 28029161
Highly Cited. Review.
Epigenetic Modifications in ANCA-Associated Vasculitis: Potential for Insights into Disease Pathogenesis and Prediction of Outcome?
Thomas Oates, Alan D Salama.
J Am Soc Nephrol, 2017 Jan 05; 28(4). PMID: 28049651    Free PMC article.
The emerging landscape of dynamic DNA methylation in early childhood.
Cheng-Jian Xu, Marc Jan Bonder, +20 authors, Gerard H Koppelman.
BMC Genomics, 2017 Jan 07; 18(1). PMID: 28056824    Free PMC article.
Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease.
Katrina Soderquest, Arnulf Hertweck, +9 authors, Graham M Lord.
PLoS Genet, 2017 Feb 12; 13(2). PMID: 28187197    Free PMC article.
Detection of Imprinted Genes by Single-Cell Allele-Specific Gene Expression.
Federico A Santoni, Georgios Stamoulis, +4 authors, Stylianos E Antonarakis.
Am J Hum Genet, 2017 Feb 14; 100(3). PMID: 28190458    Free PMC article.
A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation.
Owen J L Rackham, Sarah R Langley, +7 authors, Enrico Petretto.
Genetics, 2017 Feb 19; 205(4). PMID: 28213474    Free PMC article.
Epigenetics studies of fetal alcohol spectrum disorder: where are we now?
Alexandre A Lussier, Joanne Weinberg, Michael S Kobor.
Epigenomics, 2017 Feb 25; 9(3). PMID: 28234026    Free PMC article.
Review.
Developmental pathways to adiposity begin before birth and are influenced by genotype, prenatal environment and epigenome.
Xinyi Lin, Ives Yubin Lim, +19 authors, GUSTO study group.
BMC Med, 2017 Mar 08; 15(1). PMID: 28264723    Free PMC article.
Time-dependent genetic effects on gene expression implicate aging processes.
Julien Bryois, Alfonso Buil, +8 authors, Emmanouil T Dermitzakis.
Genome Res, 2017 Mar 18; 27(4). PMID: 28302734    Free PMC article.
Associations of self-reported smoking, cotinine levels and epigenetic smoking indicators with oxidative stress among older adults: a population-based study.
Xu Gao, Xīn Gào, +3 authors, Hermann Brenner.
Eur J Epidemiol, 2017 Apr 24; 32(5). PMID: 28434075
ANRIL Promoter DNA Methylation: A Perinatal Marker for Later Adiposity.
Karen Lillycrop, Robert Murray, +32 authors, Keith M Godfrey.
EBioMedicine, 2017 May 06; 19. PMID: 28473239    Free PMC article.
A complete tool set for molecular QTL discovery and analysis.
Olivier Delaneau, Halit Ongen, +3 authors, Emmanouil T Dermitzakis.
Nat Commun, 2017 May 19; 8. PMID: 28516912    Free PMC article.
Highly Cited.
Associating cellular epigenetic models with human phenotypes.
Tuuli Lappalainen, John M Greally.
Nat Rev Genet, 2017 May 31; 18(7). PMID: 28555657
Highly Cited. Review.
Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes.
Judith F Kribelbauer, Oleg Laptenko, +5 authors, Harmen J Bussemaker.
Cell Rep, 2017 Jun 15; 19(11). PMID: 28614722    Free PMC article.
Highly Cited.
Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression.
Carolyn J Vivian, Amanda E Brinker, +5 authors, Danny R Welch.
Cancer Res, 2017 Jul 01; 77(22). PMID: 28663334    Free PMC article.
Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling.
Yelena Chernyavskaya, Raksha Mudbhary, +10 authors, Kirsten C Sadler.
Development, 2017 Jul 13; 144(16). PMID: 28698226    Free PMC article.
Epigenomics of Major Depressive Disorders and Schizophrenia: Early Life Decides.
Anke Hoffmann, Vincenza Sportelli, Michael Ziller, Dietmar Spengler.
Int J Mol Sci, 2017 Aug 05; 18(8). PMID: 28777307    Free PMC article.
Review.
The impact of methylation quantitative trait loci (mQTLs) on active smoking-related DNA methylation changes.
Xu Gao, Hauke Thomsen, +2 authors, Hermann Brenner.
Clin Epigenetics, 2017 Aug 22; 9. PMID: 28824732    Free PMC article.
An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome.
Bernard Ng, Charles C White, +9 authors, Philip L De Jager.
Nat Neurosci, 2017 Sep 05; 20(10). PMID: 28869584    Free PMC article.
Highly Cited.
Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy.
Matthias Heinig, Michiel E Adriaens, +28 authors, Norbert Hubner.
Genome Biol, 2017 Sep 15; 18(1). PMID: 28903782    Free PMC article.
Data Resources for Human Functional Genomics.
Kristin G Ardlie, Roderic Guigó.
Curr Opin Syst Biol, 2017 Oct 11; 1. PMID: 28989986    Free PMC article.
Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease.
eGTEx Project.
Nat Genet, 2017 Oct 12; 49(12). PMID: 29019975    Free PMC article.
Highly Cited.
Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change.
Pejman Mohammadi, Stephane E Castel, Andrew A Brown, Tuuli Lappalainen.
Genome Res, 2017 Oct 13; 27(11). PMID: 29021289    Free PMC article.
Mapping eQTL by leveraging multiple tissues and DNA methylation.
Chaitanya R Acharya, Kouros Owzar, Andrew S Allen.
BMC Bioinformatics, 2017 Oct 20; 18(1). PMID: 29047346    Free PMC article.
Measuring quantitative effects of methylation on transcription factor-DNA binding affinity.
Zheng Zuo, Basab Roy, +2 authors, Gary D Stormo.
Sci Adv, 2017 Nov 22; 3(11). PMID: 29159284    Free PMC article.
Epigenetic regulation of AXL and risk of childhood asthma symptoms.
Lu Gao, Joshua Millstein, +6 authors, Carrie V Breton.
Clin Epigenetics, 2017 Nov 28; 9. PMID: 29177020    Free PMC article.
Choice of surrogate tissue influences neonatal EWAS findings.
Xinyi Lin, Ai Ling Teh, +15 authors, Neerja Karnani.
BMC Med, 2017 Dec 06; 15(1). PMID: 29202839    Free PMC article.
Impact of regulatory variation across human iPSCs and differentiated cells.
Nicholas E Banovich, Yang I Li, +13 authors, Yoav Gilad.
Genome Res, 2017 Dec 07; 28(1). PMID: 29208628    Free PMC article.
Highly Cited.
Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection.
Konstantin Popadin, Stephan Peischl, +10 authors, Stylianos E Antonarakis.
Genome Res, 2017 Dec 15; 28(1). PMID: 29237728    Free PMC article.
Locus-specific hypomethylation of the mouse IAP retrotransposon is associated with transcription factor-binding sites.
Ken-Ichi Shimosuga, Kei Fukuda, Hiroyuki Sasaki, Kenji Ichiyanagi.
Mob DNA, 2017 Dec 20; 8. PMID: 29255492    Free PMC article.
TET2 Loss Dysregulates the Behavior of Bone Marrow Mesenchymal Stromal Cells and Accelerates Tet2-/--Driven Myeloid Malignancy Progression.
Rong Li, Yuan Zhou, +11 authors, Zhigang Zhao.
Stem Cell Reports, 2018 Jan 02; 10(1). PMID: 29290626    Free PMC article.
Gene variants and educational attainment in cannabis use: mediating role of DNA methylation.
Maria Carla Gerra, Subramaniam Jayanthi, +5 authors, Claudia Donnini.
Transl Psychiatry, 2018 Jan 23; 8(1). PMID: 29353877    Free PMC article.
Genetic estimators of DNA methylation provide insights into the molecular basis of polygenic traits.
Virginie Freytag, Vanja Vukojevic, +10 authors, Andreas Papassotiropoulos.
Transl Psychiatry, 2018 Feb 01; 8(1). PMID: 29382824    Free PMC article.
Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci.
Matthias Thurner, Martijn van de Bunt, +12 authors, Mark I McCarthy.
Elife, 2018 Feb 08; 7. PMID: 29412141    Free PMC article.
Highly Cited.
Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms.
Brandon L Pierce, Lin Tong, +12 authors, Habibul Ahsan.
Nat Commun, 2018 Feb 25; 9(1). PMID: 29476079    Free PMC article.
Distinct chromatin signatures of DNA hypomethylation in aging and cancer.
Raúl F Pérez, Juan Ramón Tejedor, +2 authors, Mario F Fraga.
Aging Cell, 2018 Mar 06; 17(3). PMID: 29504244    Free PMC article.
The association between copy number aberration, DNA methylation and gene expression in tumor samples.
Wei Sun, Paul Bunn, +6 authors, Dan-Yu Lin.
Nucleic Acids Res, 2018 Mar 13; 46(6). PMID: 29529299    Free PMC article.
DNA methylation of the BRD2 promoter is associated with juvenile myoclonic epilepsy in Caucasians.
Shilpa Pathak, James Miller, +2 authors, David A Greenberg.
Epilepsia, 2018 Apr 03; 59(5). PMID: 29608786    Free PMC article.
DNA methylation and transcriptome aberrations mediated by ERα in mouse seminal vesicles following developmental DES exposure.
Yin Li, Katherine J Hamilton, +11 authors, Kenneth S Korach.
Proc Natl Acad Sci U S A, 2018 Apr 19; 115(18). PMID: 29666266    Free PMC article.
Identification of rare de novo epigenetic variations in congenital disorders.
Mafalda Barbosa, Ricky S Joshi, +21 authors, Andrew J Sharp.
Nat Commun, 2018 May 29; 9(1). PMID: 29802345    Free PMC article.
An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells.
Elizabeth M Kennedy, George N Goehring, +6 authors, Karen N Conneely.
BMC Genomics, 2018 Jun 20; 19(1). PMID: 29914364    Free PMC article.
Genomic approaches for the elucidation of genes and gene networks underlying cardiovascular traits.
M E Adriaens, C R Bezzina.
Biophys Rev, 2018 Jun 24; 10(4). PMID: 29934864    Free PMC article.
Review.
Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data.
Xin Zhou, Zhibin Chen, Xiaodong Cai.
Epigenetics, 2018 Jun 27; 13(5). PMID: 29940789    Free PMC article.
Integrating -Omics Approaches into Human Population-Based Studies of Prenatal and Early-Life Exposures.
Todd M Everson, Carmen J Marsit.
Curr Environ Health Rep, 2018 Jul 29; 5(3). PMID: 30054820    Free PMC article.
Review.
Characterizing genetic and environmental influences on variable DNA methylation using monozygotic and dizygotic twins.
Eilis Hannon, Olivia Knox, +8 authors, Jonathan Mill.
PLoS Genet, 2018 Aug 10; 14(8). PMID: 30091980    Free PMC article.
Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci.
Vitor Onuchic, Eugene Lurie, +16 authors, Aleksandar Milosavljevic.
Science, 2018 Aug 25; 361(6409). PMID: 30139913    Free PMC article.
Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline.
Shinya Tasaki, Chris Gaiteri, +4 authors, David A Bennett.
Front Genet, 2018 Aug 25; 9. PMID: 30140277    Free PMC article.
Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci.
Boxiang Liu, Milos Pjanic, +11 authors, Thomas Quertermous.
Am J Hum Genet, 2018 Aug 28; 103(3). PMID: 30146127    Free PMC article.
Children's biobehavioral reactivity to challenge predicts DNA methylation in adolescence and emerging adulthood.
Sarah J Goodman, Danielle S Roubinov, +7 authors, W Thomas Boyce.
Dev Sci, 2018 Sep 04; 22(2). PMID: 30176105    Free PMC article.
Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment.
Rui Sun, Haoyi Weng, +5 authors, Maggie Haitian Wang.
BMC Proc, 2018 Sep 29; 12(Suppl 9). PMID: 30263051    Free PMC article.
A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome.
Paras Garg, Ricky S Joshi, Corey Watson, Andrew J Sharp.
PLoS Genet, 2018 Oct 03; 14(10). PMID: 30273333    Free PMC article.
Smoking induces coordinated DNA methylation and gene expression changes in adipose tissue with consequences for metabolic health.
Pei-Chien Tsai, Craig A Glastonbury, +18 authors, Jordana T Bell.
Clin Epigenetics, 2018 Oct 22; 10(1). PMID: 30342560    Free PMC article.
Leveraging DNA-Methylation Quantitative-Trait Loci to Characterize the Relationship between Methylomic Variation, Gene Expression, and Complex Traits.
Eilis Hannon, Tyler J Gorrie-Stone, +6 authors, Jonathan Mill.
Am J Hum Genet, 2018 Nov 08; 103(5). PMID: 30401456    Free PMC article.
Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders.
Heath E O'Brien, Eilis Hannon, +12 authors, Nicholas J Bray.
Genome Biol, 2018 Nov 14; 19(1). PMID: 30419947    Free PMC article.
Prioritization of PLEC and GRINA as Osteoarthritis Risk Genes Through the Identification and Characterization of Novel Methylation Quantitative Trait Loci.
Sarah J Rice, Maria Tselepi, +8 authors, John Loughlin.
Arthritis Rheumatol, 2019 Feb 08; 71(8). PMID: 30730609    Free PMC article.
DNA Methylation: Shared and Divergent Features across Eukaryotes.
Robert J Schmitz, Zachary A Lewis, Mary G Goll.
Trends Genet, 2019 Aug 11; 35(11). PMID: 31399242    Free PMC article.
Review.
IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis.
Yue Fan, Tauras P Vilgalys, +3 authors, Xiang Zhou.
Genome Biol, 2019 Oct 28; 20(1). PMID: 31651351    Free PMC article.
Edematous severe acute malnutrition is characterized by hypomethylation of DNA.
Katharina V Schulze, Shanker Swaminathan, +17 authors, Neil A Hanchard.
Nat Commun, 2019 Dec 21; 10(1). PMID: 31857576    Free PMC article.
The influence of DNA methylation on monoallelic expression.
Simão Teixeira da Rocha, Anne-Valerie Gendrel.
Essays Biochem, 2019 Nov 30; 63(6). PMID: 31782494    Free PMC article.
Review.
LINC00261 Is an Epigenetically Regulated Tumor Suppressor Essential for Activation of the DNA Damage Response.
Shandy Shahabi, Vishaly Kumaran, +12 authors, Crystal N Marconett.
Cancer Res, 2019 Feb 24; 79(12). PMID: 30796052    Free PMC article.
Highly Cited.
Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation.
Mariângela B C Maldonado, Nelson B de Rezende Neto, +8 authors, Flavia L Lopes.
PLoS One, 2019 Sep 13; 14(9). PMID: 31513639    Free PMC article.
The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region.
Nora Fernandez-Jimenez, Koldo Garcia-Etxebarria, +12 authors, Jose Ramon Bilbao.
Sci Rep, 2019 Feb 06; 9(1). PMID: 30718669    Free PMC article.
Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle.
D Leland Taylor, Anne U Jackson, +19 authors, Francis S Collins.
Proc Natl Acad Sci U S A, 2019 May 12; 116(22). PMID: 31076557    Free PMC article.
Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation.
Lucas T Husquin, Maxime Rotival, +8 authors, Lluis Quintana-Murci.
Genome Biol, 2018 Dec 20; 19(1). PMID: 30563547    Free PMC article.
Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation.
Sumaiya A Islam, Sarah J Goodman, +4 authors, Michael S Kobor.
Epigenetics Chromatin, 2019 Jan 04; 12(1). PMID: 30602389    Free PMC article.
Association of a placental Interleukin-6 genetic variant (rs1800796) with DNA methylation, gene expression and risk of acute chorioamnionitis.
Chaini Konwar, Giulia F Del Gobbo, Jefferson Terry, Wendy P Robinson.
BMC Med Genet, 2019 Feb 24; 20(1). PMID: 30795743    Free PMC article.
Leveraging brain cortex-derived molecular data to elucidate epigenetic and transcriptomic drivers of complex traits and disease.
Charlie Hatcher, Caroline L Relton, Tom R Gaunt, Tom G Richardson.
Transl Psychiatry, 2019 Mar 02; 9(1). PMID: 30820025    Free PMC article.
Integrative analysis of DNA methylation in discordant twins unveils distinct architectures of systemic sclerosis subsets.
Paula S Ramos, Kip D Zimmerman, +3 authors, Carol A Feghali-Bostwick.
Clin Epigenetics, 2019 Apr 06; 11(1). PMID: 30947741    Free PMC article.
In-utero epigenetic factors are associated with early-onset myopia in young children.
Wei Jie Seow, Cheryl S Ngo, +10 authors, Seang Mei Saw.
PLoS One, 2019 May 18; 14(5). PMID: 31100065    Free PMC article.
Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns.
Darina Czamara, Gökçen Eraslan, +31 authors, Elisabeth B Binder.
Nat Commun, 2019 Jun 13; 10(1). PMID: 31186427    Free PMC article.
Early-life determinants of hypoxia-inducible factor 3A gene (HIF3A) methylation: a birth cohort study.
Toby Mansell, Anne-Louise Ponsonby, +7 authors, Barwon Infant Study Investigator Team.
Clin Epigenetics, 2019 Jul 03; 11(1). PMID: 31262346    Free PMC article.
Identification of DNA motifs that regulate DNA methylation.
Mengchi Wang, Kai Zhang, +9 authors, Wei Wang.
Nucleic Acids Res, 2019 Jul 25; 47(13). PMID: 31334813    Free PMC article.
Collective effects of long-range DNA methylations predict gene expressions and estimate phenotypes in cancer.
Soyeon Kim, Hyun Jung Park, Xiangqin Cui, Degui Zhi.
Sci Rep, 2020 Mar 05; 10(1). PMID: 32127627    Free PMC article.
Profiling haplotype specific CpG and CpH methylation within a schizophrenia GWAS locus on chromosome 14 in schizophrenia and healthy subjects.
Margarita Alfimova, Nikolay Kondratyev, Arkadiy Golov, Vera Golimbet.
Sci Rep, 2020 Mar 15; 10(1). PMID: 32170143    Free PMC article.
Learning Causal Biological Networks With the Principle of Mendelian Randomization.
Md Bahadur Badsha, Audrey Qiuyan Fu.
Front Genet, 2019 Jun 06; 10. PMID: 31164902    Free PMC article.
Contrasting DNA methylation responses of inbred fish lines to different rearing environments.
Waldir M Berbel-Filho, Deiene Rodríguez-Barreto, +2 authors, Sofia Consuegra.
Epigenetics, 2019 May 31; 14(10). PMID: 31144573    Free PMC article.
Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci.
Maria Gutierrez-Arcelus, Yuriy Baglaenko, +16 authors, Soumya Raychaudhuri.
Nat Genet, 2020 Feb 19; 52(3). PMID: 32066938    Free PMC article.
Multi-omics integrative analysis identified SNP-methylation-mRNA: Interaction in peripheral blood mononuclear cells.
Yi-Hua Lu, Bing-Hua Wang, +6 authors, Shu-Feng Lei.
J Cell Mol Med, 2019 May 21; 23(7). PMID: 31106970    Free PMC article.
DNA methylation and cis-regulation of gene expression by prostate cancer risk SNPs.
James Y Dai, Xiaoyu Wang, +8 authors, Janet L Stanford.
PLoS Genet, 2020 Apr 01; 16(3). PMID: 32226005    Free PMC article.
The signature of HBV-related liver disease in peripheral blood mononuclear cell DNA methylation.
Kang Li, Ling Qin, +8 authors, Yonghong Zhang.
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Epigenome-wide association study of whole blood gene expression in Framingham Heart Study participants provides molecular insight into the potential role of CHRNA5 in cigarette smoking-related lung diseases.
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