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  
  • PMID: 23755361
  •     56 References
  •     195 citations


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:

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

Common regulatory variation impacts gene expression in a cell type-dependent manner.
Antigone S Dimas, Samuel Deutsch, +12 authors, Stylianos E Antonarakis.
Science, 2009 Aug 01; 325(5945). PMID: 19644074    Free PMC article.
Highly Cited.
Human DNA methylomes at base resolution show widespread epigenomic differences.
Ryan Lister, Mattia Pelizzola, +15 authors, Joseph R Ecker.
Nature, 2009 Oct 16; 462(7271). PMID: 19829295    Free PMC article.
Highly Cited.
ENCODE whole-genome data in the UCSC Genome Browser.
Kate R Rosenbloom, Timothy R Dreszer, +15 authors, W James Kent.
Nucleic Acids Res, 2009 Nov 19; 38(Database issue). PMID: 19920125    Free PMC article.
Highly Cited.
BEDTools: a flexible suite of utilities for comparing genomic features.
Aaron R Quinlan, Ira M Hall.
Bioinformatics, 2010 Jan 30; 26(6). PMID: 20110278    Free PMC article.
Highly Cited.
Genetic control of individual differences in gene-specific methylation in human brain.
Dandan Zhang, Lijun Cheng, +7 authors, Chunyu Liu.
Am J Hum Genet, 2010 Mar 11; 86(3). PMID: 20215007    Free PMC article.
Highly Cited.
Transcriptome genetics using second generation sequencing in a Caucasian population.
Stephen B Montgomery, Micha Sammeth, +5 authors, Emmanouil T Dermitzakis.
Nature, 2010 Mar 12; 464(7289). PMID: 20220756    Free PMC article.
Highly Cited.
Understanding mechanisms underlying human gene expression variation with RNA sequencing.
Joseph K Pickrell, John C Marioni, +7 authors, Jonathan K Pritchard.
Nature, 2010 Mar 12; 464(7289). PMID: 20220758    Free PMC article.
Highly Cited.
Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain.
J Raphael Gibbs, Marcel P van der Brug, +13 authors, Andrew B Singleton.
PLoS Genet, 2010 May 21; 6(5). PMID: 20485568    Free PMC article.
Highly Cited.
Conserved role of intragenic DNA methylation in regulating alternative promoters.
Alika K Maunakea, Raman P Nagarajan, +23 authors, Joseph F Costello.
Nature, 2010 Jul 09; 466(7303). PMID: 20613842    Free PMC article.
Highly Cited.
Discovery and characterization of chromatin states for systematic annotation of the human genome.
Jason Ernst, Manolis Kellis.
Nat Biotechnol, 2010 Jul 27; 28(8). PMID: 20657582    Free PMC article.
Highly Cited.
Integrating common and rare genetic variation in diverse human populations.
International HapMap 3 Consortium, David M Altshuler, +86 authors, Jean E McEwen.
Nature, 2010 Sep 03; 467(7311). PMID: 20811451    Free PMC article.
Highly Cited.
Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks.
Maria A Hahn, Xiwei Wu, +2 authors, Gerd P Pfeifer.
PLoS One, 2011 Apr 29; 6(4). PMID: 21526191    Free PMC article.
Mapping and analysis of chromatin state dynamics in nine human cell types.
Jason Ernst, Pouya Kheradpour, +11 authors, Bradley E Bernstein.
Nature, 2011 Mar 29; 473(7345). PMID: 21441907    Free PMC article.
Highly Cited.
Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment.
Emily Hodges, Antoine Molaro, +9 authors, Gregory J Hannon.
Mol Cell, 2011 Sep 20; 44(1). PMID: 21924933    Free PMC article.
Highly Cited.
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines.
Jordana T Bell, Athma A Pai, +5 authors, Jonathan K Pritchard.
Genome Biol, 2011 Jan 22; 12(1). PMID: 21251332    Free PMC article.
Highly Cited.
Identification of genetic elements that autonomously determine DNA methylation states.
Florian Lienert, Christiane Wirbelauer, +3 authors, Dirk Schübeler.
Nat Genet, 2011 Oct 04; 43(11). PMID: 21964573
Highly Cited.
DNA-binding factors shape the mouse methylome at distal regulatory regions.
Michael B Stadler, Rabih Murr, +9 authors, Dirk Schübeler.
Nature, 2011 Dec 16; 480(7378). PMID: 22170606
Highly Cited.
Functions of DNA methylation: islands, start sites, gene bodies and beyond.
Peter A Jones.
Nat Rev Genet, 2012 May 30; 13(7). PMID: 22641018
Highly Cited. Review.
Plasticity of DNA methylation in mouse T cell activation and differentiation.
Yan Li, Guobing Chen, +4 authors, Jun Y Fan.
BMC Mol Biol, 2012 May 31; 13. PMID: 22642378    Free PMC article.
An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium.
Nature, 2012 Sep 08; 489(7414). PMID: 22955616    Free PMC article.
Highly Cited.
The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, +59 authors, John A Stamatoyannopoulos.
Nature, 2012 Sep 08; 489(7414). PMID: 22955617    Free PMC article.
Highly Cited.
Architecture of the human regulatory network derived from ENCODE data.
Mark B Gerstein, Anshul Kundaje, +53 authors, Michael Snyder.
Nature, 2012 Sep 08; 489(7414). PMID: 22955619    Free PMC article.
Highly Cited.
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.
Marta Kulis, Simon Heath, +38 authors, José I Martín-Subero.
Nat Genet, 2012 Oct 16; 44(11). PMID: 23064414
Highly Cited.
An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium, Goncalo R Abecasis, +7 authors, Gil A McVean.
Nature, 2012 Nov 07; 491(7422). PMID: 23128226    Free PMC article.
Highly Cited.
Molecular biology. Epigenetic islands in a genetic ocean.
Dirk Schübeler.
Science, 2012 Nov 10; 338(6108). PMID: 23139324
Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects.
Kristel R van Eijk, Simone de Jong, +11 authors, Roel A Ophoff.
BMC Genomics, 2012 Nov 20; 13. PMID: 23157493    Free PMC article.
Highly Cited.
Genome-wide methylation profiles reveal quantitative views of human aging rates.
Gregory Hannum, Justin Guinney, +13 authors, Kang Zhang.
Mol Cell, 2012 Nov 28; 49(2). PMID: 23177740    Free PMC article.
Highly Cited.
Mediators and dynamics of DNA methylation.
Robert Shoemaker, Wei Wang, Kun Zhang.
Wiley Interdiscip Rev Syst Biol Med, 2010 Sep 30; 3(3). PMID: 20878927
Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, +254 authors, International Human Genome Sequencing Consortium.
Nature, 2001 Mar 10; 409(6822). PMID: 11237011
Highly Cited.
DNA methylation patterns and epigenetic memory.
Adrian Bird.
Genes Dev, 2002 Jan 10; 16(1). PMID: 11782440
Highly Cited. Review.
Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, Peg3.
Joomyeong Kim, Angela Kollhoff, Anne Bergmann, Lisa Stubbs.
Hum Mol Genet, 2003 Jan 30; 12(3). PMID: 12554678
Statistical significance for genomewide studies.
John D Storey, Robert Tibshirani.
Proc Natl Acad Sci U S A, 2003 Jul 29; 100(16). PMID: 12883005    Free PMC article.
Highly Cited.
The UCSC Table Browser data retrieval tool.
Donna Karolchik, Angela S Hinrichs, +4 authors, W James Kent.
Nucleic Acids Res, 2003 Dec 19; 32(Database issue). PMID: 14681465    Free PMC article.
Highly Cited.
DNA modification mechanisms and gene activity during development.
R Holliday, J E Pugh.
Science, 1975 Jan 24; 187(4173). PMID: 1111098
Highly Cited.
X inactivation, differentiation, and DNA methylation.
A D Riggs.
Cytogenet Cell Genet, 1975 Jan 01; 14(1). PMID: 1093816
Highly Cited. Review.
Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region.
G C Prendergast, E B Ziff.
Science, 1991 Jan 11; 251(4990). PMID: 1987636
Highly Cited.
Targeted mutation of the DNA methyltransferase gene results in embryonic lethality.
E Li, T H Bestor, R Jaenisch.
Cell, 1992 Jun 12; 69(6). PMID: 1606615
Highly Cited.
An integrative genomics approach to infer causal associations between gene expression and disease.
Eric E Schadt, John Lamb, +18 authors, Aldons J Lusis.
Nat Genet, 2005 Jun 21; 37(7). PMID: 15965475    Free PMC article.
Highly Cited.
DNA methylation and human disease.
Keith D Robertson.
Nat Rev Genet, 2005 Sep 02; 6(8). PMID: 16136652
Highly Cited. Review.
High-throughput DNA methylation profiling using universal bead arrays.
Marina Bibikova, Zhenwu Lin, +14 authors, Jian-Bing Fan.
Genome Res, 2006 Feb 02; 16(3). PMID: 16449502    Free PMC article.
Highly Cited.
GENCODE: producing a reference annotation for ENCODE.
Jennifer Harrow, France Denoeud, +12 authors, Roderic Guigo.
Genome Biol, 2006 Aug 24; 7 Suppl 1. PMID: 16925838    Free PMC article.
Highly Cited.
Gene body-specific methylation on the active X chromosome.
Asaf Hellman, Andrew Chess.
Science, 2007 Feb 27; 315(5815). PMID: 17322062
Highly Cited.
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.
Michael Weber, Ines Hellmann, +4 authors, Dirk Schübeler.
Nat Genet, 2007 Mar 06; 39(4). PMID: 17334365
Highly Cited.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium, Ewan Birney, +316 authors, Pieter J de Jong.
Nature, 2007 Jun 16; 447(7146). PMID: 17571346    Free PMC article.
Highly Cited.
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Shaun Purcell, Benjamin Neale, +8 authors, Pak C Sham.
Am J Hum Genet, 2007 Aug 19; 81(3). PMID: 17701901    Free PMC article.
Highly Cited.
Population genomics of human gene expression.
Barbara E Stranger, Alexandra C Nica, +11 authors, Emmanouil T Dermitzakis.
Nat Genet, 2007 Sep 18; 39(10). PMID: 17873874    Free PMC article.
Highly Cited.
High-resolution mapping and characterization of open chromatin across the genome.
Alan P Boyle, Sean Davis, +5 authors, Gregory E Crawford.
Cell, 2008 Feb 05; 132(2). PMID: 18243105    Free PMC article.
Highly Cited.
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
Jun Zhu, Bin Zhang, +5 authors, Eric E Schadt.
Nat Genet, 2008 Jun 17; 40(7). PMID: 18552845    Free PMC article.
Highly Cited.
Genome-scale DNA methylation maps of pluripotent and differentiated cells.
Alexander Meissner, Tarjei S Mikkelsen, +10 authors, Eric S Lander.
Nature, 2008 Jul 05; 454(7205). PMID: 18600261    Free PMC article.
Highly Cited.
An Sp1/Sp3 binding polymorphism confers methylation protection.
Yanis A Boumber, Yutaka Kondo, +6 authors, Jean-Pierre J Issa.
PLoS Genet, 2008 Aug 30; 4(8). PMID: 18725933    Free PMC article.
DNA methylation profiles in monozygotic and dizygotic twins.
Zachary A Kaminsky, Thomas Tang, +13 authors, Art Petronis.
Nat Genet, 2009 Jan 20; 41(2). PMID: 19151718
Highly Cited.
A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals.
Brian L Browning, Sharon R Browning.
Am J Hum Genet, 2009 Feb 10; 84(2). PMID: 19200528    Free PMC article.
Highly Cited.
Disentangling molecular relationships with a causal inference test.
Joshua Millstein, Bin Zhang, Jun Zhu, Eric E Schadt.
BMC Genet, 2009 May 29; 10. PMID: 19473544    Free PMC article.
Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity.
Christian Schmidl, Maja Klug, +4 authors, Michael Rehli.
Genome Res, 2009 Jun 06; 19(7). PMID: 19494038    Free PMC article.
Highly Cited.
Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin.
Bioinformatics, 2009 May 20; 25(14). PMID: 19451168    Free PMC article.
Highly Cited.
The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, +7 authors, 1000 Genome Project Data Processing Subgroup.
Bioinformatics, 2009 Jun 10; 25(16). PMID: 19505943    Free PMC article.
Highly Cited.
The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome.
M Reza Sailani, Periklis Makrythanasis, +27 authors, Stylianos E Antonarakis.
Genome Res, 2013 Jun 21; 23(9). PMID: 23783273    Free PMC article.
Gene expression: Disentangling DNA methylation.
Mary Muers.
Nat Rev Genet, 2013 Jun 26; 14(8). PMID: 23797851
DNA methylation, genotype and gene expression: who is driving and who is along for the ride?
Meaghan J Jones, Anthony P Fejes, Michael S Kobor.
Genome Biol, 2013 Aug 01; 14(7). PMID: 23899167    Free PMC article.
Epigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosis.
Diego M Marzese, Richard A Scolyer, +16 authors, Dave S B Hoon.
Hum Mol Genet, 2013 Sep 10; 23(1). PMID: 24014427    Free PMC article.
Bridging the gap between genetic associations and molecular mechanisms for type 2 diabetes.
Hui Jin Ng, Anna L Gloyn.
Curr Diab Rep, 2013 Oct 16; 13(6). PMID: 24127137
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.
Helena Kilpinen, Sebastian M Waszak, +23 authors, Emmanouil T Dermitzakis.
Science, 2013 Oct 19; 342(6159). PMID: 24136355    Free PMC article.
Highly Cited.
Genetic and epigenetic regulation of human lincRNA gene expression.
Konstantin Popadin, Maria Gutierrez-Arcelus, Emmanouil T Dermitzakis, Stylianos E Antonarakis.
Am J Hum Genet, 2013 Nov 26; 93(6). PMID: 24268656    Free PMC article.
Epigenetic epidemiology: promises for public health research.
Kelly M Bakulski, M Daniele Fallin.
Environ Mol Mutagen, 2014 Jan 23; 55(3). PMID: 24449392    Free PMC article.
Comprehensive functional annotation of 77 prostate cancer risk loci.
Dennis J Hazelett, Suhn Kyong Rhie, +15 authors, Gerhard A Coetzee.
PLoS Genet, 2014 Feb 06; 10(1). PMID: 24497837    Free PMC article.
Highly Cited.
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts.
James R Wagner, Stephan Busche, +3 authors, Mathieu Blanchette.
Genome Biol, 2014 Feb 22; 15(2). PMID: 24555846    Free PMC article.
Highly Cited.
Random monoallelic gene expression increases upon embryonic stem cell differentiation.
Mélanie A Eckersley-Maslin, David Thybert, +3 authors, David L Spector.
Dev Cell, 2014 Mar 01; 28(4). PMID: 24576421    Free PMC article.
The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes.
Ai Ling Teh, Hong Pan, +22 authors, Joanna D Holbrook.
Genome Res, 2014 Apr 09; 24(7). PMID: 24709820    Free PMC article.
Highly Cited.
Random monoallelic expression: regulating gene expression one allele at a time.
Mélanie A Eckersley-Maslin, David L Spector.
Trends Genet, 2014 May 02; 30(6). PMID: 24780084    Free PMC article.
A symbiotic liaison between the genetic and epigenetic code.
Holger Heyn.
Front Genet, 2014 May 14; 5. PMID: 24822056    Free PMC article.
Stability of gene expression and epigenetic profiles highlights the utility of patient-derived paediatric acute lymphoblastic leukaemia xenografts for investigating molecular mechanisms of drug resistance.
Nicholas C Wong, Vivek A Bhadri, +5 authors, Richard B Lock.
BMC Genomics, 2014 Jun 03; 15. PMID: 24885906    Free PMC article.
Contribution of genetic variation to transgenerational inheritance of DNA methylation.
Allan F McRae, Joseph E Powell, +7 authors, Grant W Montgomery.
Genome Biol, 2014 Jun 03; 15(5). PMID: 24887635    Free PMC article.
Highly Cited.
Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations.
Santhi K Ganesh, Daniel I Chasman, +52 authors, Aravinda Chakravarti.
Am J Hum Genet, 2014 Jul 01; 95(1). PMID: 24975945    Free PMC article.
Cis and trans effects of human genomic variants on gene expression.
Julien Bryois, Alfonso Buil, +9 authors, Emmanouil T Dermitzakis.
PLoS Genet, 2014 Jul 11; 10(7). PMID: 25010687    Free PMC article.
Relating gene expression evolution with CpG content changes.
Huan Yang, Dawei Li, Chao Cheng.
BMC Genomics, 2014 Aug 22; 15. PMID: 25142157    Free PMC article.
Two-stage genome-wide methylation profiling in childhood-onset Crohn's Disease implicates epigenetic alterations at the VMP1/MIR21 and HLA loci.
Alex T Adams, Nicholas A Kennedy, +10 authors, Jack Satsangi.
Inflamm Bowel Dis, 2014 Aug 22; 20(10). PMID: 25144570    Free PMC article.
Integrating transcriptome and epigenome: putting together the pieces of the type 2 diabetes pathogenesis puzzle.
Swapan Kumar Das.
Diabetes, 2014 Aug 26; 63(9). PMID: 25146470    Free PMC article.
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels.
Nicholas E Banovich, Xun Lan, +6 authors, Yoav Gilad.
PLoS Genet, 2014 Sep 19; 10(9). PMID: 25233095    Free PMC article.
Highly Cited.
Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies.
Nikolaos I Panousis, Maria Gutierrez-Arcelus, Emmanouil T Dermitzakis, Tuuli Lappalainen.
Genome Biol, 2014 Sep 23; 15(9). PMID: 25239376    Free PMC article.
Genetic and epigenetic regulation of gene expression in fetal and adult human livers.
Marc Jan Bonder, Silva Kasela, +17 authors, Lili Milani.
BMC Genomics, 2014 Oct 06; 15. PMID: 25282492    Free PMC article.
Evolving insights on how cytosine methylation affects protein-DNA binding.
Ana Carolina Dantas Machado, Tianyin Zhou, +5 authors, Remo Rohs.
Brief Funct Genomics, 2014 Oct 17; 14(1). PMID: 25319759    Free PMC article.
The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences.
N Ari Wijetunga, Fabien Delahaye, +4 authors, John M Greally.
Nat Commun, 2014 Oct 21; 5. PMID: 25327398    Free PMC article.
Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning.
Nilmini Hettiarachchi, Kirill Kryukov, Kenta Sumiyama, Naruya Saitou.
Genome Biol Evol, 2014 Nov 05; 6(9). PMID: 25364802    Free PMC article.
Genome-wide associations between genetic and epigenetic variation influence mRNA expression and insulin secretion in human pancreatic islets.
Anders H Olsson, Petr Volkov, +6 authors, Charlotte Ling.
PLoS Genet, 2014 Nov 07; 10(11). PMID: 25375650    Free PMC article.
Highly Cited.
The Influences of Genetic and Environmental Factors on Methylome-wide Association Studies for Human Diseases.
Yan V Sun.
Curr Genet Med Rep, 2014 Nov 26; 2(4). PMID: 25422794    Free PMC article.
The era of integrative genomics: more data or better methods?
Devin C Koestler, Meaghan J Jones, +2 authors, Michael Kobor.
Epigenomics, 2014 Nov 29; 6(5). PMID: 25431938    Free PMC article.
Approaches for establishing the function of regulatory genetic variants involved in disease.
Julian Charles Knight.
Genome Med, 2014 Dec 05; 6(10). PMID: 25473428    Free PMC article.
Gene age predicts the strength of purifying selection acting on gene expression variation in humans.
Konstantin Y Popadin, Maria Gutierrez-Arcelus, +10 authors, Stylianos E Antonarakis.
Am J Hum Genet, 2014 Dec 07; 95(6). PMID: 25480033    Free PMC article.
Relationship between expression and methylation of obesity-related genes in children.
Veronica Davé, Paul Yousefi, +2 authors, Nina Holland.
Mutagenesis, 2015 Jan 16; 30(3). PMID: 25589532    Free PMC article.
Function and information content of DNA methylation.
Dirk Schübeler.
Nature, 2015 Jan 17; 517(7534). PMID: 25592537
Highly Cited. Review.
Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing.
Maria Gutierrez-Arcelus, Halit Ongen, +18 authors, Emmanouil T Dermitzakis.
PLoS Genet, 2015 Jan 31; 11(1). PMID: 25634236    Free PMC article.
Highly Cited.
Discordance of DNA methylation variance between two accessible human tissues.
Ruiwei Jiang, Meaghan J Jones, +4 authors, Michael S Kobor.
Sci Rep, 2015 Feb 11; 5. PMID: 25660083    Free PMC article.
The role of regulatory variation in complex traits and disease.
Frank W Albert, Leonid Kruglyak.
Nat Rev Genet, 2015 Feb 25; 16(4). PMID: 25707927
Highly Cited. Review.
Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci.
Mathieu Lemire, Syed H E Zaidi, +14 authors, Thomas J Hudson.
Nat Commun, 2015 Feb 27; 6. PMID: 25716334    Free PMC article.
Highly Cited.
Role of mecp2 in experience-dependent epigenetic programming.
Christoph A Zimmermann, Anke Hoffmann, Florian Raabe, Dietmar Spengler.
Genes (Basel), 2015 Mar 11; 6(1). PMID: 25756305    Free PMC article.
Post-conversion targeted capture of modified cytosines in mammalian and plant genomes.
Qing Li, Masako Suzuki, +10 authors, John M Greally.
Nucleic Acids Res, 2015 Mar 31; 43(12). PMID: 25813045    Free PMC article.
Assessing allele-specific expression across multiple tissues from RNA-seq read data.
Matti Pirinen, Tuuli Lappalainen, +5 authors, Manuel A Rivas.
Bioinformatics, 2015 Mar 31; 31(15). PMID: 25819081    Free PMC article.
A pooling-based approach to mapping genetic variants associated with DNA methylation.
Irene M Kaplow, Julia L MacIsaac, +3 authors, Hunter B Fraser.
Genome Res, 2015 Apr 26; 25(6). PMID: 25910490    Free PMC article.
DNA methylation and healthy human aging.
Meaghan J Jones, Sarah J Goodman, Michael S Kobor.
Aging Cell, 2015 Apr 29; 14(6). PMID: 25913071    Free PMC article.
Highly Cited. Review.
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
Manu J Dubin, Pei Zhang, +16 authors, Magnus Nordborg.
Elife, 2015 May 06; 4. PMID: 25939354    Free PMC article.
Highly Cited.
The landscape of genomic imprinting across diverse adult human tissues.
Yael Baran, Meena Subramaniam, +20 authors, Tuuli Lappalainen.
Genome Res, 2015 May 09; 25(7). PMID: 25953952    Free PMC article.
Highly Cited.
Regulators associated with clinical outcomes revealed by DNA methylation data in breast cancer.
Matthew H Ung, Frederick S Varn, Shaoke Lou, Chao Cheng.
PLoS Comput Biol, 2015 May 23; 11(5). PMID: 25996148    Free PMC article.
HIF3A association with adiposity: the story begins before birth.
Hong Pan, Xinyi Lin, +18 authors, GUSTO Study Group.
Epigenomics, 2015 May 27; 7(6). PMID: 26011824    Free PMC article.
Human body epigenome maps reveal noncanonical DNA methylation variation.
Matthew D Schultz, Yupeng He, +16 authors, Joseph R Ecker.
Nature, 2015 Jun 02; 523(7559). PMID: 26030523    Free PMC article.
Highly Cited.
Integrative analysis of methylome and transcriptome in human blood identifies extensive sex- and immune cell-specific differentially methylated regions.
Shimrat Mamrut, Nili Avidan, +4 authors, Ariel Miller.
Epigenetics, 2015 Aug 21; 10(10). PMID: 26291385    Free PMC article.
Life course socioeconomic status and DNA methylation in genes related to stress reactivity and inflammation: The multi-ethnic study of atherosclerosis.
Belinda L Needham, Jennifer A Smith, +7 authors, Ava V Diez Roux.
Epigenetics, 2015 Aug 22; 10(10). PMID: 26295359    Free PMC article.
DNA-Methylation Patterns in Trisomy 21 Using Cells from Monozygotic Twins.
M Reza Sailani, Federico A Santoni, +12 authors, Stylianos E Antonarakis.
PLoS One, 2015 Sep 01; 10(8). PMID: 26317209    Free PMC article.
Tools and best practices for data processing in allelic expression analysis.
Stephane E Castel, Ami Levy-Moonshine, +2 authors, Tuuli Lappalainen.
Genome Biol, 2015 Sep 19; 16. PMID: 26381377    Free PMC article.
Highly Cited.
Omic personality: implications of stable transcript and methylation profiles for personalized medicine.
Rubina Tabassum, Ambily Sivadas, +3 authors, Greg Gibson.
Genome Med, 2015 Sep 24; 7. PMID: 26391122    Free PMC article.
Epigenome-wide association study suggests that SNPs in the promoter region of RETN influence plasma resistin level via effects on DNA methylation at neighbouring sites.
Masahiro Nakatochi, Sahoko Ichihara, +9 authors, Mitsuhiro Yokota.
Diabetologia, 2015 Sep 26; 58(12). PMID: 26404063
Functional genomics bridges the gap between quantitative genetics and molecular biology.
Tuuli Lappalainen.
Genome Res, 2015 Oct 03; 25(10). PMID: 26430152    Free PMC article.
Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers.
Sarah Voisin, Markus Sällman Almén, +11 authors, Helgi B Schiöth.
Genome Med, 2015 Oct 10; 7. PMID: 26449484    Free PMC article.
Methylation quantitative trait locus analysis of osteoarthritis links epigenetics with genetic risk.
Michael D Rushton, Louise N Reynard, +7 authors, John Loughlin.
Hum Mol Genet, 2015 Oct 16; 24(25). PMID: 26464490    Free PMC article.
Differentially methylated obligatory epialleles modulate context-dependent LAM gene expression in the honeybee Apis mellifera.
Laura Wedd, Robert Kucharski, Ryszard Maleszka.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Clin Epigenetics, 2020 Jun 10; 12(1). PMID: 32513305    Free PMC article.
The Role of Transcription Factor 21 in Epicardial Cell Differentiation and the Development of Coronary Heart Disease.
Haochang Hu, Shaoyi Lin, Shuangshuang Wang, Xiaomin Chen.
Front Cell Dev Biol, 2020 Jun 26; 8. PMID: 32582717    Free PMC article.
Genetic-Epigenetic Interactions in Asthma Revealed by a Genome-Wide Gene-Centric Search.
Vladimir Kogan, Joshua Millstein, +9 authors, Carrie V Breton.
Hum Hered, 2019 Jan 23; 83(3). PMID: 30669148    Free PMC article.
Gene-methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk.
Julia Romanowska, Øystein A Haaland, +7 authors, Håkon K Gjessing.
Clin Epigenetics, 2020 Jul 18; 12(1). PMID: 32678018    Free PMC article.
Epigenetics and evolution.
I Mendizabal, T E Keller, J Zeng, Soojin V Yi.
Integr Comp Biol, 2014 May 20; 54(1). PMID: 24838745    Free PMC article.
Association Between the Methylation Statuses at CpG Sites in the Promoter Region of the SLCO1B3, RNA Expression and Color Change in Blue Eggshells in Lushi Chickens.
Zhuanjian Li, Tuanhui Ren, +9 authors, Xiangtao Kang.
Front Genet, 2019 Mar 14; 10. PMID: 30863430    Free PMC article.
Predicting gene expression using DNA methylation in three human populations.
Huan Zhong, Soyeon Kim, Degui Zhi, Xiangqin Cui.
PeerJ, 2019 May 21; 7. PMID: 31106051    Free PMC article.
Association of CNVs with methylation variation.
Xinghua Shi, Saranya Radhakrishnan, +7 authors, Sunita R Setlur.
NPJ Genom Med, 2020 Oct 17; 5. PMID: 33062306    Free PMC article.
HIF3A cord blood methylation and systolic blood pressure at 4 years - a population-based cohort study.
Toby Mansell, David Burgner, +6 authors, Richard Saffery.
Epigenetics, 2020 Jun 13; 15(12). PMID: 32530724    Free PMC article.
The other side of the coin: Hypersociability.
Miklos Toth.
Genes Brain Behav, 2018 Aug 14; 18(1). PMID: 30101538    Free PMC article.
Oxidative stress and epigenetic mortality risk score: associations with all-cause mortality among elderly people.
Xu Gao, Xīn Gào, +3 authors, Hermann Brenner.
Eur J Epidemiol, 2019 Feb 17; 34(5). PMID: 30771035
Expression Quantitative Trait Methylation Analysis Reveals Methylomic Associations With Gene Expression in Childhood Asthma.
Soyeon Kim, Erick Forno, +8 authors, Juan C Celedón.
Chest, 2020 Jun 23; 158(5). PMID: 32569636    Free PMC article.
Drug Response Associated With and Prognostic lncRNAs Mediated by DNA Methylation and Transcription Factors in Colon Cancer.
Jiayu Zhang, Zhen Shen, +3 authors, Tiancheng Zhao.
Front Genet, 2020 Dec 18; 11. PMID: 33329694    Free PMC article.
The long non-coding RNA TSLC8 inhibits colorectal cancer by stabilizing puma.
Zhian Du, Tao Yu, +2 authors, Gang Liu.
Cell Cycle, 2020 Nov 22; 19(23). PMID: 33218295    Free PMC article.
Combined effects of genotype and childhood adversity shape variability of DNA methylation across age.
Darina Czamara, Elleke Tissink, +21 authors, Elisabeth B Binder.
Transl Psychiatry, 2021 Feb 03; 11(1). PMID: 33526782    Free PMC article.
Gene regulation contributes to explain the impact of early life socioeconomic disadvantage on adult inflammatory levels in two cohort studies.
Cristian Carmeli, Zoltán Kutalik, +18 authors, Silvia Stringhini.
Sci Rep, 2021 Feb 06; 11(1). PMID: 33542415    Free PMC article.
Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer's disease risk genes.
Jeremy Schwartzentruber, Sarah Cooper, +10 authors, Andrew Bassett.
Nat Genet, 2021 Feb 17; 53(3). PMID: 33589840    Free PMC article.
Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis.
DeAnna Baker Frost, Willian da Silveira, +9 authors, Paula S Ramos.
Genes (Basel), 2021 Jan 28; 12(2). PMID: 33498390    Free PMC article.
Global discovery of lupus genetic risk variant allelic enhancer activity.
Xiaoming Lu, Xiaoting Chen, +13 authors, Leah C Kottyan.
Nat Commun, 2021 Mar 14; 12(1). PMID: 33712590    Free PMC article.
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.
Chen Yao, Roby Joehanes, +11 authors, Daniel Levy.
Clin Epigenetics, 2021 Mar 24; 13(1). PMID: 33752734    Free PMC article.
Role of DNA Methylation in Mediating Genetic Risk of Psychiatric Disorders.
Anna Starnawska, Ditte Demontis.
Front Psychiatry, 2021 Apr 20; 12. PMID: 33868039    Free PMC article.
Genetic impacts on DNA methylation: research findings and future perspectives.
Sergio Villicaña, Jordana T Bell.
Genome Biol, 2021 May 02; 22(1). PMID: 33931130    Free PMC article.
The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1.
Sreejana Ray, Aniekanabasi Ufot, +5 authors, Charles Vinson.
Biochim Biophys Acta Gene Regul Mech, 2019 Mar 03; 1862(4). PMID: 30825655    Free PMC article.
Effect of DNA methylation on gene transcription is associated with the distribution of methylation sites across the genome in osteoarthritis.
Peng Yi, Xiongfeng Xu, Jiawei Yao, Bo Qiu.
Exp Ther Med, 2021 May 20; 22(1). PMID: 34007328    Free PMC article.