Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era

被引：101

作者：

Do, Catherine ^{[1
,2
]}

Shearer, Alyssa ^{[1
,2
]}

Suzuki, Masako ^{[3
]}

Terry, Mary Beth ^{[2
,4
]}

Gelernter, Joel ^{[5
,6
,7
]}

Greally, John M. ^{[3
]}

Tycko, Benjamin ^{[8
,9
]}

机构：

[1] Columbia Univ, Inst Canc Genet, New York, NY 10032 USA

[2] Columbia Univ, Herbert Irving Comprehens Canc Ctr, New York, NY 10032 USA

[3] Albert Einstein Coll Med, Dept Genet, Ctr Epigen, Bronx, NY 10461 USA

[4] Columbia Univ, Mailman Sch Publ Hlth, Dept Epidemiol, New York, NY 10032 USA

[5] Yale Univ, Sch Med, Dept Psychiat, New Haven, CT 06520 USA

[6] Yale Univ, Sch Med, Dept Genet, New Haven, CT 06520 USA

[7] Yale Univ, Sch Med, Dept Neurobiol, New Haven, CT 06520 USA

[8] Taub Inst Res Alzheimers Dis & Aging Brain, Inst Canc Genet, Herbert Irving Comprehens Canc Ctr, New York, NY 10032 USA

[9] Columbia Univ, Dept Pathol & Cell Biol, New York, NY 10032 USA

来源：

GENOME BIOLOGY | 2017年 / 18卷

关键词：

TRANSCRIPTION FACTOR-BINDING; EPIGENOME-WIDE ASSOCIATION; ALLELE-SPECIFIC METHYLATION; HUMAN ADIPOSE-TISSUE; BODY-MASS INDEX; DNA METHYLATION; FUNCTIONAL VARIATION; BREAST-CANCER; HUMAN BLOOD; EXPRESSION;

D O I：

10.1186/s13059-017-1250-y

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Studies on genetic-epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in the post-genome-wide-association-study (GWAS) era. Such maps can nominate regulatory sequence variants that underlie GWAS signals for common diseases, ranging from neuropsychiatric disorders to cancers. Conversely, mQTLs need to be filtered out when searching for non-genetic effects in epigenome-wide association studies (EWAS). Sequence variants in CCCTC-binding factor (CTCF) and transcription factor binding sites have been mechanistically linked to mQTLs and hap-ASM. Identifying these sites can point to disease-associated transcriptional pathways, with implications for targeted treatment and prevention.

引用

页数：22

共 189 条

[131] Epigenome-wide association studies for common human diseases [J].

Rakyan, Vardhman K. ;

Down, Thomas A. ;

Balding, David J. ;

Beck, Stephan .

NATURE REVIEWS GENETICS, 2011, 12 (08) :529-541

[132] Effects of sequence variation on differential allelic transcription factor occupancy and gene expression [J].

Reddy, Timothy E. ;

Gertz, Jason ;

Pauli, Florencia ;

Kucera, Katerina S. ;

Varley, Katherine E. ;

Newberry, Kimberly M. ;

Marinov, Georgi K. ;

Mortazavi, Ali ;

Williams, Brian A. ;

Song, Lingyun ;

Crawford, Gregory E. ;

Wold, Barbara ;

Willard, Huntington F. ;

Myers, Richard M. .

GENOME RESEARCH, 2012, 22 (05) :860-869

[133] Incidence of Breast Cancer and Its Subtypes in Relation to Individual and Multiple Low-Penetrance Genetic Susceptibility Loci [J].

Reeves, Gillian K. ;

Travis, Ruth C. ;

Green, Jane ;

Bull, Diana ;

Tipper, Sarah ;

Baker, Krys ;

Beral, Valerie ;

Peto, Richard ;

Bell, John ;

Zelenika, Diana ;

Lathrop, Mark .

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION, 2010, 304 (04) :426-434

[134] CpG methylation regulates allelic expression of GDF5 by modulating binding of SP1 and SP3 repressor proteins to the osteoarthritis susceptibility SNP rs143383 [J].

Reynard, Louise N. ;

Bui, Catherine ;

Syddall, Catherine M. ;

Loughlin, John .

HUMAN GENETICS, 2014, 133 (08) :1059-1073

[135] Collapsed methylation quantitative trait loci analysis for low frequency and rare variants [J].

Richardson, Tom G. ;

Shihab, Hashem A. ;

Hemani, Gibran ;

Zheng, Jie ;

Hannon, Eilis ;

Mill, Jonathan ;

Carnero-Montoro, Elena ;

Bell, Jordana T. ;

Lyttleton, Oliver ;

McArdle, Wendy L. ;

Ring, Susan M. ;

Rodriguez, Santiago ;

Campbell, Colin ;

Smith, George Davey ;

Relton, Caroline L. ;

Timpson, Nicholas J. ;

Gaunt, Tom R. .

HUMAN MOLECULAR GENETICS, 2016, 25 (19) :4339-4349

[136] Impact of age, BMI and HbA1c levels on the genome-wide DNA methylation and mRNA expression patterns in human adipose tissue and identification of epigenetic biomarkers in blood [J].

Ronn, Tina ;

Volkov, Petr ;

Gillberg, Linn ;

Kokosar, Milana ;

Perfilyev, Alexander ;

Jacobsen, Anna Louisa ;

Jorgensen, Sine W. ;

Brons, Charlotte ;

Jansson, Per-Anders ;

Eriksson, Karl-Fredrik ;

Pedersen, Oluf ;

Hansen, Torben ;

Groop, Leif ;

Stener-Victorin, Elisabet ;

Vaag, Allan ;

Nilsson, Emma ;

Ling, Charlotte .

HUMAN MOLECULAR GENETICS, 2015, 24 (13) :3792-3813

[137] Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans [J].

Rotival, Maxime ;

Zeller, Tanja ;

Wild, Philipp S. ;

Maouche, Seraya ;

Szymczak, Silke ;

Schillert, Arne ;

Castagne, Raphaele ;

Deiseroth, Arne ;

Proust, Carole ;

Brocheton, Jessy ;

Godefroy, Tiphaine ;

Perret, Claire ;

Germain, Marine ;

Eleftheriadis, Medea ;

Sinning, Christoph R. ;

Schnabel, Renate B. ;

Lubos, Edith ;

Lackner, Karl J. ;

Rossmann, Heidi ;

Muenzel, Thomas ;

Rendon, Augusto ;

Erdmann, Jeanette ;

Deloukas, Panos ;

Hengstenberg, Christian ;

Diemert, Patrick ;

Montalescot, Gilles ;

Ouwehand, Willem H. ;

Samani, Nilesh J. ;

Schunkert, Heribert ;

Tregouet, David-Alexandre ;

Ziegler, Andreas ;

Goodall, Alison H. ;

Cambien, Francois ;

Tiret, Laurence ;

Blankenberg, Stefan .

PLOS GENETICS, 2011, 7 (12)

[138] Bison: bisulfite alignment on nodes of a cluster [J].

Ryan, Devon Patrick ;

Ehninger, Dan .

BMC BIOINFORMATICS, 2014, 15

[139] Genetics of gene expression surveyed in maize, mouse and man [J].

Schadt, EE ;

Monks, SA ;

Drake, TA ;

Lusis, AJ ;

Che, N ;

Colinayo, V ;

Ruff, TG ;

Milligan, SB ;

Lamb, JR ;

Cavet, G ;

Linsley, PS ;

Mao, M ;

Stoughton, RB ;

Friend, SH .

NATURE, 2003, 422 (6929) :297-302

[140] Mapping the genetic architecture of gene expression in human liver [J].

Schadt, Eric E. ;

Molony, Cliona ;

Chudin, Eugene ;

Hao, Ke ;

Yang, Xia ;

Lum, Pek Y. ;

Kasarskis, Andrew ;

Zhang, Bin ;

Wang, Susanna ;

Suver, Christine ;

Zhu, Jun ;

Millstein, Joshua ;

Sieberts, Solveig ;

Lamb, John ;

GuhaThakurta, Debraj ;

Derry, Jonathan ;

Storey, John D. ;

Avila-Campillo, Iliana ;

Kruger, Mark J. ;

Johnson, Jason M. ;

Rohl, Carol A. ;

van Nas, Atila ;

Mehrabian, Margarete ;

Drake, Thomas A. ;

Lusis, Aldons J. ;

Smith, Ryan C. ;

Guengerich, F. Peter ;

Strom, Stephen C. ;

Schuetz, Erin ;

Rushmore, Thomas H. ;

Ulrich, Roger .

PLOS BIOLOGY, 2008, 6 (05) :1020-1032

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