SNPs located at CpG sites modulate genome-epigenome interaction

Epigenetics

Volumn 8, Issue 8, 2013, Pages 802-806

  Zhi, Degui ^a   Aslibekyan, Stella ^a   Irvin, Marguerite R ^a   Claas, Steven A ^a   Borecki, Ingrid B ^b   Ordovas, Jose M ^c   Absher, Devin M ^d   Arnett, Donna K ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b WASHINGTON UNIVERSITY   (United States)

^c TUFTS UNIVERSITY   (United States)

^d HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

Author keywords

DNA methylation; Epigenome wide study; Infinium human methylation 450K beadchip; meQTL; meSNP

Indexed keywords

ALLELE; ARTICLE; CD4+ T LYMPHOCYTE; CPG ISLAND; DNA METHYLATION; EPIGENETICS; GENE EXPRESSION; GENE FREQUENCY; GENE INTERACTION; GENETIC ASSOCIATION; GENETIC REGULATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; MICROARRAY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA METHYLATION; EPIGENOME-WIDE STUDY; INFINIUM HUMAN METHYLATION 450K BEADCHIP; MEQTL; MESNP;

CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; GENOME, HUMAN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84880972450     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.25501     Document Type: Article

References (14)

1. Maher B. Personal genomes: The case of the missing heritability. Nature 2008; 456:18-21; PMID:18987709; http://dx.doi.org/10.1038/456018a
2. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai SL, et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 2010; 6:e1000952; PMID:20485568; http://dx.doi.org/10.1371/journal. pgen.1000952
3. Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol 2011; 12:R10; PMID:21251332; http://dx.doi.org/10.1186/gb-2011-12-1-r10
4. Shoemaker R, Deng J, Wang W, Zhang K. Allelespecific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res 2010; 20:883-9; PMID:20418490; http://dx.doi. org/10.1101/gr.104695.109
5. Zhang D, Cheng L, Badner JA, Chen C, Chen Q, Luo W, et al. Genetic control of individual differences in gene-specific methylation in human brain. Am J Hum Genet 2010; 86:411-9; PMID:20215007; http:// dx.doi.org/10.1016/j.ajhg.2010.02.005
6. Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, et al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet 2011; 7:e1002228; PMID:21852959; http://dx.doi. org/10.1371/journal.pgen.1002228
7. Hellman A, Chess A. Extensive sequence-influenced DNA methylation polymorphism in the human genome. Epigenetics Chromatin 2010; 3:11; PMID:20497546; http://dx.doi.org/10.1186/1756-8935-3-11
8. Lai CQ, Arnett DK, Corella D, Straka RJ, Tsai MY, Peacock JM, et al. Fenofibrate effect on triglyceride and postprandial response of apolipoprotein A5 variants: the GOLDN study. Arterioscler Thromb Vasc Biol 2007; 27:1417-25; PMID:17431185; http://dx.doi. org/10.1161/ATVBAHA.107.140103
9. Irvin MR, Kabagambe EK, Tiwari HK, Parnell LD, Straka RJ, Tsai MY, et al. Apolipoprotein E polymorphisms and postprandial triglyceridemia before and after fenofibrate treatment in the Genetics of Lipid Lowering and Diet Network (GOLDN) Study. Circ Cardiovasc Genet 2010; 3:462-7; PMID:20729559; http://dx.doi. org/10.1161/CIRCGENETICS.110.950667
10. Aslibekyan S, Kabagambe EK, Irvin MR, Straka RJ, Borecki IB, Tiwari HK, et al. A genome-wide association study of inflammatory biomarker changes in response to fenofibrate treatment in the Genetics of Lipid Lowering Drug and Diet Network. Pharmacogenet Genomics 2012; 22:191-7; PMID:22228203; http:// dx.doi.org/10.1097/FPC.0b013e32834fdd41
11. Atkinson B, Therneau T. kinship: mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees. 2007; R package version 1.1.0-17.
12. Liang L, Morar N, Dixon AL, Lathrop GM, Abecasis GR, Moffatt MF, et al. A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines. [Epub ahead of print]. Genome Res 2013; 23:716-26; PMID:23345460; http://dx.doi.org/10.1101/gr.142521.112
13. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 2010; 464:768-72; PMID:20220758; http://dx.doi.org/10.1038/ nature08872
14. Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, Runarsson A, et al. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol 2013; 31:142-7; PMID:23334450; http://dx.doi. org/10.1038/nbt.2487