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자연과학대학
생명과학전공
Journal papers
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Association of CNVs with methylation variation
Title
Association of CNVs with methylation variation
Authors
Shi X.
;
Radhakrishnan S.
;
Wen J.
;
Chen J.Y.
;
Chen J.
;
Lam B.A.
;
Mills R.E.
;
Stranger B.E.
;
Lee C.
;
Setlur S.R.
Ewha Authors
Charles Lee
SCOPUS Author ID
Charles Lee
Issue Date
2020
Journal Title
npj Genomic Medicine
ISSN
2056-7944
Citation
npj Genomic Medicine vol. 5, no. 1
Publisher
Nature Research
Indexed
SCIE; SCOPUS
Document Type
Article
Abstract
Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long-range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype. © 2020, The Author(s).
DOI
10.1038/s41525-020-00145-w
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