Intermediate DNA methylation is a conserved signature of genome regulation
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ncomms7363.pdf
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Author(s)
Elliott, GiNell
Hong, Chibo
Xing, Xiaoyun
Zhou, Xin
Li, Daofeng
Coarfa, Cristian
Bell, Robert J.A.
Maire, Cecile L.
Ligon, Keith L.
Sigaroudinia, Mahvash
Date Issued
February 2015
Journal
Nature Communications
Publisher
Nature Publishing Group
Citation
Elliott, GiNell et al. “Intermediate DNA Methylation Is a Conserved Signature of Genome Regulation.” Nature Communications 6, 1 (February 2015): 6363 © 2015 Macmillan Publishers Limited
Version
Final published version
Abstract
The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions of intermediate methylation and their quantitative relationship with gene activity, we apply integrative and comparative epigenomics to 25 human primary cell and tissue samples. We report 18,452 intermediate methylation regions located near 36% of genes and enriched at enhancers, exons and DNase I hypersensitivity sites. Intermediate methylation regions average 57% methylation, are predominantly allele-independent and are conserved across individuals and between mouse and human, suggesting a conserved function. These regions have an intermediate level of active chromatin marks and their associated genes have intermediate transcriptional activity. Exonic intermediate methylation correlates with exon inclusion at a level between that of fully methylated and unmethylated exons, highlighting gene context-dependent functions. We conclude that intermediate DNA methylation is a conserved signature of gene regulation and exon usage.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
Creative Commons Attribution 4.0 International License
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DOI of Published Version
https://doi.org/10.1038/NCOMMS7363
