A diverse epigenetic landscape at human exons with implication for expression

Nucleic Acids Research
Meromit SingerYael Mandel-Gutfreund

Abstract

DNA methylation is an important epigenetic marker associated with gene expression regulation in eukaryotes. While promoter methylation is relatively well characterized, the role of intragenic DNA methylation remains unclear. Here, we investigated the relationship of DNA methylation at exons and flanking introns with gene expression and histone modifications generated from a human fibroblast cell-line and primary B cells. Consistent with previous work we found that intragenic methylation is positively correlated with gene expression and that exons are more highly methylated than their neighboring intronic environment. Intriguingly, in this study we identified a unique subset of hypomethylated exons that demonstrate significantly lower methylation levels than their surrounding introns. Furthermore, we observed a negative correlation between exon methylation and the density of the majority of histone modifications. Specifically, we demonstrate that hypo-methylated exons at highly expressed genes are associated with open chromatin and have a characteristic histone code comprised of significantly high levels of histone markings. Overall, our comprehensive analysis of the human exome supports the presence of regulatory hypomethylated...Continue Reading

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Jan 26, 2016·Current Biology : CB·Romain LibbrechtDaniel Jan Christoph Kronauer
Jun 12, 2016·Briefings in Functional Genomics·Veronique G LeBlanc, Marco A Marra
May 31, 2017·American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons·S V BonthaV R Mas
Apr 18, 2019·The Journal of International Medical Research·Zheng YangLuo Zhang
Mar 15, 2020·American Journal of Physical Anthropology·Genevieve HousmanAnne C Stone
Oct 3, 2020·World Journal of Gastrointestinal Oncology·Sandra FaiasCristina Albuquerque
Oct 23, 2019·Evolution Letters·Hollie MarshallEamonn B Mallon
Apr 3, 2019·Brain Tumor Pathology·Kosuke Aoki, Atsushi Natsume

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Methods Mentioned

BETA
RNA-Seq
ChIP-Seq

Software Mentioned

Tophat
UCSC genome browser
Cufflinks
R

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