Back to Search Start Over

Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.

Authors :
Jia Zhou
Sears, Renee L.
Xiaoyun Xing
Bo Zhang
Daofeng Li
Rockweiler, Nicole B.
Hyo Sik Jang
Choudhary, Mayank N. K.
Hyung Joo Lee
Lowdon, Rebecca F.
Arand, Jason
Tabers, Brianne
Gu, C. Charles
Cicero, Theodore J.
Ting Wang
Source :
BMC Genomics; 9/12/2017, Vol. 18, p1-17, 17p, 3 Charts, 5 Graphs
Publication Year :
2017

Abstract

Background: Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic mechanism in mammalian development, little is known about the conservation of tissue-specific genome-wide DNA methylation patterns. Results: Using a comparative epigenomics approach, we identified and compared the tissue-specific DNAmethylation patterns of rat against those of mouse and human across three shared tissue types. We confirmed that tissue-specific differentially methylated regions are strongly associated with tissue-specific regulatory elements. Comparisons between species revealed that at a minimum 11-37% of tissue-specific DNA methylation patterns are conserved, a phenomenon that we define as epigenetic conservation. Conserved DNA methylation is accompanied by conservation of other epigenetic marks including histone modifications. Although a significant amount of locus-specific methylation is epigenetically conserved, the majority of tissue-specific DNA methylation is not conserved across the species and tissue types that we investigated. Examination of the genetic underpinning of epigenetic conservation suggests that primary sequence conservation is a driving force behind epigenetic conservation. In contrast, evolutionary dynamics of tissue-specific DNA methylation are best explained by the maintenance or turnover of binding sites for important transcription factors. Conclusions: Our study extends the limited literature of comparative epigenomics and suggests a new paradigm for epigenetic conservation without genetic conservation through analysis of transcription factor binding sites. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
14712164
Volume :
18
Database :
Complementary Index
Journal :
BMC Genomics
Publication Type :
Academic Journal
Accession number :
125118963
Full Text :
https://doi.org/10.1186/s12864-017-4115-6