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Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation
- Source :
- BMC Genomics, Vol 18, Iss 1, Pp 1-17 (2017), BMC Genomics
- Publication Year :
- 2017
- Publisher :
- BMC, 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 DNA methylation 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. Electronic supplementary material The online version of this article (10.1186/s12864-017-4115-6) contains supplementary material, which is available to authorized users.
- Subjects :
- Epigenomics
0301 basic medicine
lcsh:QH426-470
lcsh:Biotechnology
Biology
Evolution, Molecular
Mice
03 medical and health sciences
lcsh:TP248.13-248.65
Genetics
Animals
Humans
Epigenetics
Conserved Sequence
Binding Sites
DNA methylation
Comparative epigenomics
Tissue-specific
Comparative genomics
Methylation
Epigenome
Epigenetic conservation
Rats
DNA binding site
lcsh:Genetics
030104 developmental biology
Differentially methylated regions
Histone
Organ Specificity
biology.protein
Transcription Factors
Research Article
Biotechnology
Subjects
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 18
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....b80a18f0e288ed66ed03f4e915a27759