Single Base-Resolution Methylome of the Dizygotic Sheep

PLoS One. 2015 Nov 4;10(11):e0142034. doi: 10.1371/journal.pone.0142034. eCollection 2015.

Abstract

Sheep is an important livestock in the world for meat, dairy and wool production. The third version of sheep reference genome has been recently assembled, but sheep DNA methylome has not been profiled yet. In this study, we report the comprehensive sheep methylome with 94.38% cytosine coverage at single base resolution by sequencing DNA samples from Longissimus dorsi of dizygotic Sunit sheep, which were bred in different habitats. We also compared methylomes between the twin sheep. DNA methylation status at genome-scale differentially methylated regions (DMRs), functional genomic regions and 248 DMR-containing genes were identified between the twin sheep. Gene ontology (GO) and KEGG annotations of these genes were performed to discover computationally predicted function. Lipid metabolism, sexual maturity and tumor-associated categories were observed to significantly enrich DMR-containing genes. These findings could be used to illustrate the relationship between phenotypic variations and gene methylation patterns.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CpG Islands*
  • Cytosine / metabolism
  • DNA Methylation*
  • Epigenesis, Genetic*
  • Female
  • Gene Expression Profiling
  • Genomics / methods*
  • Sequence Analysis, DNA
  • Sheep
  • Transcription, Genetic

Substances

  • Cytosine

Grants and funding

This work was supported by the Chinese 863 program (2013AA102506), the National Natural Science Foundations of China (31201773 and 31560623), the open project of the State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (GREKF13-02) to JW, and the China Postdoctoral Science Foundation (2014M562351) to JW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.