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Front Physiol. 2014 Jun 17;5:224. doi: 10.3389/fphys.2014.00224. eCollection 2014.

Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes.

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1
School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA.

Abstract

DNA methylation patterns and functions are variable across invertebrate taxa. In order to provide a better understanding of DNA methylation in the Pacific oyster (Crassostrea gigas), we characterized the genome-wide DNA methylation profile in male gamete cells using whole-genome bisulfite sequencing. RNA-Seq analysis was performed to examine the relationship between DNA methylation and transcript expression. Methylation status of over 7.6 million CpG dinucleotides was described with a majority of methylated regions occurring among intragenic regions. Overall, 15% of the CpG dinucleotides were determined to be methylated and the mitochondrial genome lacked DNA methylation. Integrative analysis of DNA methylation and RNA-Seq data revealed a positive association between methylation status, both in gene bodies and putative promoter regions, and expression. This study provides a comprehensive characterization of the distribution of DNA methylation in the oyster male gamete tissue and suggests that DNA methylation is involved in gene regulatory activity.

KEYWORDS:

DNA methylation; bivalves; epigenetics; gene expression; oyster

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