A Comprehensive Methylome for Crassostrea gigas Provides Insight into the Role of DNA Methylation in Bivalves

Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation.  However, previous studies have been limited to in silico analyses or single gene characterization of DNA methylation. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. Results indicate that methylation varies spatially across the genome with a majority of methylated loci mapping to intra-genic regions. Bisulfite sequencing results were coupled with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.