Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc

Abstract

Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. 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. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined 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.

Anti-viral gene induction is absent upon secondary challenge with double-stranded RNA in the Pacific oyster, Crassostrea gigas

“…We decided to target the upstream region of anti-viral genes due to the importance of methylation in regulatory regions controlling immune gene expression in mammalian and plant models [20,22,26]. However, after this study was initiated, Gavery and Roberts [31,32] reported that DNA methylation varies spatially across the C. gigas genome with the majority of methylated sites mapping to intra-genic regions. Therefore, even if DNA methylation is an epigenetic mechanism involved, we might not expect to find evidence to support our hypothesis that injection of dsRNA changes the DNA methylation levels upstream of specific anti-viral genes ( Table 2).…”

Ecological Epigenetics in Marine Metazoans

“…Gavery and Roberts were the first to report DNA methylation in C. gigas (Gavery and Roberts, 2010), and continued in a second study with BS-seq analysis. In the latter study, Gavery and Roberts correlated methylated genes in the C. gigas methylome with high transcript abundance in the transcriptome (Gavery and Roberts, 2013). The abundance of publications with C. gigas as the study organism is likely due to its economic importance in combination with the early availability of genomic resources (Zhang et al, 2012).…”

Analysis of DNA methylation in tissues and development stages of pearl oyster Pinctada fucata

“…In shellfish, associations have been found between genetic and DNA methylation profiles (P \ 0.01) and the influence of DNA methylation on gene expression and early development of Crassostrea gigas (Gavery and Roberts 2010;Jiang et al 2013b;Riviere et al 2013). The methylated genes in C. gigas were also found to associate with high transcript abundance and low variation in expression between tissue types (Gavery and Roberts 2013). No studies of DNA methylation have however been reported for P. fucata.…”