Function and Evolution of DNA Methylation in Nasonia vitripennis

Abstract

The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. One-third of genes show extensive methylation over the gene body, yet methylated DNA is not found in non-coding regions and rarely in transposons. Methylated genes occur in small clusters across the genome. Methylation demarcates exon-intron boundaries, with elevated levels over exons, primarily in the 5′ regions of genes. It is also elevated near the sites of translational initiation and termination, with reduced levels in 5′ and 3′ UTRs. Methylated genes have higher median expression levels and lower expression variation across development stages than non-methylated genes. There is no difference in frequency of differential splicing between methylated and non-methylated genes, and as yet no established role for methylation in regulating alternative splicing in Nasonia. Phylogenetic comparisons indicate that many genes maintain methylation status across long evolutionary time scales. Nasonia methylated genes are more likely to be conserved in insects, but even those that are not conserved show broader expression across development than comparable non-methylated genes. Finally, examination of duplicated genes shows that those paralogs that have lost methylation in the Nasonia lineage following gene duplication evolve more rapidly, show decreased median expression levels, and increased specialization in expression across development. Methylation of Nasonia genes signals constitutive transcription across developmental stages, whereas non-methylated genes show more dynamic developmental expression patterns. We speculate that loss of methylation may result in increased developmental specialization in evolution and acquisition of methylation may lead to broader constitutive expression.

Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti

“…S5-S6, and Tables S4-S6). The strains used are highly inbred, which also reduces calling errors due to sequence heterogeneity (30). As previously described, most of Nasonia methylated CpG sites (mCpGs) were located on exons in the first 1 kb of the coding region of the gene (30).…”

“…The strains used are highly inbred, which also reduces calling errors due to sequence heterogeneity (30). As previously described, most of Nasonia methylated CpG sites (mCpGs) were located on exons in the first 1 kb of the coding region of the gene (30). Gene methylation status (methylated vs. nonmethylated genes) was determined by the same criteria in our recent N. vitripennis methylome study (>10% mCpGs in the 5′-most 1-kb coding region) (30) (SI Appendix, Methods).…”

“…In our previous work we have shown in Nasonia that methylated genes tend to be expressed in all developmental stages and that methylation is negatively correlated with expression variability across development (30). Methylated genes are also more conserved at longer evolutionary timescales (30).…”

“…In our previous work we have shown in Nasonia that methylated genes tend to be expressed in all developmental stages and that methylation is negatively correlated with expression variability across development (30). Methylated genes are also more conserved at longer evolutionary timescales (30). Furthermore, duplicated genes that had lost their methylation since the divergence of Apis and Nasonia showed greater developmental stage specialization, suggesting that nonmethylated genes tend to evolve into specialized genes (30).…”

“…All three DNA methyltranferases are present in the Nasonia genome (28), and DNA methylation is critical for many biological processes including early embryonic development (29). Recently, we analyzed the DNA methylome in N. vitripennis at a base-pair resolution using whole-genome bisulfite sequencing (WGBS-seq) (30). In this current study, we quantify the gene expression level in adult whole-body samples of males and females from two closely related Nasonia species, N. vitripennis and N. giraulti, using RNA sequencing and also compare genome-wide DNA methylation in males and females of both species by WGBS-seq with >20× haploid genome coverage.…”