Function and Evolution of DNA Methylation in Nasonia vitripennis

Xu Wang,Amanda Avery,David Wheeler,John H Werren,John K Colbourne,Jeong-Hyeon Choi,Alfredo Rago,Andrew G Clark,Claude Desplan

doi:10.1371/journal.pgen.1003872

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.

Highlights

DNA methylation is an important epigenetic modification found in many plants and animals [1,2,3,4,5]
Using a highly inbred line permitted us to precisely characterize DNA methylation, which is compared to gene expression variation across developmental stages, and contrasted to other insect species
Methylated genes exhibit more uniform expression across developmental stages for both moderately and highly expressed genes, suggesting that DNA methylation is marking the genes for constitutive expression

Summary

Introduction

DNA methylation is an important epigenetic modification found in many plants and animals [1,2,3,4,5]. DNA methylation is associated with important epigenetic processes such as genomic imprinting [6], histone modifications and X chromosome inactivation [7,8], and plays an important role in brain development [9]. Methylation at the promoter will typically result in silencing of the gene [12]. The promoters of transposable elements (TEs) are often repressed by DNA methylation [13]. Non-CpG methylation has been observed in mammals, with high percentages in embryonic stem cells [14]

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Discussion

Conclusion