Whole-Genome DNA Methylation Profile of the Jewel Wasp (Nasonia vitripennis)

Abstract

The epigenetic mark of DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, has been extensively studied in many mammalian genomes and, although it is commonly found at the promoter regions of genes, it is also involved in a number of different biological functions. In other complex animals, such as social insects, DNA methylation has been determined to be involved in caste differentiation and to occur primarily in gene bodies. The role of methylation in nonsocial insects, however, has not yet been explored thoroughly. Here, we present the whole-genome DNA methylation profile of the nonsocial hymenopteran, the jewel wasp (Nasonia vitripennis). From high-throughput sequencing of bisulfite-converted gDNA extracted from male Nasonia thoraces, we were able to determine which cytosine residues are methylated in the entire genome. We found that an overwhelming majority of methylated sites (99.7%) occur at cytosines followed by a guanine in the 3′ direction (CpG sites). Additionally, we found that a majority of methylation in Nasonia occurs within exonic regions of the genome (more than 62%). Overall, methylation is sparse in Nasonia, occurring only at 0.18% of all sites and at 0.63% of CpGs. Our analysis of the Nasonia methylome revealed that in contrast to the methylation profile typically seen in mammals, methylation is sparse and is constrained primarily to exons. This methylation profile is more similar to that of the social hymenopteran species, the honey bee (Apis mellifera). In presenting the Nasonia methylome, we hope to promote future investigation of the regulatory function of DNA methylation in both social and nonsocial hymenoptera.

DNA Methylation and Sex Allocation in the Parasitoid WaspNasonia vitripennis

“…Given that the N. vitripennis methylome has recently been sequenced (Wang et al 2013;Beeler et al 2014), future research will determine which methylated DNA sequences are involved in sex allocation. As we have recently shown that there is (so far) no detectable differential gene expression associated with facultative sex allocation in Nasonia (N. Cook, U. Trivedi, B. Pannebakker, M. Blaxter, M. Ritchie, E. Tauber, T. Sneddon, and D. Shuker, unpublished manuscript), it would appear that disrupting DNA methylation is not having its effect by changing patterns of gene expression during oviposition, but rather the effect must be upstream, perhaps changing the sex allocation machinery prior to the female actually having to allocate sex.…”

“…Recent work has confirmed genome-wide DNA methylation in Nasonia, with approximately 30% of genes having methylated CpG sequences, mostly in exons, with methylation typically associated with increased gene expression (Wang et al 2013; see also Beeler et al 2014). Here we use the demethylating agent 5-aza-2 0 -deoxycytidine (5-aza-dC) to manipulate the genome-wide DNA methylation status of female N. vitripennis.…”

DNA methylation changes induced by long and short photoperiods inNasonia

“…First, we provide a detailed genomic description of methylation in Nasonia vitripennis, which augments the recently published data sets (Wang et al 2013;Beeler et al 2014). Second, we identify differentially methylated sites in females associated with experience of long or short days.…”

Functional characterization of the transcriptional regulatory elements of three highly expressed constitutive genes in the jewel wasp, Nasonia vitripennis

“…Although NVhsp90A showed a similar pattern of expression and level of expression as NVhsp70 and NVlsdp in Sf9 cells and in somatic and germline transformed D. melanogaster, the expression pattern will require mapping in N. vitripennis during development. NVhsp90A is the only sequence examined that shows DNA methylation in the native condition (Beeler et al, 2014) yet it was as active in the Sf9 cells and in D. melanogaster, which largely lacks DNA methylation. This suggests that the methylation state of this TRE is not an essential feature of its efficacy.…”

“…This selection scheme provided sequences that had a high likelihood of containing consensus transcriptional regulatory elements for each gene but was not sufficient to include all potential enhancer or regulatory elements for each gene. From this pool, the 5' upstream sequences were examined with consideration to the state of DNA methylation based on comparisons with the bisulphiteconverted DNA libraries (Beeler et al, 2014). Based on these selection criteria, eight unmethylated genes were selected as potential candidates and an additional five methylated genes were selected (Table 1).…”