Abstract
DNA modification is a naturally occurring DNA modification in prokaryotic and eukaryotic organisms and is involved in several biological processes. Although genome-wide methylation has been studied in many insects, the understanding of global and genomic DNA methylation during insect early embryonic development, is lacking especially for insect diapause. In this study, we analyzed the relationship between DNA methylomes and transcriptomes in diapause-destined eggs compared to diapause-terminated eggs in the silkworm, Bombyx mori (B. mori). The results revealed that methylation was sparse in this species, as previously reported. Moreover, methylation levels in diapause-terminated eggs (HCl-treated) were 0.05% higher than in non-treated eggs, mainly due to the contribution of CG methylation sites. Methylation tends to occur in the coding sequences and promoter regions, especially at transcription initiation sites and short interspersed elements. Additionally, 364 methylome- and transcriptome-associated genes were identified, which showed significant differences in methylation and expression levels in diapause-destined eggs when compared with diapause-terminated eggs, and 74% of methylome and transcriptome associated genes showed both hypermethylation and elevated expression. Most importantly, Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses showed that methylation may be positively associated with Bombyx mori embryonic development, by regulating cell differentiation, metabolism, apoptosis pathways and phosphorylation. Through analyzing the G2/M phase-specific E3 ubiquitin-protein ligase (G2E3), we speculate that methylation may affect embryo diapause by regulating the cell cycle in Bombyx mori. These findings will help unravel potential linkages between DNA methylation and gene expression during early insect embryonic development and insect diapause.
Highlights
DNA methylation is an important epigenetic modification in plants and animals [1,2,3,4]
Our previous study provided functional insights into Bombyx moriDnmt1 (BmDnmt1) and Bombyx moriDnmt2 (BmDnmt2) in the regulation of silkworm embryonic development; we showed that the expression of BmDnmt1 and BmDnmt2 was elevated in diapause-terminated eggs that were hydrochloric acid (HCl)-treated when compared with diapause-destined eggs [40]
To explore gene expression mechanisms during early embryonic development in the silkworm, we compared the transcriptional profiles of diapause-terminated eggs treated with HCl (HCl-treated) and diapause-destined eggs using RNA sequencing (RNA-seq), and the raw sequencing data are available from the repository of NCBI Sequence Read Archive (SRA) with the accession No PRJNA598980
Summary
DNA methylation is an important epigenetic modification in plants and animals [1,2,3,4]. DNA methylation in animals is accomplished by two types of DNA methyltransferases (DNMTs), de novo and maintenance DNMTs [12]. De novo DNMTs are responsible for establishing new methylation patterns by the Dnmt family of proteins, and maintenance DNMTs maintain previously established methylation patterns and are represented by the Dnmt family of proteins [13]. In contrast to these DNMTs, Dnmt shows a weak methyltransferase activity towards DNA and has been characterized as an active RNA methyltransferase [12,14]. Drosophila melanogaster possesses only a single DNMT (Dnmt2), the DNA methylation rate in the genome is at a low detectable level [15]
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