DNA Methylation Is Correlated with Gene Expression during Diapause Termination of Early Embryonic Development in the Silkworm (Bombyx mori)

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.

Invertebrate DNA methylation and gene regulation

“…For the smooth cauliflower coral Stylophora pistillata (Liew et al 2018), we compared only the most extreme pH treatment (pH 7.2; N=3) to controls (pH 8.0; N=3). For silkworm Bombyx mori (Li et al 2020), we compared diapause terminated (N=3) to diapause destined (N=3) eggs. For the termite Zootermopsis nevadensis nuttingi (Glastad et al 2016), we compared winged reproductive alates of both sexes (N=4) to larval instars (workers) of both sexes (N=4).…”

“…The Anthozoan studies contrasted polyp types in the coral Acropora millepora (Dixon and Matz 2020), pH treatments in the coral Stylophora pistillata (Liew et al 2018), and symbiotic state in the sea anemone Exaiptasia pallida . Hexapoda studies included different reproductive states in ants (Ooceraea biroi)(Libbrecht et al 2016), bumblebees (Bombus terrestris) (Marshall et al 2019), and termites (Zootermopsis nevadensis) (Glastad et al 2016), different subcastes in honeybee (Apis mellifera)(Herb et al 2012), differences in maternal care in carpenter bee (Arsenault et al 2018), and different diapause states in silkworm (Bombyx mori) (Li et al 2020). Using these diverse datasets, we first confirm previous findings that baseline gbM levels are bimodally distributed across coding genes, are…”

Invertebrate DNA Methylation and Gene Regulation

“…For the smooth cauli ower coral Stylophora pistillata (Liew et al 2018), we compared only the most extreme pH treatment (pH 7.2; N=3) to controls (pH 8.0; N=3). For silkworm Bombyx mori (Li et al 2020), we compared diapause terminated (N=3) to diapause destined (N=3) eggs. For the termite Zootermopsis nevadensis nuttingi (Glastad et al 2016), we compared winged reproductive alates of both sexes (N=4) to larval instars (workers) of both sexes (N=4).…”

“…The Anthozoan studies contrasted polyp types in the coral Acropora millepora (Dixon and Matz 2020), pH treatments in the coral Stylophora pistillata (Liew et al 2018), and symbiotic state in the sea anemone Exaiptasia pallida . Hexapoda studies included different reproductive states in ants (Ooceraea biroi) (Libbrecht et al 2016), bumblebees (Bombus terrestris) (Marshall et al 2019), and termites (Zootermopsis nevadensis) (Glastad et al 2016), different subcastes in honeybee (Apis mellifera) (Herb et al 2012), differences in maternal care in carpenter bee (Arsenault et al 2018), and different diapause states in silkworm (Bombyx mori) (Li et al 2020). Using these diverse datasets, we rst con rm previous ndings that baseline gbM levels are bimodally distributed across coding genes, are positively associated with baseline transcription level, and are negatively associated with transcriptional differences between conditions.…”

Genome assembly and methylome analysis of the white wax scale insect provides insight into sexual differentiation of metamorphosis in hexapods

“…Overall, the role of DNA methylation in insects is not well understood, since its level can vary greatly among insects (Adam et al, 2016). DNA methylation has been linked to different functions and different developmental stages in a range of insects, such as the phase polyphenism in Locusta migratoria , the regulation of diapause in B. mori , or caste differentiation in A. mellifera (Kucharski et al, 2008; Li et al, 2020; Wang et al, 2013).…”