Abstract
Allele-specific expression is when one allele of a gene shows higher levels of expression compared with the other allele, in a diploid organism. Recent work has identified allele-specific expression in a number of Hymenopteran species. However, the molecular mechanism which drives this allelic expression bias remains unknown. In mammals, DNA methylation is often associated with genes which show allele-specific expression. DNA methylation systems have been described in species of Hymenoptera, providing a candidate mechanism. Using previously generated RNA-Seq and whole-genome bisulfite sequencing from reproductive and sterile bumblebee (Bombus terrestris) workers, we have identified genome-wide allele-specific expression and allele-specific DNA methylation. The majority of genes displaying allele-specific expression are common between reproductive and sterile workers and the proportion of allele-specific expression bias generally varies between genetically distinct colonies. We have also identified genome-wide allele-specific DNA methylation patterns in both reproductive and sterile workers, with reproductive workers showing significantly more genes with allele-specific methylation. Finally, there is no significant overlap between genes showing allele-specific expression and allele-specific methylation. These results indicate that cis-acting DNA methylation does not directly drive genome-wide allele-specific expression in this species.
Highlights
Allele-specific expression is when one allele of a gene shows higher levels of expression compared to the other allele, in a diploid organism
Using whole genome bisulfite sequencing and RNA-seq from reproductive and sterile B. terrestris workers from three independent colonies we have identified genome wide allele-specific expression and allele-specific methylation
The majority of genes displaying allele-specific expression are common between reproductive castes and the proportion of allele-specific expression generally varies between colonies
Summary
Allele-specific expression is when one allele of a gene shows higher levels of expression compared to the other allele, in a diploid organism. Recent research has identified parent-of-origin allele-specific expression in honeybees and bumblebees (Galbraith et al, 2016; Kocher et al, 2015; Marshall et al, 2020), with one study identifying greater paternal-allele (patrigene) expression bias in reproductive honeybee workers compared to sterile workers, as predicted by the kinship theory (Galbraith et al, 2016). Various studies have found an association between methylation and gene expression (Glastad et al, 2014; Bonasio et al, 2012; Patalano et al, 2015; Marshall et al, 2019), and alternative splicing (Lyko et al, 2010; Glastad et al, 2016) in social insects This is not uniform across all species, see Standage et al (2016). Another study did not find any relationship between allele-specific expression and methylation in a hybrid cross of two non-social wasp species, Nasonia vitripennis and Nasonia giraulti (Wang et al, 2016)
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