Bumblebee Workers Show Differences in Allele-Specific DNA Methylation and Allele-Specific Expression

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.

Keywords: Hymenoptera; bumblebee; genomic imprinting.

Fig. 1.

Overview of the theoretical proportions of reads per SNP in a gene which does not show allele-specific expression. Each red dot is an individual SNP.

Fig. 2.

(a) Scatter plot showing the allele-specific expression proportion of sterile workers plotted against the allele-specific expression proportion of reproductive workers (the allele-specific expression proportion was averaged across colonies). Each point is a gene, the red points indicate genes showing significant allele-specific expression (q<0.05 and average allele-specific expression proportion >0.65). (b) An UpSet plot showing the number of genes with allele-specific expression shared by worker reproductive state and the number unique to reproductive or sterile workers (intersection size), indicated by a joint dot or single dot, respectively. The set size shows the total genes with allele-specific expression in either reproductive or sterile workers.

Fig. 3.

The average proportion of allele-specific expression for genes found to show significant allele-specific expression in only sterile or reproductive workers across colonies. The top row shows the genes with the highest allele-specific expression bias in reproductive workers compared with sterile workers. The bottom row shows the highest allele-specific expression bias in sterile workers compared with reproductive workers.

Fig. 4.

The average proportion of allelic expression for genes found to show the most extreme allele-specific expression in both sterile and reproductive workers across colonies.

Fig. 5.

(a) UpSet plot showing the number of genes with allele-specific methylation in just reproductive and sterile workers, as well as the number of genes in common between both reproductive states. (b) Component bar plot showing the number of regions with allele-specific methylation within genes, found in exons and introns and the number without additional annotation.

Fig. 6.

(a) UpSet plot showing the overlapping genes identified as having allele-specific methylation and/or allele-specific expression in both reproductive and sterile workers. AEG, allelically expressed gene; AMG, allelically methylated gene.

Fig. 7.

Boxplots showing the proportion of allele-specific expression in reproductive and sterile workers for genes identified with allele-specific methylation in: both reproductive states, just reproductive workers or just sterile workers. Each boxplot shows the median along with the 25th and 75th percentiles. The whiskers represent 1.5× the interquartile range. Outliers are represented as additional red points and each gene is represented by a black dot.