Differentially methylated obligatory epialleles modulate context-dependentLAMgene expression in the honeybeeApis mellifera

Abstract

Differential intragenic methylation in social insects has been hailed as a prime mover of environmentally driven organismal plasticity and even as evidence for genomic imprinting. However, very little experimental work has been done to test these ideas and to prove the validity of such claims. Here we analyze in detail differentially methylated obligatory epialleles of a conserved gene encoding lysosomal a-mannosidase (AmLAM) in the honeybee. We combined genotyping of progenies derived from colonies founded by single drone inseminated queens, ultra-deep allele-specific bisulfite DNA sequencing, and gene expression to reveal how sequence variants, DNA methylation, and transcription interrelate. We show that both methylated and non-methylated states of AmLAM follow Mendelian inheritance patterns and are strongly influenced by polymorphic changes in DNA. Increased methylation of a given allele correlates with higher levels of context-dependent AmLAM expression and appears to affect the transcription of an antisense long noncoding RNA. No evidence of allelic imbalance or imprinting involved in this process has been found. Our data suggest that by generating alternate methylation states that affect gene expression, sequence variants provide organisms with a high level of epigenetic flexibility that can be used to select appropriate responses in various contexts. This study represents the first effort to integrate DNA sequence variants, gene expression, and methylation in a social insect to advance our understanding of their relationships in the context of causality.

The caste- and sex-specific DNA methylome of the termite Zootermopsis nevadensis

“…S5). This suggests that DNA methylation’s association with gene expression level and variation may be driven, at least in part, by an interaction between DNA methylation and intragenic antisense transcription1030.…”

“…Indeed, knockdown of the putative mediator of de novo DNA methylation (DNMT3) was shown to have a direct impact on the production of castes in the honey bee7. DNA methylation has further been associated with alternative splicing differences between honey bee castes89, linked to modulation of context-dependent gene expression10, and found to display differences between castes in hymenopteran social insects1112.…”

A possible role of DNA methylation in functional divergence of a fast evolving duplicate gene encoding odorant binding protein 11 in the honeybee

“…Methylation density was calculated as the percentage of methylated CpG motifs found across the OBP11 amplicons [20,21].…”

“…two brains or four antennae equivalent to 2.5 mg total RNA from brain samples and 0.5 mg total RNA from purified antennal samples were used. To assess RNA quality, 1-2 ml of each RNA sample was denatured with formamide, containing 0.01% SybrGreen and evaluated by agarose gel electrophoresis (1.5% agarose; 20 V cm 21 ).…”

“…PhiX spike was added at 5% concentration as recommended by Illumina for low-diversity libraries [20,21].…”