Robust DNA Methylation in the Clonal Raider Ant Brain

Abstract

SUMMARY Social insects are promising model systems for epigenetics due to their immense morphological and behavioral plasticity. Reports that DNA methylation differs between the queen and worker castes in social insects [1–4] have implied a role for DNA methylation in regulating division of labor. To better understand the function of DNA methylation in social insects, we performed whole-genome bisulfite sequencing on brains of the clonal raider ant Cerapachys biroi, whose colonies alternate between reproductive (queen-like) and brood care (workerlike) phases [5]. Many cytosines were methylated in all replicates (on average 29.5% of the methylated cytosines in a given replicate), indicating that a large proportion of the C. biroi brain methylome is robust. Robust DNA methylation occurred preferentially in exonic CpGs of highly and stably expressed genes involved in core functions. Our analyses did not detect any differences in DNA methylation between the queen-like and worker-like phases, suggesting that DNA methylation is not associated with changes in reproduction and behavior in C. biroi. Finally, many cytosines were methylated in one sample only, due to either biological or experimental variation. By applying the statistical methods used in previous studies [1–4, 6] to our data, we show that such sample-specific DNA methylation may underlie the previous findings of queen- and worker-specific methylation. We argue that there is currently no evidence that genome-wide variation in DNA methylation is associated with the queen and worker castes in social insects, and we call for a more careful interpretation of the available data.

Hemimetabolous genomes reveal molecular basis of termite eusociality

“…as recently shown 38,44 . In fact, DNA methylation appears to be important for the regulation of housekeeping genes because predicted methylated genes are related to general biological processes (further supported by lower CpG o/e within 1-to-1 orthologues than in non-conserved genes) 45 , while caste-specific genes are 'released' from this type of gene regulation.…”

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“…Nevertheless, a recent investigation of Nasonia revealed no direct evidence for parent-of-origin differentially methylated regions, which casts doubt on the DNA methylation-imprinting hypothesis in hymenopteran insects (Wang et al, 2016). DNA methylation has been implicated in developmental (Kucharski et al, 2008;Alvarado et al, 2015) and behavioral (Herb et al, 2012) variation in some hymenopterans (but see Libbrecht et al, 2016). Accordingly, we tested whether there were detectable differences in Dnmt expression in heads from adult S. invicta workers, gynes, and males.…”

Rapid adaptive responses to climate change in corals

“…These examples mostly implicate atypical genomic regions, for example, retrotransposons that affect the transcription of neighbouring genes 13,30 . Furthermore, the low levels of correlation found between the transcriptome and the methylome of several multicellular organisms 32,33 , combined with the lack of a CpG methylation system in some of the most widely studied model animals, including the fruit fly Drosophila and the roundworm Caenorhabditis 34,35 , weakens the case for its significance as a universal regulator of gene expression 15,36 , and hence a universal mediator of TGP. In corals, DNA methylation levels correlate strongly with gene function; broadly and uniformly expressed 'housekeeping' genes are strongly methylated, whereas genes responsible for inducible or cell-specific functions are weakly methylated 37,38 (Fig.…”