DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera

Abstract

The recent, unexpected discovery of a functional DNA methylation system in the genome of the social bee Apis mellifera underscores the potential importance of DNA methylation in invertebrates. The extent of genomic DNA methylation and its role in A. mellifera remain unknown, however. Here we show that genes in A. mellifera can be divided into 2 distinct classes, one with low-CpG dinucleotide content and the other with high-CpG dinucleotide content. This dichotomy is explained by the gradual depletion of CpG dinucleotides, a well-known consequence of DNA methylation. The loss of CpG dinucleotides associated with DNA methylation also may explain the unusual mutational patterns seen in A. mellifera that lead to AT-rich regions of the genome. A detailed investigation of this dichotomy implicates DNA methylation in A. mellifera development. High-CpG genes, which are predicted to be hypomethylated in germlines, are enriched with functions associated with developmental processes, whereas low-CpG genes, predicted to be hypermethylated in germlines, are enriched with functions associated with basic biological processes. Furthermore, genes more highly expressed in one caste than another are overrepresented among high-CpG genes. Our results highlight the potential significance of epigenetic modifications, such as DNA methylation, in developmental processes in social insects. In particular, the pervasiveness of DNA methylation in the genome of A. mellifera provides fertile ground for future studies of phenotypic plasticity and genomic imprinting.

Fig. 1.

Contrasting patterns of DNA methylation in A. mellifera genes and those of other insects, as measured by CpG_O/E. The y-axis depicts the number of genes with the specific CpG_O/E values given on the x-axis. The distribution of CpG_O/E in D. melanogaster (A), A. gambiae (B), and T. castaneum genes (C) all show unimodal distribution, reflecting a relative lack of DNA methylation in these species. In contrast, the distribution of CpG_O/E in A. mellifera genes (D) is bimodal, likely demonstrating the effects of DNA methylation of CpG dinucleotides (see text). The arrows show the position of the 5 genes [GB16767 (CpG_O/E = 0.56), GB19399 (0.66), GB18099 (0.67), GB12504 (0.75), and XP_001121083 (0.71)] found to be methylated in a previous study (6). Note that we could not map the gene GB15223 using our experimental procedure.

Fig. 2.

Caste-specific genes tend to have high CpG_O/E. (A) Caste-specificity [measured as the absolute value of log₂(queen/worker) gene expression] is correlated with CpG_O/E (Spearman's rank correlation, r_s = 0.1405; P = 2.80e-09). Mean values of CpG_O/E for equal windows of caste specificity are shown as black dots with 95% confidence interval error bars. Ten outliers beyond caste-specificity values of 1.2 are excluded from the figure, but are included in calculations of correlation and model fitting. Points in the scatterplot are divided into caste-generic and caste-specific classes according to significant differences in expression between queens and workers (32). (B) The relationship between the values of log₂-gene expression ratios between castes and CpG_O/E values shows that the enrichment of high-CpG genes holds for genes that are either queen-specific or worker-specific. Genes expressed more highly in workers have log₂-ratios < 0, whereas those expressed more highly in queens have log₂-ratios > 0. The y-axis shows the mean and 95% confidence intervals of each group. As the log₂-expression ratios between castes become more extreme (either side of the x-axis), CpG_O/E tends to become more elevated.