PMC

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 (). Note that we could not map the gene GB15223 using our experimental procedure.

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 (). (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.