A Comparison of Digital Gene Expression Profiling and Methyl DNA Immunoprecipitation as Methods for Gene Discovery in Honeybee (Apis mellifera) Behavioral Genomic Analyses
The honey bee has a well-organized system of division of labor among workers. Workers typically progress through a series of discrete behavioral castes as they age, and this has become an important case study for exploring how dynamic changes in gene expression can influence behavior. Here we applied both digital gene expression analysis and methyl DNA immunoprecipitation analysis to nurse, forager and reverted nurse bees (nurses that have returned to the nursing state after a period spent foraging) from the same colony in order to compare the outcomes of these different forms of genomic analysis. A total of 874 and 710 significantly differentially expressed genes were identified in forager/nurse and reverted nurse/forager comparisons respectively. Of these, 229 genes exhibited reversed directions of gene expression differences between the forager/nurse and reverted nurse/forager comparisons. Using methyl-DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) we identified 366 and 442 significantly differentially methylated genes in forager/nurse and reverted nurse/forager comparisons respectively. Of these, 165 genes were identified as differentially methylated in both comparisons. However, very few genes were identified as both differentially expressed and differentially methylated in our comparisons of nurses and foragers. These findings confirm that changes in both gene expression and DNA methylation are involved in the nurse and forager behavioral castes, but the different analytical methods reveal quite distinct sets of candidate genes.