Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee (ChIP-Seq).

Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we produce the first genome- wide maps of chromatin accessibility across all three adult honey bee phenotypes. We identify ~ 3000 regulatory regions in queen, ~ 4500 in worker and ~ 4000 in drone, with the vast majority of these sites located within intronic regions. Integrating ATAC-seq, RNA-seq and ChIP-seq data, we show a positive correlation between chromatin accessibility at introns, flanking H3K27ac modified nucleosomes and abundance of the respective mRNA transcript. Importantly, we find that these regulatory regions are enriched in transcription factor binding motifs and using ATAC-seq footprinting we identify queen, worker and drone - specific occupancy and uncover novel transcription factor networks. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications (H3K27me3, H3K27ac, H3K4me1, H3K4me3) in brains of newly-eclosed adult Q, W and D honey bees