Genome-wide analysis of bivalent histone modifications during Drosophila embryogenesis

In eukaryotes, histone modifications are key epigenetic regulators that are associated with distinct chromatin features. Bivalent histone modifications describe a situation where a subset of promoters have with both activating (H3K4me3) and repressive (H3K27me3) markers in pluripotent cells (e.g., ESCs). However, it remains to be understood whether bivalent histone modifications are stable throughout developmental stages. Here, by systematically analyzing ChIP-seq data of H3K4me3 and H3K27me3, we provided the first panoramic view of bivalent histone modifications in Drosophila from embryonic 0–4 to 20–24 hr. In our study, we found that bivalent histone modifications occur at other locations in the genome in addition to the promoter region. Additionally, the different genomic regions occupied by bivalent histone modifications exhibit spatiotemporal specificity at each stage. Furthermore, gene ontology and motif analysis reflected continuous and gradual changes of target genes during different developmental process. In summary, we suggest that bivalent histone modifications have potential regulatory functions throughout Drosophila embryonic stage.