Epigenomic landscape of enhancer elements duringHydrahead organizer formation

Background Axis patterning during development is accompanied by large-scale gene expression changes. These are brought about by changes in the histone modifications leading to dynamic alterations in chromatin architecture. Thecisregulatory DNA elements also play an important role towards modulating gene expression in a context-dependent manner.Hydrabelongs to the phylum Cnidaria where the first asymmetry in the body plan was observed and the oral-aboral axis originated. Wnt signaling has been shown to determine the head organizer function in the basal metazoanHydra. Results To gain insights into the evolution ofcisregulatory elements and associated chromatin signatures, we ectopically activated the Wnt signaling pathway inHydraand monitored the genome-wide alterations in key histone modifications. Motif analysis of putative intergenic enhancer elements fromHydrarevealed the conservation of bilateriancisregulatory elements that play critical roles in development. Differentially regulated enhancer elements were identified upon ectopic activation of Wnt signaling and found to regulate many head organizer specific genes. Enhancer activity of many of the identifiedcisregulatory elements was confirmed by luciferase reporter assay. Quantitative chromatin immunoprecipitation analysis upon activation of Wnt signaling further confirmed the enrichment of H3K27ac on the enhancer elements ofHv_Wnt5a,Hv_Wnt11and head organizer genesHv_Bra1,CnGscandHv_Pitx1. Additionally, perturbation of the putative H3K27me3 eraser activity using a specific inhibitor affected the ectopic activation of Wnt signaling indicating the importance of the dynamic changes in the H3K27 modifications towards regulation of the genes involved in the head organizer activity. Conclusions The activation-associated histone marks H3K4me3, H3K27ac and H3K9ac mark chromatin in a similar manner as seen in bilaterians. We identified intergeniccisregulatory elements which harbor sites for key transcription factors involved in developmental processes. Differentially regulated enhancers exhibited motifs for many zinc-finger, T-box and ETS related TFs whose homologs have a head specific expression inHydraand could be a part of the pioneer TF network in the patterning of the head. The ability to differentially modify the H3K27 residue is critical for the patterning ofHydraaxis revealing a dynamic acetylation/methylation switch to regulate gene expression and chromatin architecture.