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Fig. 3 | Epigenetics & Chromatin

Fig. 3

From: Epigenomic landscape of enhancer elements during Hydra head organizer formation

Fig. 3

Dynamic regulation of enhancer-like elements during axis patterning in Hydra. a The occupancy of the H3K27ac, H3K4me3 and H3K9ac on the enriched peak regions identified by activation of Wnt signaling using Alsterpaullone (ALP). Four k-means clusters were obtained based on the combinatorial presence of the three modifications. The average profile of the modifications is depicted below the heatmap of each modification with the colors denoting different clusters. b Distribution of Gene ontology (GO) terms for transcription factors (GO:0003700, GO:0043565) and Wnt signaling pathway members (GO:0016055) for the nearest neighbour genes of the intergenic regions across the four clusters. c Comparison of head specific genes identified by performing differential gene expression analysis using RNA-Seq from head and foot regions (SRR6815024-29) with the nearest neighbour genes of the intergenic regions from clusters 1 & 2 (cluster1_2) and clusters 3 & 4 (cluster3_4). d The 774 head specific genes which exhibit enriched H3K27ac mark upon ALP treatment were subjected to network analysis using STRING [38]. Cluster analysis of the network generated showed a large cluster enriched with Wnt signaling pathway members. e The transcription factor binding motifs/sites (TFBS) that show central enrichment in the intergenic H3K27ac peak regions of the 774 genes (intersection of head specific and cluster3_4 genes). The logos of motifs for the TFBS are shown in the first column and the total number of sites identified by DREME (black font) or FIMO (red font) are shown in the second column. The third column shows the transcription factors identified by TOMTOM. f Integrative Genomics Viewer (IGV) [39] track plots depict differential occupancy of H3K27ac and H3K4me3 upon ALP treatment on the gene body and upstream regulatory regions of Hv_Bra1 which plays a role in head patterning in Hydra. The regions showing enriched H3K27ac peaks are depicted in grey in the last track

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