Fig. 2
From: A genome-wide assessment of the ancestral neural crest gene regulatory network
Profiling of chromatin dynamics in the developing NC. a Schematics indicating the region of DNT or head dissected from T20, T21 and T23 lamprey embryos for ATAC-seq and the number of biologically independent samples analysed. b Genomic functional annotation of our ATAC-seq peaksets for all stages. c Mean ATAC-seq read coverage map at each stage over our consensus promoter peakset (i.e. peaks associated with T21 enriched genes), showing higher read coverage at T21. d Heatmaps depicting k-means linear enrichment clustering of ATAC-seq reads at all stages across consensus intergenic and intronic peaksets. Boxes indicated the large “EMT” clusters that show enriched signal at T21 and T23. e Violin plots visualising the distribution of mean normalised T21 read counts for genes associated with k-means clusters. Gene expression associated with promoter peak clusters (annotated and novel promoters) is higher and less variable than that for genes associated with intergenic and intronic clusters. f Mean ATAC-seq read coverage maps at each stage for “EMT” clusters (intergenic cluster 5 in blue; intronic cluster 4 in red), showing higher coverage at T21 and T23. g, h, j TF-binding motif enrichment analysis for intergenic (g), intronic (h) and promoter (annotated and novel) (j), k-means clusters. NC master regulator motifs are highlighted in red. Similar motifs shared between intergenic and intronic cluster 1 and promoter clusters are highlighted in orange. Canonical promoter motifs are highlighted in brown. i TFs that were significantly enriched in pair-wise in silico co-binding analyses conducted on intergenic k-means cluster 5. cl, cluster; Pc, peak centre
