Fig. 1

Dynamics of RARαa binding to chromatin during zebrafish embryonic development. (A) Heatmaps of the 8084 RARαa BSs obtained from ChIP-seq in 80% of epiboly, 5 somites and 24 hpf stages (n = 2 biological replicates per stage). Peaks were clustered using k-means clustering, obtaining six clusters, with three of them showing a clear dynamic behavior: cluster 4 (n = 672), or early BSs, cluster 5 (n = 2059) or intermediate BSs, and cluster 3 (n = 1764) or late BSs. Average profiles of clusters 4, 5 and 3 are shown on top. (B) Motif enrichment analysis of the early (top), intermediate (medium) and late (bottom) RARαa BSs. Five representative motifs of the top-10 were chosen. Motif logos are represented with their position in the top-10, the TF names, the enrichment p-values and the percentage of sites showing the motif. (C) Zebrafish wild-type expression terms enriched for the genes associated with dynamic RARαa BSs. The top-10 terms for each stage have been combined. (D) Genome tracks of RARαa ChIP-seq at the indicated developmental stages showing signal intensities in the dhrs3b locus. The Genes track represents ENSEMBL annotated genes.