Fig. 7.

Prdm1a directly binds to and regulates limb genes. (A) Lateral view of EGFP-positive pectoral fins from the Tg(Mmu:Prx1-EGFP) zebrafish line at 24 hpf before CUT&RUN was performed. Scale bar: 200 µm. (B,C) Coverage heatmaps of (B) H3K27Ac and (C) Prdm1a binding across the genome 1.5 kb upstream and downstream of the peak center. (D) Annotation of enriched binding sites by Prdm1a. (E) Enriched Prdm1a peaks were subjected to Gene Ontology (GO) terms analysis using ChIPseeker's enrichGO function. (F) Prdm1a peaks were subjected to motif analysis using HOMER. The top ten motifs as well as known limb-related motifs are shown along with q-values. (G) Tracks showing H3K27Ac enrichment (open chromatin) and Prdm1a-binding sites for fgfr1a, dlx5a, dlx6a and smo. There is variability between replicates, but the overall trends are comparable (see Fig. S5). e, eye; pf, pectoral fin; TF, transcription factor; y, yolk.