Fig. 2

Epigenetic reprogramming of PAX3 binding sites. a HiChIP normalized matrix from 6-day Pax3-induced cells displaying the Myf5 locus shows that the region characterizing increased contacts (triangle) undergoes changes in deposition of H3K4me1 and H3K27Ac marks over time. Scale: maxrange = 0.2. IGV snapshot displaying the ChIP-seq tracks for H3K27Ac, H3K27me3, H3K4me3, and H3K4me1 in non-induced, 1-day and 6-day induced iPax3 cells is shown below. Green boxes represent intergenic regions. Black arrow represents the transcription start site. b k-means clustering of H3K4me1, H3K4me3, H3K27me3, and H3K27Ac ChIP-seq data from 1-day Pax3-induced (+) and non-induced (−) EB cultures. Mapped data were used to generate a Density Tag Map centered on 3780 PAX3 peaks ±3 kb. Cluster 1: 960 peaks; Cluster 2: 566 peaks; Cluster 3: 136 peaks; Cluster 4: 2122 peaks. c Distribution of H3K4me1, H3K4me3, H3K27me3, and H3K27Ac ChIP-seq reads across the PAX3 peak center ±3 kb for clusters 1 and 4 shown in panel b. d–f IGV track displaying H3K4me1, H3K4me3, H3K27Ac, H3K27me3, and PAX3 genomic occupancy at representative PAX3-bound loci from clusters 1 (Gas1) and 4 (Adamts5) in 1-day Pax3-induced (+) and non-induced (−) EBs cultures. Dashed black squares indicate PAX3-bound loci. Green boxes represent intergenic regions. Black arrow represents the transcription start site. e–g Images of E11.5 transgenic embryos expressing LacZ under the control of VISTA elements overlapping to Pax3 peaks. mm745, adjacent to the Gas1 locus, is expressed in both somite and neural tube. hs1684, within Adamts5 gene, is expressed in the somite. Published images were downloaded from https://enhancer.lbl.gov