Fig. 4
Ldb1 recruitment at Pax3 sites is associated with enhanced chromatin remodeling and looping. a k-means clustering of ChIP-seq data for LDB1, SMC1, and CTCF in 1-day Pax3-induced (+) and non-induced (−) EBs. Density Tag Map centered on 3780 PAX3 peaks shows the recruitment of LDB1 upon Pax3 induction at a subset of loci (cluster 1), and reveals that PAX3-mediated LDB1 recruitment is independent from SMC1-CTCF complex. Cluster 1: 595 peaks; Cluster 2: 168 peaks; Cluster 3: 324 peaks; Cluster 4: 2693 peaks. b IGV track displaying PAX3, LDB1, SMC1, and CTCF genome occupancy at the Megf10 locus in 1-day Pax3-induced (+) and non-induced (−) EBs. Dashed black square indicate PAX3-mediated LDB1 recruitment. Green boxes represent intergenic regions. Black arrow represents the transcription start site. c Graph shows distribution of ChIP-seq reads for the selected marks at loci characterized by PAX3 + LDB1 recruitment (violet) and PAX3-only binding (green). Loci bound by both LDB1 and PAX3 display higher remodeling compared with PAX3-only bound sites. d HiChIP normalized matrix from 6-day Pax3-induced cells displaying the Megf10 locus demonstrates long-range interactions involving the 1-day bound PAX3 + LDB1 site (dashed black square from panel b). Position of PAX3 peaks, genes and chromosome coordinates are showed below the matrix. Scale: maxrange = 0.2. Arcs indicate looping interactions identified by FitHiChIP. e GREAT functional annotation of peaks characterized by PAX3-mediated LDB1 recruitment (cluster from Fig. 4a)
