Fig. 1

Pax3-bound elements establish long-range interactions. a Schematic representation of Pax3-induced myogenesis during mouse ES cell differentiation. Pax3 is induced at day 3 of differentiation using a doxycycline-dependent system. Twenty-four hours post Pax3-induction (1-day), only Myf5 transcript is detectable. Myod and Myog are expressed in the later stages of myogenic commitment (transcripts are detectable following 3/4-day Pax3 induction). b IGV track displaying PAX3 binding at Myf5, Megf10, Met, and Prex1 loci in 1-day and 6-day Pax3-induced cells. Dashed black squares indicate PAX3-bound loci. Green boxes represent intergenic regions. Black arrow represents the transcription start site. c Functional annotation of PAX3 peaks from 1-day and 6-day Pax3-induced cells. d Number of long-range interactions (loops) detected by PAX3 HiChIP. e Long-range interactions at the Met, Myf5, and Prex1 loci in 1-day and 6-day Pax3-induced cultures. The contact maps were normalized for sequencing depth and visualized as ratio relative to the background (non-induced PAX3 HiChIP). Triangles indicate domains of long-range chromatin interactions involving PAX3-bound sites (position of PAX3 peaks, genes, and chromosome coordinates are showed below). Scale: maxrange = 0.2. Arcs indicate looping interactions identified by FitHiChIP