Fig. 5
Myogenic differentiation and looping are impaired upon Ldb1 knockdown. a–c Ldb1 knockdown in iPax3 differentiating cells impairs myogenic differentiation. Western blot (a) shows reduced levels of eMYHC, MYOG, and LDB1 in differentiated cultures from 6-day Pax3-induced Ldb1-knockdown (shLdb1) and control (shSCR) ES cells. Similar results were obtained by immunostaining using eMYHC (b) and gene expression analysis of Pax3-regulated genes. Scale bar: 100 µm (c). Graph represents mean + s.e.m of n ≥ 3 independent biological replicates. Student’s t-test **p < 0.01, ***p < 0.001. d Knockdown of Ldb1 in iPax3 cells (collected upon 6-day Pax3 induction) impairs the deposition of H3K4me1 at PAX3 + LDB1 sites. Graph represents mean + s.e.m. of n = 3 independent biological replicates. Student’s t-test *p < 0.05, **p < 0.01, ***p < 0.001. e Ldb1 knockdown impairs chromatin looping at Pax3 sites. Graph shows the number of contacts detected at PAX3 + LDB1 sites. f Number of long-range interactions (loops) detected by Pax3 HiChIP in shSCR and shLdb1 cells. g HiChIP normalized matrix from shSCR and shLdb1 6-day Pax3-induced cells displaying the Dbx1 and Prex1 loci. The contact maps were normalized for sequencing depth and visualized as ratio relative to the background (HiChIP in non-induced cells). Black arrows indicate the loss in interaction frequency between two loci. Position of PAX3 peaks, genes, and chromosome coordinates are showed below the matrix. Scale: maxrange = 0.2. Arcs indicate looping interactions identified by FitHiChIP. Source data are provided as a Source Data file
