Fig. 6

Isl1 recognizes its DNA binding motif on DNA wrapped around nucleosomes and its binding correlates with sites of open chromatin. a EMSA with increasing amount of recombinant Isl1 protein (0, 0.2, 0.4, 0.6, 0.8 and 1 µM) and free Ttn DNA fragment harbouring Isl1 binding sites (left panels) and the same fragment assembled into nucleosomes (right panels). b Competition assay showing the specificity of Isl1 binding to free and nucleosomal Ttn DNA using specific Isl1 binding oligo and nonspecific oligo as competitors at 80× molar ratio excess. S, specific competitor; NS, nonspecific competitor. c Overlap of all Isl1 ChIP-Seq and ATAC-Seq peaks (top; n = 2, each) or peaks at Transcription Start Sites (TSS)±10 kb in mESC-derived CPCs. Only high confidence peaks, found in two Isl1 ChIP-Seq and ATAC-Seq replicates, were used in the analysis. d Examples of genes bound by Isl1, showing open chromatin configuration at Isl1 binding sites in mESC-derived CPCs. Genome tracks of Isl1 ChIP-Seq and ATAC-Seq reads of mESC-derived CPCs. e Overlap of all Isl1 ChIP-Seq (n = 2), GATA4 ChIP-exo⁵ (n = 3) and ATAC-Seq peaks (n = 2) (top) or peaks at Transcription Start Sites (TSS)±10 kb in CPCs. f Heatmap (top) and aggregation plot (bottom) of mapped reads of Isl1 ChIP-Seq, GATA4 ChIP-exo and ATAC-Seq at  2 kb around peak midpoints of Isl1, GATA4 and ATAC (IGA); Isl1 and GATA4 (IG); Isl1 and ATAC (IA); GATA4 and ATAC (GA) occupancy groups