Fig. 1: EWS-WT1 is associated with highly active distal regulatory sites in DSRCT tumors.

a Left: pie chart shows genomic locations of EWS-WT1 binding sites in the DSRCT cell line JN-DSRCT1. Two antibodies targeting the WT1 C-terminal region present in the fusion protein were used for the EWS-WT1 ChIP-seq profiling (WT1 ab1 and WT1 ab2). Consensus peaks were defined as those shared by both WT1 antibodies tested. Right: whole genome distribution of promoter, intragenic and intergenic regions in the human genome. b Left: Heatmaps of WT1, H3K4me1, H3K4me3, H3K27ac and H3K27me3 ChIP-seq signal densities in the DSRCT cell line JN-DSRCT1. Right: Heatmaps of H3K4me1 and H3K27ac in DSRCT primary tumors. 10-kb windows in each panel are centered on EWS-WT1 binding sites identified in the JN-DSRCT1 cell line as in Fig. 1a. c DNA Motif enrichment analysis at distal EWS-WT1 binding sites from the JN-DSRCT1 cell line as in Fig. 1a. The consensus WT1 motif CTCCC(A/C)C and the TCC repeat motif score first and third respectively. Associated transcription factors for the motifs were EGR1 and ZNF263 respectively. See also Supplementary Fig. S1D. p values were calculated based on the binomial test by the Homer software. d Boxplots show ChIP-seq signal intensity for H3K27ac and EWS-WT1 in JN-DSRCT1 cells at subsets of EWS-WT1 binding sites identified. Each category contains 5871 and 952 EWS-WT1 binding sites (n), respectively. H3K27ac (2 kb window) and EWS-WT1 (500 bp window). Median value is shown as a line within the boxplot, which spans from the 25th to 75th percentiles. p values were calculated using two-sided t tests. e Representative example of EWS-WT1 binding sites containing CTCCC clusters near the PDGFA locus, enriched in H3K27ac ChIP-seq signals in the JN-DSRCT1 cell line and DSRCT primary tumors. Regions of interest are highlighted in light gray. Each CTCCC motif detected at EWS-WT1 binding site is depicted as a box below.