Fig. 4

Determination of physiologically relevant enriched transcription factors in H3.3K27M and H3.3 wild-type cells. a, b Motifs identified using MEME–ChIP and number of times that motif occurred in the ATAC-seq peaks was determined using FIMO. Background was calculated by scrambling DNA sequence and inputting that sequence into FIMO. Threshold for significant fold enrichment was set to 2 (black dashed line). ***p value < 0.001 as described in MEME–ChIP output. c, d HINT–ATAC identified DNA binding footprints in ATAC-seq data made by transcription factors. Those that were statistically significant (p value < 0.05, black dashed line) and of interest from MEME–ChIP analysis are plotted for c parental and d wild-type. e HINT–ATAC line plots showing the differential footprints of transcription factors significantly differentially bound in XIII (HEY1) and XVII (Pax2), and f XIII-WT (LHX6 and FOSL1::JUN)