Fig. 5

TEAD and NFI motifs are enriched in YAP1-bound cis-regulatory elements in ST-EPN-YAP1s. a Ranked group-specific enhancers that overlap with group-specific YAP1 peaks. Selected genes with highest correlation in respective topology-associated domains of enhancers are indicated. Right side from dashed line represents super-enhancers. b YAP1 and H3K27ac ChIP-Seq data across human primary ST-EPN-YAP1 and ST-EPN-RELA tumor samples (n = 3 for each entity) in the NDEL1 locus. YAP1-binding regions and H3K27Ac-marked enhancer regions of ST-EPN-YAP1 and ST-EPN-RELA colored cyan and red, respectively. TEAD and NFI motifs are shown by black bars. c Box plot of NDEL1 gene expression level across molecular groups of human ependymal tumors. The center line, box limits, whiskers, and points indicate the median, upper/lower quartiles, 1.5× interquartile range and outliers respectively. d Gene ontology (GO) analysis of 129 genes that showed highest correlation within topology-associated domains in ST-EPN-YAP1-specific enhancers that overlap with ST-EPN-YAP1-specific YAP1 peaks. Darker color intensity reflects a smaller p-value of GO term enrichment, while the bubble size reflects the term frequency. e Top five transcriptional factor-binding motifs enriched within YAP1 peaks specific to ST-EPN-YAP1 tumors. The enrichment p-values are computed by HOMER tool using binomial test. f, g Transcription factor motif enrichment in group-specific YAP1 peaks overlapping with group-specific enhancers/super-enhancers in human ST-EPN-YAP1 f or ST-EPN-RELA g tumors. Colored lines indicate location of TEAD1–4-binding motifs