Fig. 4

Cell type-specific chromatin association of ncRNAs. a Number of chromatin-enriched RNAs in mESC, MEF, and NPC. b Unsupervised clustering of the Pearson correlation coefficient matrix of the histone modification-specific PIRCh-seq profiles in mESC, MEF, and NPC, based on the enrichment scores from the 458 chromatin-associated ncRNAs in each cell type. c Ratio of the chromatin-enriched ncRNA under each chemical modification over the total number of enriched ncRNAs in mESC, MEF, and NPC. d Schematic illustration of how RNAs enriched on both the repressive and active chromatin (bi-chromatin enriched) and either the repressive or active chromatin (mono-chromatin enriched). e UCSC tracks of the normalized PIRCh-seq signal at the lncRNA uc008bcq.1 locus in mESC, MEF, and NPC. uc008bcq.1 is bi-chromatin enriched in mESC, but mono-chromatin enriched in MEF and NPC. f Number of ncRNAs that are bi-chromatin enriched or mono-chromatin enriched in mESC, MEF, and NPC (***P < 0.001, *P < 0.05, chi-square test)