Fig. 3

PIRCh-seq classifies functional ncRNAs via chromatin state association. a Summary of histone modifications representing distinct regulatory patterns. b The enrichment of the 7sk ChIRP-seq peaks overlap with different histone modification ChIP-seq peaks in the same cell line (mESC). A positive value indicates the ChIRP-seq peaks are highly enriched with ChIP-seq peaks compared to random, and a negative value indicates depletion. c The PIRCh enrichment score of the lncRNA 7sk in mESC from distinct histone modification-specific PIRCh-seq experiments. A positive value means enriched, and a negative value means depleted. d Classification of the PIRCh-seq identified chromatin-associated ncRNAs (n = 258) in mESC. Scatter plot shows the t-SNE result on PIRCh-seq enrichment score matrix and annotated by K-means clustering. e Functional classification of histone-specific chromatin-RNA association patterns defined by chromHMM algorithm. f Box plot of the expression of the coding genes nearby (± 100 Kb) each group of PIRCh-clustered ncRNAs defined in d. Center lines represent mean values; box limits represent the interquartile range. The expression of the coding genes that are close to the ncRNAs in the “repressed” group is significantly lower than those in the “active promoter/enhancer” group (P < 0.05, two-tailed Welch’s T test). Genes close to un-enriched ncRNAs are shown as controls