Fig. 2

ncRNAs are enriched on chromatin compared with protein coding transcripts. a Ratio of intronic over exonic reads obtained from different chromatin-RNA association sequencing technologies (MARGI, GRID, CPE, CAR, and PIRCh) versus input controls in multiple cell lines. b Normalized average read coverage around introns from different chromatin-RNA association sequencing technologies (MARGI, GRID, CPE, CAR, and PIRCh) versus input controls in multiple cell lines. c Normalized average read coverage around introns from histone modification-specific PIRCh-seq profiles (colored) and inputs (black) in mouse embryonic stem cells (mESCs). d Gene set enrichment analysis (GSEA) shows highly statistical enriched (FDR = 0, P < 0.0001) non-coding genes (green) and depleted coding genes (blue) on histone H3 in mESCs. Genes were ranked by their histone H3 PIRCh enrichment scores. e Average fold enrichment (calculated by limma in R) of the coding gene, lncRNA, pre-miRNA, snoRNA, and other ncRNAs from histone modification-specific PIRCh-seq profiles (namely H3, H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K9me3, and H4K16ac) in mESC. Error bar shows the standard deviation from the mean. f Average variation score of the PIRCh-seq signals for the coding versus non-coding genes (****P < 0.0001, two-tailed Welch’s T test). Error bar shows the standard deviation from the mean. g Heatmap displaying the ranking of the ChIP-seq enrichment of the chromatin binding sites of 23 lncRNA. The 23 lncRNAs are chromatin enriched from PIRCh-seq, and the chromatin binding sites are obtained from ChIRP/CHART/RAP/GRID-seq profiles from the LnChrom database. Colors represent ranking from 1 to 5. h Heatmap shows the ranking of PIRCh-seq enrichment of the same lncRNAs in g. Colors represent ranking from 1 to 5. i Bar plot of the Spearman correlation coefficients between the ranking in g and h for each lncRNA versus random permutation (****P < 0.0001, two-tailed Welch’s T test). j Unsupervised clustering of the Pearson correlation coefficients matrix of the histone modification-specific PIRCh-seq profiles based on the enrichment scores from the 258 chromatin-associated ncRNAs in mESC