Fig. 5

RNAs with single strand are more likely to associate with chromatin. a UCSC track of the normalized input (black) and H3 (red) and H3K4me3 (green) PIRCh-seq signals of lncRNA Malat1 in mESC. Dash lines represent fold change of PIRCh-seq over input and smoothed by 500 bp sliding windows. The boxed region represents the most enriched domain on Malat1. Bottom peaks are chromatin-enriched sites on Malat1. b Structure profile from icSHAPE and structural prediction from RNAfold around a zoom in chromatin-associated peak on lncRNA Malat1. c Computational workflow to integrate RNA secondary structure information from icSHAPE and chromatin enrichment information from PIRCh-seq to study the structural preference of chromatin-RNA association. d Average diagram of icSHAPE scores around all PIRCh-seq peaks under different histone modifications (colored solid line) versus a randomly selected background (gray solid line). P values (colored dash line) were estimated by using two-tailed Welch’s T test on every position between PIRCh-seq profiles over background. e Box plot of the icSHAPE score of PIRCh-seq enriched vs depleted RNAs (***P < 0.001, two-tailed Welch’s T test). Center lines represent mean values; box limits represent the interquartile range; whiskers each extend 1.5 times the interquartile range; dots represent outliers. f Box plot of the PIRCh-seq enrichment scores of the top 100 most single-stranded RNAs versus the top 100 most double-stranded RNAs based on icSHAPE scores (**P < 0.01 two-tailed Welch’s T test). Center lines represent mean values; box limits represent the interquartile range; whiskers each extend 1.5 times the interquartile range; dots represent outliers. g Relative allele-specific RNA expression and chromatin enrichment of lncRNAs Xist, Gas5, and Malat1 in the 129S1 allele versus the CAST allele of NPC. The Y-axis represents the log2 fold change of the allelic signals in 129S1 over CAST. The 129S1 version of lncRNA Xist is highly expressed and also enriched at chromatin with H3K27me3 modification. Both alleles of lncRNA Malat1 were almost equally expressed and enriched. The 129S1 version of Gas5 was lowly expressed but highly enriched on chromatin compared to the CAST version of the same gene. h Normalized allele-specific input and histone H3K27me3 PIRCh-seq signals in the 129S1 and CAST alleles. Top shows single nucleotide polymorphisms (SNP) positions that distinguish the alleles