Fig. 2: SWI/SNF preferentially binds trans-acting lncRNAs.

a Correlation between BRG1 iCLIP coverage and RNA-seq coverage, normalized to RNA length. Reads per kilobase million (RPKM). b Analysis of RNA classes based on normalized iCLIP coverage. Log₂(iCLIP coverage/RNA-seq coverage) values are plotted to compare RNA classes (lncRNAs, mRNAs, snoRNAs, snRNAs, and miRNAs). Reads per kilobase million (RPKM). Box plots are defined as follows: “miRNA” minima: -4.8725, maxima: 3.2751, center: -0.5896, lower bound (25th percentile): -1.8241, upper bound (75th percentile): 0.2226; “snRNA” minima: -4.4778, maxima: 3.1295, center: -0.4113, lower bound (25th percentile): -1.8856, upper bound (75th percentile): 0.4326; “Protein coding” minima: -3.9667, maxima: 4.2052, center: 0.1668, lower bound (25th percentile): −0.9103, upper bound (75th percentile): 1.1378; “snoRNA” minima: −4.9670, maxima: 6.9218, center: 0.2799, lower bound (25th percentile): −1.0903, upper bound (75th percentile): 2.1851; “lncRNA” minima: −2.5777, maxima: 5.2470, center: 1.5063, lower bound (25th percentile): 0.3676, upper bound (75th percentile): 2.3317. Whiskers extend from lower bound to minima and from upper bound to maxima. c Proportion of RNA classes enriched in BRG1 iCLIP (counts per million > 5). d Statistical analysis comparing the expected (based on relative basal expression) versus observed frequency of BRG1 binding sites within lncRNAs and mRNAs. Fisher’s exact test was performed within each condition, n = 4 technical replicates. e Stratification to identify the top bound lncRNAs. Initial screen for lncRNA presence in Red-C, BRG1 RedChIP, BRG1 iCLIP and RNA-seq. LncRNAs were then ranked compared to a mean scaled value for all lncRNAs for their degree of iCLIP coverage (RPKM), their expression level (RPKM), normalized enrichment score (iCLIP normalized to expression and RNA length) and number of iCLIP binding sites. f Scaled value plots for the top 16 lncRNA candidates based on selection criteria compared to the mean scaled value for all identified lncRNAs. g Comparative analysis of trans- and cis-acting lncRNAs identified in BRG1 RedChIP and iCLIP datasets. h Visualization of selected lncRNAs (PVT1 and LINC00607) and their BRG1 iCLIP strand-specific binding profiles. Called iCLIP binding sites are displayed. Reads per kilobase million (RPKM). Source data are provided as a Source Data file.