Fig. 1: Trans-acting lncRNAs are enriched with SWI/SNF at cell type-specific enhancers.

a Schematic representation of the Red-C, RedChIP and CUT&RUN experimental workflow. HUVEC underwent crosslinking, followed by bridging of DNA and RNA ends with an oligonucleotide-adapter. BRG1 was pulled down, followed by a biotin pulldown of the RNA-DNA-bridge adapter interactions. Red-C served as a control for the global RNA-DNA background. BRG1 CUT&RUN provided high-confidence BRG1 DNA binding sites. TSS (Transcription Start Site), seq (sequencing), pAG-Mnase (protein A and G Micrococcal Nuclease). b, c Quantitative assessment of unique RNAs (b) and DNAs (c) involved in the interactions identified by Red-C and BRG1 RedChIP. d Unique RNA-DNA interactions identified by Red-C and BRG1 RedChIP, and corresponding fold-change, in interaction frequency bins. e Comparison of the number of unique RNA-DNA interactions density across increasing interaction frequency bins. f Frequency of both Red-C and RedChIP RNA-DNA interactions within BRG1 CUT&RUN peaks. Box plots are defined as follows: “Red-C False” minima: 0.1791, maxima: 10.7481, center: 1.7913, lower bound (25^th percentile): 0.5374, upper bound (75^th percentile): 4.6575; “Red-C True” minima: 0.1791, maxima: 15.7638, center: 3.4036, lower bound (25^th percentile): 1.0748, upper bound (75^th percentile): 6.9862; “RedChIP False” minima: 0.0837, maxima: 13.2273, center: 1.0046, lower bound (25^th percentile): 0.0837, upper bound (75^th percentile): 5.3579; “RedChIP True” minima: 0.0837, maxima: 21.8502, center: 2.9301, lower bound (25^th percentile): 0.3349, upper bound (75^th percentile): 8.9577. Whiskers extend from lower bound to minima and from upper bound to maxima. A Wilcoxon signed-rank test was performed within each condition (n = 1, Red-C and RedChIP). g Classification of BRG1 CUT&RUN peaks based on the absence (None) or presence of trans-acting or cis-acting RNAs. h Enrichment of RNA classes (trans, cis, mixed or none) across different DNA elements (intergenic, intronic and promoter) bound by BRG1. i Absolute number of trans-acting RNA-DNA interaction sites within HUVEC-specific features (intergenic enhancers, intronic enhancers and promoters). j Heatmap of HUVEC-specific features where trans-acting RNAs bind, with the classification of each feature in different cell types. k Visualization of selected BRG1-associated lncRNAs (PVT1, MALAT1 and MIR100HG) from RedChIP and their proximity to BRG1 CUT&RUN peaks. The red window superimposed onto the BRG1 CUT&RUN trace represents a 5 kb RNA binding site from RedChIP. Source data are provided as a Source Data file.