Genome-wide identification of stable RNA-chromatin interactions

RNA-chromatin interactions play crucial roles in gene regulation and genome organization, but the interaction landscape remains poorly understood. In this study, we conducted an in-depth analysis of a previously published dataset on RNase-treated in situ mapping of the RNA–genome interactome in human embryonic stem cells. This dataset globally profiles RNase-insensitive RNA-chromatin interactions. Our analysis revealed that RNase treatment selectively preserved long-range RNA-chromatin interactions while removing promiscuous interactions resulting from the local diffusion of nascent transcripts. RNase-insensitive chromatin-associated RNAs (RI-caRNAs) exhibited high sequence conservation and preferentially localized to functional genomic regions, including promoters, transcription factor binding sites, and regions with specific histone modifications. Interestingly, coding and non-coding RNA transcripts showed distinct sensitivities to RNase, with lncRNAs and disease-associated transcripts being enriched among RI-caRNAs. Furthermore, we identified specific caRNA classes associated with individual transcription factors and histone modifications. Altogether, our findings reveal a RNase-inaccessible regulatory RNA-chromatin interactome and provide a resource for understanding RNA-mediated chromatin regulation.