The FANTOM consortium has long focused on decoding the regulation of mammalian genome, and notably unveiled its pervasive transcription into RNA, such as introns, antisense strands, repetitive elements and non-coding RNAs. While recent studies have uncovered that many of these RNAs associated with chromatin, the mechanisms and roles of these interactions remain to be comprehensively elucidated. We thus integrated multiple genome-wide technologies such as CAGE, CUT&Tag, ATAC-seq, Hi-C, Cap-trap full-length cDNA seq, and RADICL-seq across 16 human cell types to study the RNA–DNA interactome in a cell type specific context.
Our analyses show that chromatin associated RNAs (caRNAs) derived from both coding and non-coding loci, including newly identified transcripts, form a highly structured and dynamic network of interactions during cellular differentiation. These interactions are not random; caRNAs preferentially target regulatory elements and exhibit strong cell type specificity. Their enrichment at disease-relevant loci underscores the importance of RNA–DNA interactions in maintaining cellular identity and function.
A subset of caRNAs, identified as key breaking points in the RNA–DNA interaction networks, connect to numerous transcription start sites and appear to influence gene activity as either activators or repressors, suggesting a direct role in transcriptional control. In particular, many of these key caRNAs both colocalize and are predicted to interact with RNA binding protein and epigenetic factors at their target regulatory elements.
Functional enrichment analyses link these regulatory caRNAs to crucial biological processes such as cell cycle regulation in iPSCs, neuronal development in neurons, and immune functions in macrophages. Our findings thus shed light on a previously underappreciated layer of genome regulation mediated by caRNAs and provide a foundation for future studies on their roles in differentiation and disease.