Simultaneous Capture of Chromatin-Associated RNA and Global RNA–RNA Interactions With Reduced Input Requirements

Chromatin-associated RNAs (caRNAs) have been increasingly recognized as key regulators of gene expression and genome architecture. A few technologies, such as ChRD-PET and RedChIP, have emerged to assess protein-mediated RNA–chromatin interactions, but each has limitations. Here, we describe the TaDRIM-seq (targeted DNA-associated RNA and RNA–RNA interaction mapping by sequencing) technique, which combines Protein G (PG)-Tn5-targeted DNA tagmentation with in situ proximity ligation to simultaneously profile caRNAs across genomic regions and capture global RNA–RNA interactions within intact nuclei. This approach reduces the required cell input, shortens the experimental duration compared to existing protocols, and is applicable to both mammalian and plant systems. Key features • A multi-omics sequencing strategy. • Compatible with mammalian and plant systems. • Profiling of epigenome, RNA–DNA, and RNA–RNA interactomes.