Comprehensive analysis of RNA–chromatin, RNA–, and DNA–protein interactions

RNA–chromatin interactome data are considered to be one of the noisiest types of data in biology. This is due to protein-coding RNA contacts and nonspecific interactions between RNA and chromatin caused by protocol specifics. Therefore, finding regulatory interactions between certain transcripts and genome loci requires a wide range of filtering techniques to obtain significant results. Using data on pairwise interactions between these molecules, we propose a concept of triad interaction involving RNA, protein, and a DNA locus. The constructed triads show significantly less noise contacts and are more significant when compared to a background model for generating pairwise interactions. RNA–chromatin contacts data can be used to validate the proposed triad object as positive (Red-ChIP experiment) or negative (RADICL-seq NPM) controls. Our approach also filters RNA–chromatin contacts in chromatin regions associated with protein functions based on ChromHMM annotation.