Large-scale analysis of RNA-DNA interactions

We have performed large-scale analysis of RNADNA contacts in chromatin based on our own experimental data for K562 human cells and GRID-Seq. We have devised RNA-Seq controls and validated the resulting interactions with known chromatin-associated RNAs. We propose a pipeline for the analysis of RNA-DNA interactions, a noise correction procedure and clustering by the distance preference approach. We have compared the obtained interactomes with DNA-DNA contacts (Hi-C) for the same cell line and report the association of contacts with active compartment A and boundaries of topologically associating domains (TADs). We have detected a fraction of chromatin-enriched RNAs and report their chromatin properties. We also describe classes of RNAs by their contact preferences with DNA.