RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

Nuclear noncoding RNAs are key regulators of gene expression and chromatin organization. Here we present RedChIP, a technique combining RNA-DNA proximity ligation and chromatin immunoprecipitation for identification of RNAs associated with genomic regions occupied by a protein of interest. We identify a spectrum of cis and trans acting lincRNAs enriched at Polycomb and CTCF binding sites, which may be involved in Polycomb mediated gene repression and chromatin looping. The RedChIP experimental procedure for mapping RNA-DNA interactome mediated by protein of interest is based on Red-C protocol with protein immunoprecipitation step followed by high-throughput sequencing of the chimeric RNA-DNA molecules. BioProject: PRJNA728474; SRA Study accession: SRP319077