RedChIP: protocol to identify RNAs mediating protein interactions with chromatin

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 the 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.