Brief Report: RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins |
| |
Authors: | Alexey A. Gavrilov Rinat I. Sultanov Mikhail D. Magnitov Aleksandra A. Galitsyna Erdem B. Dashinimaev Erez Lieberman Aiden Sergey V. Razin |
| |
Abstract: | Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However, neither of these techniques examines proteins involved in RNA–chromatin interactions. Here, we introduce RedChIP, a technique combining RNA–DNA proximity ligation and chromatin immunoprecipitation for identifying RNA–chromatin interactions mediated by a particular protein. Using antibodies against architectural protein CTCF and the EZH2 subunit of the Polycomb repressive complex 2, we identify a spectrum of cis- and trans-acting ncRNAs enriched at Polycomb- and CTCF-binding sites in human cells, which may be involved in Polycomb-mediated gene repression and CTCF-dependent chromatin looping. By providing a protein-centric view of RNA–DNA interactions, RedChIP represents an important tool for studies of nuclear ncRNAs. |
| |
Keywords: | noncoding RNA, cell nucleus, RNA– DNA interactome, CTCF, Polycomb |
|
|