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

• DOI: 10.1073/pnas.2116222119
• Publication Date: 2021-12-30T22:11:30Z
• Authors: Alexey A. Gavrilov; Rinat I. Sultanov; Mikhail D. Magnitov; Aleksandra A. Gal...; Erdem B. Dashinimaev; Erez Lieberman Aiden; Sergey V. Razin
• Keywords: CTCF; ChIA-PET; Polycomb-group proteins

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 genome-wide spectrum contacts with chromatin. To address this question, a panel RNA-DNA proximity ligation techniques has been developed. However, neither these examines proteins involved RNA-chromatin interactions. Here, we introduce RedChIP, technique combining immunoprecipitation for identifying interactions mediated by particular protein. Using antibodies against architectural protein CTCF EZH2 subunit Polycomb repressive complex 2, cis- trans-acting enriched at Polycomb- CTCF-binding sites human cells, which may be Polycomb-mediated repression CTCF-dependent looping. By providing protein-centric view interactions, RedChIP represents an important tool studies ncRNAs.