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

Proc Natl Acad Sci U S A. 2022 Jan 4;119(1):e2116222119. doi: 10.1073/pnas.2116222119.

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: CTCF; Polycomb; RNA–DNA interactome; cell nucleus; noncoding RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CCCTC-Binding Factor / metabolism*
  • Chromatin Immunoprecipitation
  • DNA-Binding Proteins / metabolism
  • Humans
  • Polycomb-Group Proteins / metabolism*
  • RNA, Untranslated / metabolism*

Substances

  • CCCTC-Binding Factor
  • DNA-Binding Proteins
  • Polycomb-Group Proteins
  • RNA, Untranslated