Open AccessRedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins
Author(s) -
А. В. Гаврилов,
Rinat Sultanov,
Mikhail Magnitov,
Aleksandra A. Galitsyna,
Erdem Dashinimaev,
E Aiden,
Sergey V. Razin
Publication year - 2021
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.2116222119
Subject(s) - chromatin , ctcf , rna , biology , chia pet , non coding rna , computational biology , genetics , dna , polycomb group proteins , gene , microbiology and biotechnology , chromatin remodeling , gene expression , repressor , enhancer
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 ofcis - andtrans -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.