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Updated: Dec 20, 2025

CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells
Published on: May 25, 2018
Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals
Alexey A Gavrilov1,2, Anastasiya A Zharikova1,3,4,5, Aleksandra A Galitsyna1,3,4,6
1Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
Abstract:
Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA-DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA-DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.
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