Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

Alexey A. Gavrilov, Anastasiya A. Zharikova, Aleksandra A. Galitsyna, Artem V. Luzhin, Natalia M. Rubanova, Arkadiy K. Golov, Nadezhda V. Petrova, Maria D. Logacheva, Omar L. Kantidze, Sergey V. Ulianov, Mikhail D. Magnitov, Andrey A. Mironov, Sergey V. Razin

Research output: Contribution to journalArticlepeer-review

11 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)6699-6714
Number of pages16
JournalNucleic Acids Research
Volume48
Issue number12
DOIs
Publication statusPublished - 9 Jul 2020

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