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


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.

SUBMITTER: Gavrilov AA 

PROVIDER: S-EPMC7337940 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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

Gavrilov Alexey A AA   Zharikova Anastasiya A AA   Galitsyna Aleksandra A AA   Luzhin Artem V AV   Rubanova Natalia M NM   Golov Arkadiy K AK   Petrova Nadezhda V NV   Logacheva Maria D MD   Kantidze Omar L OL   Ulianov Sergey V SV   Magnitov Mikhail D MD   Mironov Andrey A AA   Razin Sergey V SV  

Nucleic acids research 20200701 12


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  ...[more]

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