Journal
NUCLEIC ACIDS RESEARCH
Volume 48, Issue 12, Pages 6699-6714Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkaa457
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Funding
- Russian Science Foundation [18-14-00011]
- Skoltech Center of Life Sciences Systems Biology Fellowship Program
- Russian Science Foundation [18-14-00011] Funding Source: Russian Science Foundation
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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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