Journal
NUCLEIC ACIDS RESEARCH
Volume 47, Issue 5, Pages 2306-2321Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gky1305
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Funding
- DFG [GR475/22-2, SFB1036]
- CellNetworks (EcTop Survey 2014)
- Baden-Wurttemberg Stiftung
- Aachen Interdisciplinary Center for Clinical Research (IZKF)
- Excellence Initiative of the German federal and state governments
- Start program of the RWTH Aachen Medical Faculty
- German Cancer Research Center (DKFZ), Molecular Biology of the Cell II
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RNA can directly bind to purine-rich DNA via Hoogsteen base pairing, forming a DNA:RNA triple helical structure that anchors the RNA to specific sequences and allows guiding of transcription regulators to distinct genomic loci. To unravel the prevalence of DNA:RNA triplexes in living cells, we have established a fast and cost-effective method that allows genome-wide mapping of DNA:RNA triplex interactions. In contrast to previous approaches applied for the identification of chromatin-associated RNAs, this method uses protein-free nucleic acids isolated from chromatin. High-throughput sequencing and computational analysis of DNA-associated RNA revealed a large set of RNAs which originate from non-coding and coding loci, including super-enhancers and repeat elements. Combined analysis of DNA-associated RNA and RNA-associated DNA identified genomic DNA:RNA triplex structures. The results suggest that triplex formation is a general mechanism of RNA-mediated target-site recognition, which has major impact on biological functions.
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