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Updated: Jan 31, 2026
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Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin
Published on: January 20, 2016
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Isolation and genome-wide characterization of cellular DNA:RNA triplex structures
Nevcin Sentürk Cetin1, Chao-Chung Kuo2, Teodora Ribarska1
1Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany.
Nucleic Acids Research
|January 4, 2019
Summary
Researchers developed a new method to map DNA:RNA triplexes genome-wide. This reveals that DNA:RNA triplexes are common and play a key role in RNA-mediated gene regulation.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- RNA can bind to DNA through Hoogsteen base pairing, forming DNA:RNA triplexes.
- These triplexes anchor RNA to specific DNA sequences, guiding regulatory factors to genomic sites.
Purpose of the Study:
- To develop a fast, cost-effective, genome-wide method for mapping DNA:RNA triplex interactions in cells.
- To investigate the prevalence and biological significance of DNA:RNA triplexes.
Main Methods:
- Established a novel method using protein-free nucleic acids isolated from chromatin.
- Employed high-throughput sequencing and computational analysis of DNA-associated RNA.
- Combined analysis of DNA-associated RNA and RNA-associated DNA.
Main Results:
- Identified a large set of RNAs originating from non-coding and coding loci, including super-enhancers and repeat elements.
- Successfully mapped genome-wide DNA:RNA triplex interactions.
- Confirmed the formation of genomic DNA:RNA triplex structures.
Conclusions:
- DNA:RNA triplex formation is a prevalent mechanism for RNA-mediated target-site recognition.
- These triplexes significantly impact biological functions, including gene regulation.
- The new method provides a powerful tool for studying RNA-DNA interactions in vivo.
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