ArticleNucleic acids research2019
Isolation and genome-wide characterization of cellular DNA:RNA triplex structures.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Long non-coding RNA triplex-dependent regulation of melanoma gene networks.NAR genomics and bioinformatics · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- The Chromaverse Is Colored by Triplexes Formed Through the Interactions of Noncoding RNAs with HNPRNPU, TP53, AGO, REL Proteins, Intrinsically-Disordered Regions, and Flipons.International journal of molecular sciences · 2026Article
- Functional Genomic Evidence for Candidate Small Viral RNA-Mediated Epigenetic Interference in SARS-CoV-1 and SARS-CoV-2.Computational and structural biotechnology journal · 2026Article
- The evolutionary entanglement of flipons with zinc fingers and retroelements has engendered a large family of Z-DNA and G-quadruplex binding proteins.Open biology · 2025Article
- Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.Cell genomics · 2025Article
- Defining the transcriptional routes controlling lncRNA NEAT1 expression: implications in cellular stress response, inflammation, and differentiation.Discover oncology · 2025Review
- Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates.International journal of molecular sciences · 2025Review
- Biomolecules Interacting with Long Noncoding RNAs.Biology · 2025Review
- Flipons enable genomes to learn by intermediating the exchange of energy for information.Journal of the Royal Society, Interface · 2025Review
- Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism.Nucleic acids research · 2025Article
- HSATII RNA-dependent triplex formation in early human embryogenesis as a potential mechanism for Y chromosome loss in Turner syndrome.Frontiers in molecular biosciences · 2025Article
- Peptidylprolyl isomerase A guides SENP5/GAU1 DNA-lncRNA triplex generation for driving tumorigenesis.Nature communications · 2024Article
- Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates.NAR genomics and bioinformatics · 2024Article
- EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter.Epigenetics & chromatin · 2023Article
- Noncoding RNA-chromatin association: Functions and mechanisms.Fundamental research · 2023Review
- Integrative modeling of lncRNA-chromatin interaction maps reveals diverse mechanisms of nuclear retention.BMC genomics · 2023Article
- The long non-coding RNA NEAT1 is a ΔNp63 target gene modulating epidermal differentiation.Nature communications · 2023Article
- Tumour mutations in long noncoding RNAs enhance cell fitness.Nature communications · 2023Article
- TRIPBASE: a database for identifying the human genomic DNA and lncRNA triplexes.NAR genomics and bioinformatics · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.