ArticleNucleic acids research2019
Detection of RNA-DNA binding sites in long noncoding RNAs.
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 109 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
109 citing papers in PubMed, 186 citations in OpenAlex.
- Long non-coding RNA triplex-dependent regulation of melanoma gene networks.NAR genomics and bioinformatics · 2026Article
- RNA•DNA:DNA triplex formation byRNA (New York, N.Y.) · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- The role of positive feedback loop between LINC00862 and RBM47 in hepatocellular carcinoma suppression.Genes & diseases · 2026Article
- Relevance of DNA tridimensional shape in RNA:DNA:DNA triple helix formation.Computational and structural biotechnology journal · 2026Article
- Machine Learning Approaches for Predicting RNA-RNA/DNA Interactions.Methods in molecular biology (Clifton, N.J.) · 2026Review
- LncRNA:DNA Binding Prediction Using LongTarget and Its Revised Version.Methods in molecular biology (Clifton, N.J.) · 2026Article
- TripLexicon: prediction and analysis of gene regulatory RNA-DNA interactions.Bioinformatics (Oxford, England) · 2025Article
- Gain of Alternative Allele Expression of LINC02449 at rs149707223 in Schizophrenia and Bipolar Disorder: Inducing Synaptic Transmission and Behavioral Deficits in Mice.Nature communications · 2025Article
- The lincRNA Pantr1 is a FOXG1 target gene conferring site-specific chromatin binding of FOXG1.Nucleic acids research · 2025Article
- Lnc-RAINY regulates genes involved in radiation susceptibility through DNA:DNA:RNA triplex-forming interactions and has tumor therapeutic potential in lung cancers.Non-coding RNA research · 2025Article
- Transcription regulation by RNA-induced structural strain in duplex DNA.Nucleic acids research · 2025Article
- 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
- The Role of Long Non-Coding RNAs in Human Endoderm Differentiation.Non-coding RNA · 2025Review
- Three- and four-stranded nucleic acid structures and their ligands.RSC chemical biology · 2025Review
- LncRNANon-coding RNA · 2025Article
- 3plex Web: An interactive platform for RNA:DNA triplex prediction and analysis.Computational and structural biotechnology journal · 2025Article
- Easy triplex: An online tool for predicting the formation of DNA-RNA triple helices.Computational and structural biotechnology journal · 2025Article
- Peptidylprolyl isomerase A guides SENP5/GAU1 DNA-lncRNA triplex generation for driving tumorigenesis.Nature communications · 2024Article
49 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long non-coding RNAs (lncRNAs) can act as scaffolds that promote the interaction of proteins, RNA, and DNA. There is increasing evidence of sequence-specific interactions of lncRNAs with DNA via triple-helix (triplex) formation. This process allows lncRNAs to recruit protein complexes to specific genomic regions and regulate gene expression. Here we propose a computational method called Triplex Domain Finder (TDF) to detect triplexes and characterize DNA-binding domains and DNA targets statistically. Case studies showed that this approach can detect the known domains of lncRNAs Fendrr, HOTAIR and MEG3. Moreover, we validated a novel DNA-binding domain in MEG3 by a genome-wide sequencing method. We used TDF to perform a systematic analysis of the triplex-forming potential of lncRNAs relevant to human cardiac differentiation. We demonstrated that the lncRNA with the highest triplex-forming potential, GATA6-AS, forms triple helices in the promoter of genes relevant to cardiac development. Moreover, down-regulation of GATA6-AS impairs GATA6 expression and cardiac development. These data indicate the unique ability of our computational tool to identify novel triplex-forming lncRNAs and their target genes.
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Registered trials
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.