ArticleGenome research2012
Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
128 citing papers in PubMed, 1 synthesis or guideline pooled it, 246 citations in OpenAlex.
- Antisense Versus Antigene in the Computer-Aided Design of Triplex-Forming Oligonucleotides (TFO): Insights from a Dual-Method Review, Combining Bibliometric and Systematic Review.International journal of molecular sciences · 2025Pooled it
- HSeeker: an algorithm for systematic H-DNA sequence identification.bioRxiv : the preprint server for biology · 2026Article
- RNA•DNA:DNA triplex formation byRNA (New York, N.Y.) · 2026Article
- Multiomic single-cell perturbation screens reveal critical lncRNA regulators of senescence.Nature aging · 2026Article
- Thermodynamic and kinetic considerations in DNA triplex formation revealed by ITC.European biophysics journal : EBJ · 2026Article
- Epigenetic-Genetic Coupling and Understanding the Molecular and Cellular Basis of Lamarckian Inheritance.International journal of molecular sciences · 2026Review
- Non-B DNA structures and their contributions to genetic diversity, aging, and disease.Nucleic acids research · 2026Review
- Decoding RNA triple helices: identification from sequence and secondary structure.Briefings in bioinformatics · 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
- 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
- How DNA secondary structures drive replication fork instability.DNA repair · 2025Review
- Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.Cell genomics · 2025Article
- Take the bull by the horns: A computational framework to predict lncRNA function.Cell genomics · 2025Article
- Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs.Genome 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
- Three- and four-stranded nucleic acid structures and their ligands.RSC chemical biology · 2025Review
68 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
4 authors at 3 institutions in 1 country.
Funding
Abstract
Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand in its major groove. This sequence-specific process offers a potent mechanism for targeting genomic loci of interest that is of great value for biotechnological and gene-therapeutic applications. It is likely that nature has leveraged this addressing system for gene regulation, because computational studies have uncovered an abundance of putative triplex target sites in various genomes, with enrichment particularly in gene promoters. However, to draw a more complete picture of the in vivo role of triplexes, not only the putative targets but also the sequences acting as the third strand and their capability to pair with the predicted target sites need to be studied. Here we present Triplexator, the first computational framework that integrates all aspects of triplex formation, and showcase its potential by discussing research examples for which the different aspects of triplex formation are important. We find that chromatin-associated RNAs have a significantly higher fraction of sequence features able to form triplexes than expected at random, suggesting their involvement in gene regulation. We furthermore identify hundreds of human genes that contain sequence features in their promoter predicted to be able to form a triplex with a target within the same promoter, suggesting the involvement of triplexes in feedback-based gene regulation. With focus on biotechnological applications, we screen mammalian genomes for high-affinity triplex target sites that can be used to target genomic loci specifically and find that triplex formation offers a resolution of ~1300 nt.
Indexed as
Identifiers
What OpenQuestion holds
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.