ArticleNucleic acids research2016
Re-evaluation of G-quadruplex propensity with G4Hunter.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 371 papers, 1 of them a synthesis that pooled it.
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Who cites it
371 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops.Briefings in bioinformatics · 2022Pooled it
- DNM1L depletion leads to accelerated heteroplasmy shifting of m.10191C allele through ATG7-dependent pathways.Mitochondrion · 2026Article
- Repeat-length variation generates stable TTGGG-family G-quadruplex motifs in plant mitochondrial genomes.Planta · 2026Article
- Structural Basis and Conformational Switching of Capture-SELEX Aptamers for Designing Equol Sensors.ACS omega · 2026Article
- Dibenzoacridinium derivatives: a new class of G-quadruplex ligands with anti-HIV-1 properties.RSC medicinal chemistry · 2026Article
- Dual native G-quadruplex folding is associated with chromatin looping at the MYC locus.FEBS open bio · 2026Article
- Detangling knots: the intricate roles of G-quadruplexes in herpesvirus replication.Journal of virology · 2026Review
- Variation and selection at predicted G-quadruplexes across the human pangenome.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.Nucleic acids research · 2026Article
- Metabolic disease variants rewire gene regulation through disruption of DNA G-quadruplex structures.Genome biology · 2026Article
- The presence and impact of G-quadruplexes in plant chloroplast DNA.BMC plant biology · 2026Article
- QuaDB: A streamlined web tool for identifier-based rapid prediction of putative quadruplex sequences.Human genomics · 2026Article
- Strand-asymmetric G-runs and G4s downstream of TSS modulate tumor suppressor gene transcription.Oncogene · 2026Article
- Uncertainty-aware benchmarking reveals ambiguous transcripts in mRNA-lncRNA classification.bioRxiv : the preprint server for biology · 2026Article
- RPA hyperphosphorylation hinders the resolution of R-loops and G-quadruplex-associated R-loops during RAS-driven senescence.Nucleic acids research · 2026Article
- Illuminating Mitochondrial RNA G-Quadruplexes as Structural Brakes on RNA Granule Assembly and OXPHOS.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Systematic identification of variant-specific RNA structure-small molecule interactions exemplified by RNA G-quadruplexes.Nature communications · 2026Article
- Substitution Spectrum and Selection at G-quadruplexes in Great Ape Telomere-to-Telomere Genomes.Genome biology and evolution · 2026Article
- Integrative Analysis Reveals Conserved R-Loop Features in Mouse Embryonic Stem Cells.Epigenomes · 2026Article
- The UTRs of Leishmania donovani vary in length and are enriched in potential regulatory structures.PLoS pathogens · 2026Article
311 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Critical evidence for the biological relevance of G-quadruplexes (G4) has recently been obtained in seminal studies performed in a variety of organisms. Four-stranded G-quadruplex DNA structures are promising drug targets as these non-canonical structures appear to be involved in a number of key biological processes. Given the growing interest for G4, accurate tools to predict G-quadruplex propensity of a given DNA or RNA sequence are needed. Several algorithms such as Quadparser predict quadruplex forming propensity. However, a number of studies have established that sequences that are not detected by these tools do form G4 structures (false negatives) and that other sequences predicted to form G4 structures do not (false positives). Here we report development and testing of a radically different algorithm, G4Hunter that takes into account G-richness and G-skewness of a given sequence and gives a quadruplex propensity score as output. To validate this model, we tested it on a large dataset of 392 published sequences and experimentally evaluated quadruplex forming potential of 209 sequences using a combination of biophysical methods to assess quadruplex formation in vitro. We experimentally validated the G4Hunter algorithm on a short complete genome, that of the human mitochondria (16.6 kb), because of its relatively high GC content and GC skewness as well as the biological relevance of these quadruplexes near instability hotspots. We then applied the algorithm to genomes of a number of species, including humans, allowing us to conclude that the number of sequences capable of forming stable quadruplexes (at least in vitro) in the human genome is significantly higher, by a factor of 2-10, than previously thought.
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