ArticleNucleic acids research2014
New scoring system to identify RNA G-quadruplex folding.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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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
68 citing papers in PubMed, 129 citations in OpenAlex.
- Systematic identification of variant-specific RNA structure-small molecule interactions exemplified by RNA G-quadruplexes.Nature communications · 2026Article
- In Search of the Most Significant Potential G-Quadruplexes in SARS-CoV-2 RNA: Genomic Analysis.Viruses · 2026Article
- G-quadruplexes in the proximity 3'-UTR enhances alternative polyadenylation of Neogenin 1.iScience · 2025Article
- G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data.Nature communications · 2025Article
- Synthetic G-quadruplex components for predictable, precise two-level control of mammalian recombinant protein expression.Nucleic acids research · 2025Article
- Perspectives on NcRNAs in HBV/cccDNA-driven HCC progression.Cancer cell international · 2025Review
- RNA G‑Quadruplex Reprogramming with Guanine-Rich Antisense Oligonucleotides Inhibits Monoamine Oxidase B's Translation.ACS bio & med chem Au · 2025Article
- A Dataset Curated for the Assessment of G4s in the LncRNAs Dysregulated in Various Human Cancers.Scientific data · 2025Article
- 5'-UTR G-Quadruplex-Mediated Translation Regulation in Eukaryotes: Current Understanding and Methodological Challenges.International journal of molecular sciences · 2025Review
- The G4 resolvase Dhx36 modulates cardiomyocyte differentiation and ventricular conduction system development.Nature communications · 2024Article
- Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements.Nucleic acids research · 2024Article
- Pathogenic SNPs Affect Both RNA and DNA G-Quadruplexes' Responses to Ligands.ACS chemical biology · 2024Article
- Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation.Genome research · 2024Article
- Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: ThebioRxiv : the preprint server for biology · 2024Article
- Prediction of DNA i-motifs via machine learning.Nucleic acids research · 2024Article
- Prediction of G4 formation in live cells with epigenetic data: a deep learning approach.NAR genomics and bioinformatics · 2023Article
- G-quadruplexes from non-coding RNAs.Journal of molecular medicine (Berlin, Germany) · 2023Review
- G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)International journal of molecular sciences · 2023Article
- GAIA: G-quadruplexes in alive creature database.Nucleic acids research · 2023Article
- Toward a Better Understanding of G4 Evolution in the 3 Living Kingdoms.Evolutionary bioinformatics online · 2023Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
G-quadruplexes (G4s) are non-canonical structures involved in many important cellular processes. To date, the prediction of potential G-quadruplex structures (PG4s) has been based almost exclusively on the sequence of interest agreeing with the algorithm Gx-N-1-7-Gx-N1-7-Gx-N1-7-Gx (where x ≥ 3 and N = A, U, G or C). However, many sequences agreeing with this algorithm do not form G4s and are considered false-positive predictions. Here we show the RNA PG4 candidate in the 3'-untranslated region (UTR) of the TTYH1 gene to be one such false positive. Specifically, G4 folding was observed to be inhibited by the presence of multiple-cytosine tracks, located in the candidate's genomic context, that adopted a Watson-Crick base-paired structure. Clearly, the neighbouring sequences of a PG4 may influence its folding. The secondary structure of 12 PG4 motifs along with either 15 or 50 nucleotides of their upstream and downstream genomic contexts were evaluated by in-line probing. Data permitted the development of a scoring system for the prediction of PG4s taking into account the effect of the neighbouring sequences. The accuracy of this scoring system was assessed by probing 14 other novel PG4 candidates retrieved in human 5'-UTRs. This new scoring system can be used, in combination with the standard algorithm, to better predict the folding of RNA G4s.
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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.