ArticlePLoS genetics2009
Non-coding RNA prediction and verification in Saccharomyces cerevisiae.
Article in PLoS genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 33 citations in OpenAlex.
- Functional analysis and transcriptional profiling of non-coding RNAs in yeast.The Biochemical journal · 2025Review
- In silico genome wide identification of long non-coding RNAs differentially expressed during Candida auris host pathogenesis.Archives of microbiology · 2024Article
- Discovery of 17 conserved structural RNAs in fungi.Nucleic acids research · 2021Article
- Large-scale profiling of noncoding RNA function in yeast.PLoS genetics · 2018Article
- RNAStructuromeDB: A genome-wide database for RNA structural inference.Scientific reports · 2017Article
- Mycoplasma non-coding RNA: identification of small RNAs and targets.BMC genomics · 2016Article
- Identification of novel noncoding transcripts in telomerase-negative yeast using RNA-seq.Scientific reports · 2016Article
- Probing-directed identification of novel structured RNAs.RNA biology · 2016Article
- Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm.Nucleic acids research · 2014Article
- Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system.Genetics · 2014Review
- The conserved chimeric transcript UPGRADE2 is associated with unreduced pollen formation and is exclusively found in apomictic Boechera species.Plant physiology · 2013Article
- Article
- A comparative genome-wide study of ncRNAs in trypanosomatids.BMC genomics · 2010Article
- Non-coding RNA detection methods combined to improve usability, reproducibility and precision.BMC bioinformatics · 2010Article
- Regulatory RNAs in brain function and disorders.Brain research · 2010Review
- Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns.Trends in microbiology · 2009Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-coding RNA (ncRNA) play an important and varied role in cellular function. A significant amount of research has been devoted to computational prediction of these genes from genomic sequence, but the ability to do so has remained elusive due to a lack of apparent genomic features. In this work, thermodynamic stability of ncRNA structural elements, as summarized in a Z-score, is used to predict ncRNA in the yeast Saccharomyces cerevisiae. This analysis was coupled with comparative genomics to search for ncRNA genes on chromosome six of S. cerevisiae and S. bayanus. Sets of positive and negative control genes were evaluated to determine the efficacy of thermodynamic stability for discriminating ncRNA from background sequence. The effect of window sizes and step sizes on the sensitivity of ncRNA identification was also explored. Non-coding RNA gene candidates, common to both S. cerevisiae and S. bayanus, were verified using northern blot analysis, rapid amplification of cDNA ends (RACE), and publicly available cDNA library data. Four ncRNA transcripts are well supported by experimental data (RUF10, RUF11, RUF12, RUF13), while one additional putative ncRNA transcript is well supported but the data are not entirely conclusive. Six candidates appear to be structural elements in 5' or 3' untranslated regions of annotated protein-coding genes. This work shows that thermodynamic stability, coupled with comparative genomics, can be used to predict ncRNA with significant structural elements.
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