ArticleBMC biology2007
Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions.
Article in BMC biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 34 citations in OpenAlex.
- Functional analysis and transcriptional profiling of non-coding RNAs in yeast.The Biochemical journal · 2025Review
- Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation.Nucleic acids research · 2022Article
- Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics.BMC genomics · 2017Article
- Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions.Nucleic acids research · 2017Article
- The impact of RNA structure on coding sequence evolution in both bacteria and eukaryotes.BMC evolutionary biology · 2014Article
- Identification and characterisation of non-coding small RNAs in the pathogenic filamentous fungus Trichophyton rubrum.BMC genomics · 2013Article
- Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae.Genome biology · 2013Article
- Sequence-structure relationships in yeast mRNAs.Nucleic acids research · 2012Article
- A comparative genome-wide study of ncRNAs in trypanosomatids.BMC genomics · 2010Article
- Noncoding RNA of glutamine synthetase I modulates antibiotic production in Streptomyces coelicolor A3(2).Journal of bacteriology · 2010Article
- High-resolution transcription atlas of the mitotic cell cycle in budding yeast.Genome biology · 2010Article
- Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays.Genome biology · 2010Article
- Identification and classification of ncRNA molecules using graph properties.Nucleic acids research · 2009Article
- Non-coding RNA annotation of the genome of Trichoplax adhaerens.Nucleic acids research · 2009Article
- Non-coding RNA prediction and verification in Saccharomyces cerevisiae.PLoS genetics · 2009Article
- Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping.Nature genetics · 2008Article
- Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis.Nucleic acids research · 2008Article
- Strategies for measuring evolutionary conservation of RNA secondary structures.BMC bioinformatics · 2008Article
- Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins.PloS one · 2008Article
- Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum.Genome research · 2008Article
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Authors and funding
5 authors at 4 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNon-coding RNAs (ncRNAs) are an emerging focus for both computational analysis and experimental research, resulting in a growing number of novel, non-protein coding transcripts with often unknown functions. Whole genome screens in higher eukaryotes, for example, provided evidence for a surprisingly large number of ncRNAs. To supplement these searches, we performed a computational analysis of seven yeast species and searched for new ncRNAs and RNA motifs.
resultsA comparative analysis of the genomes of seven yeast species yielded roughly 2800 genomic loci that showed the hallmarks of evolutionary conserved RNA secondary structures. A total of 74% of these regions overlapped with annotated non-coding or coding genes in yeast. Coding sequences that carry predicted structured RNA elements belong to a limited number of groups with common functions, suggesting that these RNA elements are involved in post-transcriptional regulation and/or cellular localization. About 700 conserved RNA structures were found outside annotated coding sequences and known ncRNA genes. Many of these predicted elements overlapped with UTR regions of particular classes of protein coding genes. In addition, a number of RNA elements overlapped with previously characterized antisense transcripts. Transcription of about 120 predicted elements located in promoter regions and other, previously un-annotated, intergenic regions was supported by tiling array experiments, ESTs, or SAGE data.
conclusionOur computational predictions strongly suggest that yeasts harbor a substantial pool of several hundred novel ncRNAs. In addition, we describe a large number of RNA structures in coding sequences and also within antisense transcripts that were previously characterized using tiling arrays.
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