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.
Highlights
Non-coding RNAs 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
A plausible working hypothesis is that most of these sequences are non-coding RNAs similar to mRNA-like ncRNAs [5,6] that were erroneously annotated as protein coding genes
A large number of structured RNAs in the yeast genome We screened the genomes of the seven yeast species S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzeii, S. bayanus, S. castelli and S. kluyveri for structured RNAs
Summary
Non-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. The genomic structure of yeast is much simpler than the genomic organization of multicellular species. The genome is densely packed with known genes, leaving only short intergenic sequences with a typical size of 300–600 bases [2]. Several of them emphasize non-protein coding RNA molecules: the data in Steigele and Nieselt [3] showed an unexpected complexity of antisense transcripts, that could potentially bypass or supplement classical gene regulation. A plausible working hypothesis is that most of these sequences are non-coding RNAs (ncRNAs) similar to mRNA-like ncRNAs [5,6] that were erroneously annotated as protein coding genes
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