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Literature DB >> 12853629

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics.

Abstract

We screened for new structural non-coding RNAs (ncRNAs) in the genome sequence of the yeast Saccharomyces cerevisiae using computational comparative analysis of genome sequences from five related species of Saccharomyces. The screen identified 92 candidate ncRNA genes. Thirteen showed discrete transcripts when assayed by northern blot. Of these, eight appear to be novel ncRNAs ranging in size from 268 to 775 nt, including three new H/ACA box small nucleolar RNAs.

Entities: Gene Species

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Year: 2003 PMID： 12853629 PMCID： PMC165953 DOI： 10.1093/nar/gkg438

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

46 in total

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Authors: B E Jády; T Kiss
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2. Homologs of small nucleolar RNAs in Archaea.

Authors: A D Omer; T M Lowe; A G Russell; H Ebhardt; S R Eddy; P P Dennis
Journal: Science Date: 2000-04-21 Impact factor: 47.728

3. Identification of novel small RNAs using comparative genomics and microarrays.

Authors: K M Wassarman; F Repoila; C Rosenow; G Storz; S Gottesman
Journal: Genes Dev Date: 2001-07-01 Impact factor: 11.361

4. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse.

Authors: A Hüttenhofer; M Kiefmann; S Meier-Ewert; J O'Brien; H Lehrach; J P Bachellerie; J Brosius
Journal: EMBO J Date: 2001-06-01 Impact factor: 11.598

5. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

Authors: P F Cliften; L W Hillier; L Fulton; T Graves; T Miner; W R Gish; R H Waterston; M Johnston
Journal: Genome Res Date: 2001-07 Impact factor: 9.043

6. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli.

Authors: L Argaman; R Hershberg; J Vogel; G Bejerano; E G Wagner; H Margalit; S Altuvia
Journal: Curr Biol Date: 2001-06-26 Impact factor: 10.834

7. Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes.

Authors: A Malpertuy; F Tekaia; S Casarégola; M Aigle; F Artiguenave; G Blandin; M Bolotin-Fukuhara; E Bon; P Brottier; J de Montigny; P Durrens; C Gaillardin; A Lépingle; B Llorente; C Neuvéglise; O Ozier-Kalogeropoulos; S Potier; W Saurin; C Toffano-Nioche; M Wésolowski-Louvel; P Wincker; J Weissenbach; J Souciet; B Dujon
Journal: FEBS Lett Date: 2000-12-22 Impact factor: 4.124

8. Computational identification of noncoding RNAs in E. coli by comparative genomics.

Authors: E Rivas; R J Klein; T A Jones; S R Eddy
Journal: Curr Biol Date: 2001-09-04 Impact factor: 10.834

9. The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.

Authors: M Johnston; L Hillier; L Riles; K Albermann; B André; W Ansorge; V Benes; M Brückner; H Delius; E Dubois; A Düsterhöft; K D Entian; M Floeth; A Goffeau; U Hebling; K Heumann; D Heuss-Neitzel; H Hilbert; F Hilger; K Kleine; P Kötter; E J Louis; F Messenguy; H W Mewes; J D Hoheisel
Journal: Nature Date: 1997-05-29 Impact factor: 49.962

10. Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA.

Authors: D N Frank; C Adamidi; M A Ehringer; C Pitulle; N R Pace
Journal: RNA Date: 2000-12 Impact factor: 4.942

45 in total

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Authors: Alex Coventry; Daniel J Kleitman; Bonnie Berger
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2. Visualization of multiple genome annotations and alignments with the K-BROWSER.

Authors: Kushal Chakrabarti; Lior Pachter
Journal: Genome Res Date: 2004-04 Impact factor: 9.043

3. Fast and reliable prediction of noncoding RNAs.

Authors: Stefan Washietl; Ivo L Hofacker; Peter F Stadler
Journal: Proc Natl Acad Sci U S A Date: 2005-01-21 Impact factor: 11.205

4. Direct evolution of genetic robustness in microRNA.

Authors: Elhanan Borenstein; Eytan Ruppin
Journal: Proc Natl Acad Sci U S A Date: 2006-04-11 Impact factor: 11.205

5. Partition function and base pairing probabilities of RNA heterodimers.

Authors: Stephan H Bernhart; Hakim Tafer; Ulrike Mückstein; Christoph Flamm; Peter F Stadler; Ivo L Hofacker
Journal: Algorithms Mol Biol Date: 2006-03-16 Impact factor: 1.405

6. New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA.

Authors: Dorota Piekna-Przybylska; Wayne A Decatur; Maurille J Fournier
Journal: RNA Date: 2007-02-05 Impact factor: 4.942

7. Evolutionary patterns of non-coding RNAs.

Authors: Athanasius F Bompfünewerer; Christoph Flamm; Claudia Fried; Guido Fritzsch; Ivo L Hofacker; Jörg Lehmann; Kristin Missal; Axel Mosig; Bettina Müller; Sonja J Prohaska; Bärbel M R Stadler; Peter F Stadler; Andrea Tanzer; Stefan Washietl; Christina Witwer
Journal: Theory Biosci Date: 2005-04 Impact factor: 1.919

8. The small nucleolar ribonucleoprotein (snoRNP) database.

Authors: J Christopher Ellis; Daniel D Brown; James W Brown
Journal: RNA Date: 2010-03-02 Impact factor: 4.942

9. Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway.

Authors: Manoj Pratim Samanta; Waraporn Tongprasit; Himanshu Sethi; Chen-Shan Chin; Viktor Stolc
Journal: Proc Natl Acad Sci U S A Date: 2006-03-06 Impact factor: 11.205

Review 10. De novo prediction of structured RNAs from genomic sequences.

Authors: Jan Gorodkin; Ivo L Hofacker; Elfar Torarinsson; Zizhen Yao; Jakob H Havgaard; Walter L Ruzzo
Journal: Trends Biotechnol Date: 2009-11-26 Impact factor: 19.536