Literature DB >> 12566404

Systematic discovery of new genes in the Saccharomyces cerevisiae genome.

Marco M Kessler1, Qiandong Zeng, Sarah Hogan, Robin Cook, Arturo J Morales, Guillaume Cottarel.   

Abstract

We used genome-wide comparative analysis of predicted protein sequences to identify many novel small genes, named smORFs for small open reading frames, within the budding yeast genome. Further analysis of 117 of these new genes showed that 84 are transcribed. We extended our analysis of one smORF conserved from yeast to human. This investigation provides an updated and comprehensive annotation of the yeast genome, validates additional concepts in the study of genomes in silico, and increases the expected numbers of coding sequences in a genome with the corresponding impact on future functional genomics and proteomics studies.

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Year:  2003        PMID： 12566404      PMCID： PMC420365          DOI： 10.1101/gr.232903

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  24 in total

1.  Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae.

Authors:  J D Hughes; P W Estep; S Tavazoie; G M Church
Journal:  J Mol Biol       Date:  2000-03-10       Impact factor: 5.469

2.  Characterization of the yeast transcriptome.

Authors:  V E Velculescu; L Zhang; W Zhou; J Vogelstein; M A Basrai; D E Bassett; P Hieter; B Vogelstein; K W Kinzler
Journal:  Cell       Date:  1997-01-24       Impact factor: 41.582

3.  Multicellular ascomycetous fungal genomes contain more than 8000 genes.

Authors:  D M Kupfer; C A Reece; S W Clifton; B A Roe; R A Prade
Journal:  Fungal Genet Biol       Date:  1997-06       Impact factor: 3.495

4.  Large-scale analysis of the yeast genome by transposon tagging and gene disruption.

Authors:  P Ross-Macdonald; P S Coelho; T Roemer; S Agarwal; A Kumar; R Jansen; K H Cheung; A Sheehan; D Symoniatis; L Umansky; M Heidtman; F K Nelson; H Iwasaki; K Hager; M Gerstein; P Miller; G S Roeder; M Snyder
Journal:  Nature       Date:  1999-11-25       Impact factor: 49.962

5.  NORF5/HUG1 is a component of the MEC1-mediated checkpoint response to DNA damage and replication arrest in Saccharomyces cerevisiae.

Authors:  M A Basrai; V E Velculescu; K W Kinzler; P Hieter
Journal:  Mol Cell Biol       Date:  1999-10       Impact factor: 4.272

6.  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

7.  Overview of the yeast genome.

Authors:  H W Mewes; K Albermann; M Bähr; D Frishman; A Gleissner; J Hani; K Heumann; K Kleine; A Maierl; S G Oliver; F Pfeiffer; A Zollner
Journal:  Nature       Date:  1997-05-29       Impact factor: 49.962

8.  Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs.

Authors:  W M Olivas; D Muhlrad; R Parker
Journal:  Nucleic Acids Res       Date:  1997-11-15       Impact factor: 16.971

Review 9.  Life with 6000 genes.

Authors:  A Goffeau; B G Barrell; H Bussey; R W Davis; B Dujon; H Feldmann; F Galibert; J D Hoheisel; C Jacq; M Johnston; E J Louis; H W Mewes; Y Murakami; P Philippsen; H Tettelin; S G Oliver
Journal:  Science       Date:  1996-10-25       Impact factor: 47.728

10.  The genetic control of direct-repeat recombination in Saccharomyces: the effect of rad52 and rad1 on mitotic recombination at GAL10, a transcriptionally regulated gene.

Authors:  B J Thomas; R Rothstein
Journal:  Genetics       Date:  1989-12       Impact factor: 4.562
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  25 in total

Review 1.  Comparative genomics: methods and applications.

Authors:  Bernhard Haubold; Thomas Wiehe
Journal:  Naturwissenschaften       Date:  2004-06-25

2.  Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation.

Authors:  Vanina Castelli; Jean-Marc Aury; Olivier Jaillon; Patrick Wincker; Christian Clepet; Manuella Menard; Corinne Cruaud; Francis Quétier; Claude Scarpelli; Vincent Schächter; Gary Temple; Michel Caboche; Jean Weissenbach; Marcel Salanoubat
Journal:  Genome Res       Date:  2004-03       Impact factor: 9.043

3.  Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection.

Authors:  Betina M Porcel; Olivier Delfour; Vanina Castelli; Veronique De Berardinis; Lucie Friedlander; Corinne Cruaud; Abel Ureta-Vidal; Claude Scarpelli; Patrick Wincker; Vincent Schächter; William Saurin; Gabor Gyapay; Marcel Salanoubat; Jean Weissenbach
Journal:  Genome Res       Date:  2004-02-12       Impact factor: 9.043

4.  Ecm1 is a new pre-ribosomal factor involved in pre-60S particle export.

Authors:  Yanhua Yao; Emilie Demoinet; Cosmin Saveanu; Pascal Lenormand; Alain Jacquier; Micheline Fromont-Racine
Journal:  RNA       Date:  2010-03-26       Impact factor: 4.942

5.  Biochemical and genetic analysis of the yeast proteome with a movable ORF collection.

Authors:  Daniel M Gelperin; Michael A White; Martha L Wilkinson; Yoshiko Kon; Li A Kung; Kevin J Wise; Nelson Lopez-Hoyo; Lixia Jiang; Stacy Piccirillo; Haiyuan Yu; Mark Gerstein; Mark E Dumont; Eric M Phizicky; Michael Snyder; Elizabeth J Grayhack
Journal:  Genes Dev       Date:  2005-12-01       Impact factor: 11.361

6.  Classification and function of small open reading frames.

Authors:  Juan-Pablo Couso; Pedro Patraquim
Journal:  Nat Rev Mol Cell Biol       Date:  2017-07-12       Impact factor: 94.444

7.  Hundreds of putatively functional small open reading frames in Drosophila.

Authors:  Emmanuel Ladoukakis; Vini Pereira; Emile G Magny; Adam Eyre-Walker; Juan Pablo Couso
Journal:  Genome Biol       Date:  2011-11-25       Impact factor: 13.583

8.  Strategies and Challenges in Identifying Function for Thousands of sORF-Encoded Peptides in Meiosis.

Authors:  Ina Hollerer; Andrea Higdon; Gloria A Brar
Journal:  Proteomics       Date:  2017-10-26       Impact factor: 3.984

9.  Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

Authors:  Albert Lee; Kasper Daniel Hansen; James Bullard; Sandrine Dudoit; Gavin Sherlock
Journal:  PLoS Genet       Date:  2008-12-19       Impact factor: 5.917

10.  Introns and splicing elements of five diverse fungi.

Authors:  Doris M Kupfer; Scott D Drabenstot; Kent L Buchanan; Hongshing Lai; Hua Zhu; David W Dyer; Bruce A Roe; Juneann W Murphy
Journal:  Eukaryot Cell       Date:  2004-10
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