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dc.contributor.authorBitton, Danny A
dc.contributor.authorWood, V
dc.contributor.authorScutt, Paul J
dc.contributor.authorGrallert, Agnes
dc.contributor.authorYates, Tim
dc.contributor.authorSmith, Duncan L
dc.contributor.authorHagan, Iain M
dc.contributor.authorMiller, Crispin J
dc.date.accessioned2012-01-10T22:31:04Z
dc.date.available2012-01-10T22:31:04Z
dc.date.issued2011-04
dc.identifier.citationAugmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability. 2011, 187 (4):1207-17 Geneticsen
dc.identifier.issn1943-2631
dc.identifier.pmid21270388
dc.identifier.doi10.1534/genetics.110.123497
dc.identifier.urihttp://hdl.handle.net/10541/201529
dc.description.abstractGenome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by in silico analysis. We report a systematic reappraisal of the Schizosaccharomyces pombe genome that ignores thresholds. A complete six-frame translation was compared to a proteome data set, the Pfam domain database, and the genomes of six other fungi. Thirty-nine novel loci were identified. RT-PCR and RNA-Seq confirmed transcription at 38 loci; 33 novel gene structures were delineated by 5' and 3' RACE. Expression levels of 14 transcripts fluctuated during meiosis. Translational evidence for 10 genes, evolutionary conservation data supporting 35 predictions, and distinct phenotypes upon ORF deletion (one essential, four slow-growth, two delayed-division phenotypes) suggest that all 39 predictions encode functional proteins. The popularity of S. pombe as a model organism suggests that this augmented annotation will be of interest in diverse areas of molecular and cellular biology, while the generality of the approach suggests widespread applicability to other genomes.
dc.language.isoenen
dc.subject.meshBiological Evolution
dc.subject.meshCell Survival
dc.subject.meshDatabases, Genetic
dc.subject.meshGenes, Fungal
dc.subject.meshGenetic Loci
dc.subject.meshGenome, Fungal
dc.subject.meshGenomics
dc.subject.meshMeiosis
dc.subject.meshMolecular Sequence Annotation
dc.subject.meshProteome
dc.subject.meshRNA, Fungal
dc.subject.meshReverse Transcriptase Polymerase Chain Reaction
dc.subject.meshSchizosaccharomyces
dc.subject.meshSchizosaccharomyces pombe Proteins
dc.titleAugmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.en
dc.typeArticleen
dc.contributor.departmentCancer Research UK Applied Computational Biology and Bioinformatics Group, University of Manchester, Christie Hospital Site, Manchester M20 4BX, United Kingdom.en
dc.identifier.journalGeneticsen
html.description.abstractGenome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by in silico analysis. We report a systematic reappraisal of the Schizosaccharomyces pombe genome that ignores thresholds. A complete six-frame translation was compared to a proteome data set, the Pfam domain database, and the genomes of six other fungi. Thirty-nine novel loci were identified. RT-PCR and RNA-Seq confirmed transcription at 38 loci; 33 novel gene structures were delineated by 5' and 3' RACE. Expression levels of 14 transcripts fluctuated during meiosis. Translational evidence for 10 genes, evolutionary conservation data supporting 35 predictions, and distinct phenotypes upon ORF deletion (one essential, four slow-growth, two delayed-division phenotypes) suggest that all 39 predictions encode functional proteins. The popularity of S. pombe as a model organism suggests that this augmented annotation will be of interest in diverse areas of molecular and cellular biology, while the generality of the approach suggests widespread applicability to other genomes.


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