Literature DB >> 22817757

Non-coding RNAs in Saccharomyces cerevisiae: what is the function?

Jian Wu1, Daniela Delneri, Raymond T O'Keefe.   

Abstract

New sequencing technologies and high-resolution microarray analysis have revealed genome-wide pervasive transcription in many eukaryotes, generating a large number of RNAs with no coding capacity. The focus of current debate is whether many of these ncRNAs (non-coding RNAs) are functional, and if so, what their function is. In this review, we describe recent discoveries in the field of ncRNAs in the yeast Saccharomyces cerevisiae. Newly identified ncRNAs in this budding yeast, their functions in gene regulation and possible mechanisms of action are discussed.

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Year:  2012        PMID： 22817757      PMCID： PMC4234904          DOI： 10.1042/BST20120042

Source DB:  PubMed          Journal:  Biochem Soc Trans        ISSN： 0300-5127            Impact factor:   5.407


  35 in total

1.  Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae.

Authors:  Debrah M Thompson; Roy Parker
Journal:  Mol Cell Biol       Date:  2006-10-30       Impact factor: 4.272

2.  Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae.

Authors:  Jurgi Camblong; Nahid Iglesias; Céline Fickentscher; Guennaelle Dieppois; Françoise Stutz
Journal:  Cell       Date:  2007-11-16       Impact factor: 41.582

3.  Chromatin remodelling at promoters suppresses antisense transcription.

Authors:  Iestyn Whitehouse; Oliver J Rando; Jeff Delrow; Toshio Tsukiyama
Journal:  Nature       Date:  2007-12-13       Impact factor: 49.962

4.  The transcriptional landscape of the yeast genome defined by RNA sequencing.

Authors:  Ugrappa Nagalakshmi; Zhong Wang; Karl Waern; Chong Shou; Debasish Raha; Mark Gerstein; Michael Snyder
Journal:  Science       Date:  2008-05-01       Impact factor: 47.728

5.  A high-resolution map of transcription in the yeast genome.

Authors:  Lior David; Wolfgang Huber; Marina Granovskaia; Joern Toedling; Curtis J Palm; Lee Bofkin; Ted Jones; Ronald W Davis; Lars M Steinmetz
Journal:  Proc Natl Acad Sci U S A       Date:  2006-03-28       Impact factor: 11.205

6.  A role for noncoding transcription in activation of the yeast PHO5 gene.

Authors:  Jay P Uhler; Christina Hertel; Jesper Q Svejstrup
Journal:  Proc Natl Acad Sci U S A       Date:  2007-04-30       Impact factor: 11.205

7.  The role of nucleosome positioning in the evolution of gene regulation.

Authors:  Alexander M Tsankov; Dawn Anne Thompson; Amanda Socha; Aviv Regev; Oliver J Rando
Journal:  PLoS Biol       Date:  2010-07-06       Impact factor: 8.029

8.  Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene.

Authors:  Joseph A Martens; Lisa Laprade; Fred Winston
Journal:  Nature       Date:  2004-06-03       Impact factor: 49.962

9.  A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae.

Authors:  Julia Berretta; Marina Pinskaya; Antonin Morillon
Journal:  Genes Dev       Date:  2008-03-01       Impact factor: 11.361

10.  A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.

Authors:  Travis N Mavrich; Ilya P Ioshikhes; Bryan J Venters; Cizhong Jiang; Lynn P Tomsho; Ji Qi; Stephan C Schuster; Istvan Albert; B Franklin Pugh
Journal:  Genome Res       Date:  2008-06-12       Impact factor: 9.043
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  14 in total

1.  The Small RNA sr8384 Is a Crucial Regulator of Cell Growth in Solventogenic Clostridia.

Authors:  Yunpeng Yang; Huan Zhang; Nannan Lang; Lu Zhang; Changsheng Chai; Huiqi He; Weihong Jiang; Yang Gu
Journal:  Appl Environ Microbiol       Date:  2020-06-17       Impact factor: 4.792

2.  Control of Cdc28 CDK1 by a stress-induced lncRNA.

Authors:  Mariona Nadal-Ribelles; Carme Solé; Zhenyu Xu; Lars M Steinmetz; Eulàlia de Nadal; Francesc Posas
Journal:  Mol Cell       Date:  2014-02-06       Impact factor: 17.970

Review 3.  Refined Pichia pastoris reference genome sequence.

Authors:  Lukas Sturmberger; Thomas Chappell; Martina Geier; Florian Krainer; Kasey J Day; Ursa Vide; Sara Trstenjak; Anja Schiefer; Toby Richardson; Leah Soriaga; Barbara Darnhofer; Ruth Birner-Gruenberger; Benjamin S Glick; Ilya Tolstorukov; James Cregg; Knut Madden; Anton Glieder
Journal:  J Biotechnol       Date:  2016-04-12       Impact factor: 3.307

4.  Mapping platinum adducts on yeast ribosomal RNA using high-throughput sequencing.

Authors:  Kory Plakos; Victoria J DeRose
Journal:  Chem Commun (Camb)       Date:  2017-11-28       Impact factor: 6.222

5.  Identification of novel noncoding transcripts in telomerase-negative yeast using RNA-seq.

Authors:  Rachel O Niederer; Nickolas Papadopoulos; David C Zappulla
Journal:  Sci Rep       Date:  2016-01-20       Impact factor: 4.379

6.  A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae.

Authors:  Steven Parker; Marcin G Fraczek; Jian Wu; Sara Shamsah; Alkisti Manousaki; Kobchai Dungrattanalert; Rogerio Alves de Almeida; Diego Estrada-Rivadeneyra; Walid Omara; Daniela Delneri; Raymond T O'Keefe
Journal:  RNA       Date:  2017-05-03       Impact factor: 4.942

7.  PlantRNA_Sniffer: A SVM-Based Workflow to Predict Long Intergenic Non-Coding RNAs in Plants.

Authors:  Lucas Maciel Vieira; Clicia Grativol; Flavia Thiebaut; Thais G Carvalho; Pablo R Hardoim; Adriana Hemerly; Sergio Lifschitz; Paulo Cavalcanti Gomes Ferreira; Maria Emilia M T Walter
Journal:  Noncoding RNA       Date:  2017-03-04

Review 8.  Predicting complex phenotype-genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory.

Authors:  Duygu Dikicioglu; Pınar Pir; Stephen G Oliver
Journal:  Biotechnol J       Date:  2013-08-23       Impact factor: 4.677

9.  Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae.

Authors:  Katarzyna B Hooks; Samina Naseeb; Steven Parker; Sam Griffiths-Jones; Daniela Delneri
Journal:  Genetics       Date:  2016-05-18       Impact factor: 4.562

Review 10.  Long Noncoding RNAs in Yeast Cells and Differentiated Subpopulations of Yeast Colonies and Biofilms.

Authors:  Derek Wilkinson; Libuše Váchová; Otakar Hlaváček; Jana Maršíková; Gregor D Gilfillan; Zdena Palková
Journal:  Oxid Med Cell Longev       Date:  2018-03-25       Impact factor: 6.543
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