title: Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.
abstract: Yeast Npl3 is a highly abundant, nuclear-cytoplasmic shuttling, RNA-binding protein, related to metazoan SR proteins. Reported functions of Npl3 include transcription elongation, splicing and RNA 3' end processing. We used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites, and strand-specific tiling arrays to look at the effects of loss of Npl3 on all transcripts across the genome. We found that Npl3 binds diverse RNA species, both coding and non-coding, at sites indicative of roles in both early pre-mRNA processing and 3' end formation. Tiling arrays and RNAPII mapping data revealed 3' extended RNAPII-transcribed RNAs in the absence of Npl3, suggesting that defects in pre-mRNA packaging events result in termination readthrough. Transcription readthrough was widespread and frequently resulted in down-regulation of neighboring genes. We conclude that the absence of Npl3 results in widespread 3' extension of transcripts with pervasive effects on gene expression.
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom.
authors.forename: Rebecca K
authors.initials: RK
authors.lastname: Holmes
authors.affiliation: FMI Basel, Basel, Switzerland.|European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Alex C
authors.initials: AC
authors.lastname: Tuck
authors.affiliation: EMBL, Heidelberg, Germany.
authors.forename: Chenchen
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom.
authors.forename: Hywel R
authors.initials: HR
authors.lastname: Dunn-Davies
authors.affiliation: The Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Kudla
authors.affiliation: EMBL, Heidelberg, Germany.
authors.forename: Sandra
authors.initials: S
authors.lastname: Clauder-Munster
authors.affiliation: SynthSys, University of Edinburgh, Edinburgh, Scotland, United Kingdom.
authors.forename: Sander
authors.initials: S
authors.lastname: Granneman
authors.affiliation: EMBL, Heidelberg, Germany.
authors.forename: Lars M
authors.initials: LM
authors.lastname: Steinmetz
authors.affiliation: Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America.
authors.forename: Christine
authors.initials: C
authors.lastname: Guthrie
authors.affiliation: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Tollervey
mesh_terms: D020413:3' Untranslated Regions; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D061806:Transcription Termination, Genetic
chemical_list: D020413:3' Untranslated Regions; C077734:NPL3 protein, S cerevisiae; D009687:Nuclear Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins