Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

Handle URI:
http://hdl.handle.net/10754/598406
Title:
Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe
Authors:
Schlackow, M.; Marguerat, S.; Proudfoot, N. J.; Bahler, J.; Erban, R.; Gullerova, M.
Abstract:
Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).
Citation:
Schlackow M, Marguerat S, Proudfoot NJ, Bahler J, Erban R, et al. (2013) Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe. RNA 19: 1617–1631. Available: http://dx.doi.org/10.1261/rna.040675.113.
Publisher:
Cold Spring Harbor Laboratory Press
Journal:
RNA
KAUST Grant Number:
KUK-C1-013-04
Issue Date:
23-Oct-2013
DOI:
10.1261/rna.040675.113
PubMed ID:
24152550
PubMed Central ID:
PMC3884648
Type:
Article
ISSN:
1355-8382
Sponsors:
We thank Konrad Krawczyk for valuable advice and support. This work was supported in part by the King Abdullah University of Science and Technology (KAUST) (KUK-C1-013-04); the Engineering and Physical Sciences Research Council (to M. S.); the L'Oreal/UNESCO Woman in Science UK and Ireland award (to M. G.), the MRC Career Development Award (to M. G.); the Wellcome Trust Senior Investigator Award (to J.B.), the Wellcome Trust programme grant (to N.J.P.), and the European Research Council grant agreement (239870 to R. E.); Royal Society for a University Research Fellowship; Brasenose College, University of Oxford (to R. E.); a Nicholas Kurti Junior Fellowship (to R. E.); and the Leverhulme Trust Philip Leverhulme Prize (to R.E.).
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Full metadata record

DC FieldValue Language
dc.contributor.authorSchlackow, M.en
dc.contributor.authorMarguerat, S.en
dc.contributor.authorProudfoot, N. J.en
dc.contributor.authorBahler, J.en
dc.contributor.authorErban, R.en
dc.contributor.authorGullerova, M.en
dc.date.accessioned2016-02-25T13:20:10Zen
dc.date.available2016-02-25T13:20:10Zen
dc.date.issued2013-10-23en
dc.identifier.citationSchlackow M, Marguerat S, Proudfoot NJ, Bahler J, Erban R, et al. (2013) Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe. RNA 19: 1617–1631. Available: http://dx.doi.org/10.1261/rna.040675.113.en
dc.identifier.issn1355-8382en
dc.identifier.pmid24152550en
dc.identifier.doi10.1261/rna.040675.113en
dc.identifier.urihttp://hdl.handle.net/10754/598406en
dc.description.abstractPolyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).en
dc.description.sponsorshipWe thank Konrad Krawczyk for valuable advice and support. This work was supported in part by the King Abdullah University of Science and Technology (KAUST) (KUK-C1-013-04); the Engineering and Physical Sciences Research Council (to M. S.); the L'Oreal/UNESCO Woman in Science UK and Ireland award (to M. G.), the MRC Career Development Award (to M. G.); the Wellcome Trust Senior Investigator Award (to J.B.), the Wellcome Trust programme grant (to N.J.P.), and the European Research Council grant agreement (239870 to R. E.); Royal Society for a University Research Fellowship; Brasenose College, University of Oxford (to R. E.); a Nicholas Kurti Junior Fellowship (to R. E.); and the Leverhulme Trust Philip Leverhulme Prize (to R.E.).en
dc.publisherCold Spring Harbor Laboratory Pressen
dc.subjectFission yeasten
dc.subjectRna-seqen
dc.subjectGenome-wideen
dc.subjectTranscription Terminationen
dc.subjectPolyadenylationen
dc.subject.meshPolyadenylationen
dc.subject.meshGenes, Fungalen
dc.titleGenome-wide analysis of poly(A) site selection in Schizosaccharomyces pombeen
dc.typeArticleen
dc.identifier.journalRNAen
dc.identifier.pmcidPMC3884648en
dc.contributor.institutionUniversity of Oxford, Oxford, United Kingdomen
dc.contributor.institutionUCL, London, United Kingdomen
dc.contributor.institutionSir William Dunn School of Pathology, Oxford, United Kingdomen
kaust.grant.numberKUK-C1-013-04en

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