title: Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe.
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).
authors.forename: Margarita
authors.initials: M
authors.lastname: Schlackow
authors.forename: Samuel
authors.initials: S
authors.lastname: Marguerat
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Proudfoot
authors.forename: Jürg
authors.initials: J
authors.lastname: Bähler
authors.forename: Radek
authors.initials: R
authors.lastname: Erban
authors.forename: Monika
authors.initials: M
authors.lastname: Gullerova
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D002874:Chromosome Mapping; D015825:Chromosomes, Fungal / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D016681:Genome, Fungal; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D026723:Polyadenylation; D059367:RNA Cleavage; D012331:RNA, Fungal / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012568:Schizosaccharomyces / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D061806:Transcription Termination, Genetic
chemical_list: D020413:3' Untranslated Regions; D012331:RNA, Fungal; D012333:RNA, Messenger
keywords: RNA-Seq; fission yeast; genome-wide; polyadenylation; transcription termination