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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).

Original publication

DOI

10.1261/rna.040675.113

Type

Journal article

Journal

RNA

Publication Date

12/2013

Volume

19

Pages

1617 - 1631

Keywords

RNA-Seq, fission yeast, genome-wide, polyadenylation, transcription termination, 3' Untranslated Regions, Base Sequence, Chromosome Mapping, Chromosomes, Fungal, Gene Expression Regulation, Fungal, Genes, Fungal, Genome, Fungal, Molecular Sequence Annotation, Molecular Sequence Data, Polyadenylation, RNA Cleavage, RNA, Fungal, RNA, Messenger, Schizosaccharomyces, Sequence Analysis, RNA, Transcription Termination, Genetic