Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe.
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).
['Schlackow|Margarita|M|', 'Marguerat|Samuel|S|', 'Proudfoot|Nicholas J|NJ|', 'Bähler|Jürg|J|', 'Erban|Radek|R|', 'Gullerova|Monika|M|']
D020413:3' Untranslated Regions D001483:Base Sequence D002874:Chromosome Mapping D015825:Chromosomes, Fungal 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 D012333:RNA, Messenger D012568:Schizosaccharomyces D017423:Sequence Analysis, RNA D061806:Transcription Termination, Genetic
genome-wide polyadenylation fission yeast RNA-Seq transcription termination