E-MTAB-1824 - RNA-seq of coding RNA from fission yeast (pat1-114 strain) grown at different temperatures over an eight-hour time-course and against JB22 strain to analyse genome-wide poly(A) site selection

Status
Released on 1 September 2013, last updated on 8 May 2014
Organism
Schizosaccharomyces pombe
Samples (2)
Protocols (8)
Description
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, which 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 datasets 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 well as 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 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 are generally (on chromosome 2) 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).
Experiment types
RNA-seq of coding RNA, co-expression, strain or line
Contacts
Citation
Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe. Margarita Schlackow; Samuel Marguerat; Nicholas J. Proudfoot; Jürg Bähler; Radek Erban; Monika Gullerova. RNA 19(12):1617 (2013), Europe PMC 24152550
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-1824.idf.txt
Sample and data relationshipE-MTAB-1824.sdrf.txt
Links