E-MTAB-1642 - RNA-seq of genome-wide polyadenylation sites in fission yeast (Schizosaccharomyces pombe) with a strand-specific technique

Status
Last updated on 18 November 2013, released on 19 November 2013
Organism
Schizosaccharomyces pombe
Samples (3)
Protocols (5)
Description
Regulatory elements in the 3’ untranslated regions (UTRs) of eukaryotic mRNAs influence mRNA localization, translation, and stability. The length of these regions is determined by the location at which mRNAs are cleaved and polyadenylated. The use of alternative polyadenylation sites is common, and can be regulated in different situations. I present here a new method to identify cleavage and polyadenylation sites (CSs) at the genome-wide level. The approach is strand-specific, avoids RNA enzymatic modification steps that can introduce sequence-specific biases, and uses molecular barcodes to ensure that every identified CS originates from an individual RNA molecule. I applied to create the first comprehensive genome-wide map of polyadenylation sites in the fission yeast Schizosaccharomyces pombe, comprising the analysis of over two million individual mRNAs that defined 10,422 major CSs. CSs were identified for 90% of coding genes and 15% of non-coding RNAs. Alternative polyadenylation was prevalent in both groups, with 61% and 49% of all detected genes, respectively, displaying more than one CS. The specificity of the cleavage reaction was gene-specific, resulting in highly variable levels of heterogeneity in the length of the 3' UTRs. Finally, I show that for both coding and non-coding genes the most common regulatory motif associated with CSs in fission yeast is the canonical human AAUAAA sequence.
Experiment types
RNA-seq of non coding RNA, replicate
Contact
Citation
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-MTAB-1642.idf.txt
Sample and data relationshipE-MTAB-1642.sdrf.txt
Links