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RNA Biol. 2013 Aug;10(8):1407-14. doi: 10.4161/rna.25758. Epub 2013 Jul 16.

Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation.

Author information

1
Department of Biochemistry; University of Cambridge; Cambridge, UK.

Abstract

Regulatory elements in the 3' untranslated regions (UTRs) of eukaryotic mRNAs influence mRNA localization, translation, and stability. 3'-UTR length 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 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 unique molecular identifiers to ensure that all identified CS originates from individual RNA molecules. I applied this method to create the first comprehensive genome-wide map of polyadenylation sites of the fission yeast Schizosaccharomyces pombe, comprising the analysis of 2,021,000 individual mRNAs that defined 8,883 CSs. CSs were identified for 90% of coding genes and 50% of ncRNAs. Alternative polyadenylation was prevalent in both groups, with 41% and 45% 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 3'-UTR lengths. 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.

KEYWORDS:

Illumina sequencing; S. pombe; alternative polyadenylation; fission yeast; mRNA processing; unique molecular identifiers

PMID:
23900342
PMCID:
PMC3817161
DOI:
10.4161/rna.25758
[Indexed for MEDLINE]
Free PMC Article

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