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

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 (CS s) 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 CS s. CS s 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 CS s in fission yeast is the canonical human AAUAAA sequence. © 2013 Landes Bioscience.