title: 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 (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.
authors.affiliation: Department of Biochemistry; University of Cambridge; Cambridge, UK.
authors.forename: Juan
authors.initials: J
authors.lastname: Mata
mesh_terms: D020413:3' Untranslated Regions; D002874:Chromosome Mapping; D005800:Genes, Fungal; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D011061:Poly A / Q000378:metabolism*; D026723:Polyadenylation; D039104:RNA 3' Polyadenylation Signals; D012331:RNA, Fungal / Q000235:genetics* / Q000378:metabolism*; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012568:Schizosaccharomyces / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D020413:3' Untranslated Regions; D012331:RNA, Fungal; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D011061:Poly A
keywords: Illumina sequencing; S. pombe; alternative polyadenylation; fission yeast; mRNA processing; unique molecular identifiers
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