A probabilistic model of 3' end formation in Caenorhabditis elegans

Nucleic Acids Research
Ashwin HajarnavisRichard Durbin

Abstract

The 3' ends of mRNAs terminate with a poly(A) tail. This post-transcriptional modification is directed by sequence features present in the 3'-untranslated region (3'-UTR). We have undertaken a computational analysis of 3' end formation in Caenorhabditis elegans. By aligning cDNAs that diverge from genomic sequence at the poly(A) tract, we accurately identified a large set of true cleavage sites. When there are many transcripts aligned to a particular locus, local variation of the cleavage site over a span of a few bases is frequently observed. We find that in addition to the well-known AAUAAA motif there are several regions with distinct nucleotide compositional biases. We propose a generalized hidden Markov model that describes sequence features in C.elegans 3'-UTRs. We find that a computer program employing this model accurately predicts experimentally observed 3' ends even when there are multiple AAUAAA motifs and multiple cleavage sites. We have made available a complete set of polyadenylation site predictions for the C.elegans genome, including a subset of 6570 supported by aligned transcripts.

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Citations

Oct 31, 2012·Molecular Genetics and Genomics : MGG·Xiaohui WuYong Zeng
Jul 28, 2006·Bioinformatics·Yiming ChengBin Tian
Dec 21, 2004·Nucleic Acids Research·Haibo ZhangBin Tian
Apr 1, 2005·Nucleic Acids Research·Shibin QiuTerran Lane
Dec 31, 2005·Nucleic Acids Research·Erich M SchwarzPaul W Sternberg
Mar 7, 2007·Nucleic Acids Research·Virginie MoucadelDaniel Gautheret
Nov 8, 2007·Nucleic Acids Research·Marco MangoneKristin C Gunsalus
May 4, 2005·Genome Research·Randall H BrownMichael R Brent
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Apr 4, 2014·Briefings in Bioinformatics·Guoli JiXiaohui Wu
Dec 17, 2014·Genome Biology and Evolution·Alana V Beadell, Eric S Haag
Jul 25, 2019·Frontiers in Genetics·Sheng ZhuGuoli Ji

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