Lecture Notes in Computer Science, 2009, Volume 5462/2009, 353-361, DOI: 10.1007/978-3-642-00727-9_33

Computational Prediction of Genes Translationally Regulated by Cytoplasmic Polyadenylation Elements

Eric C. Rouchka, Xiangping Wang, James H. Graham and Nigel G. F. Cooper

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Abstract

Cytoplasmic post-transcriptional modification of mRNA transcripts in the form of polyadenylated (poly(A)) tails plays a key role in their translational control. The timing and degree of polyadenylation has been shown to be due in part to a consensus nucleotide sequence – cytoplasmic polyadenylation elements (CPEs) which can be detected by a polyadenylation element binding protein (CPEB). An individual mRNA transcript controlled by CPEB may contain one or more CPE sites occurring upstream of a consensus hexamer poly-(A) signal. A probabilistic model, CPEDetector, is presented for predicting whether or not a gene’s translation is mediated by CPEB. CPEDetector takes into account detected CPE sites, poly-A sites, and distance metrics between the detected locations. This approach is tested against the 3’ untranslated regions (UTRs) of known genes using the UTRdb database.

Keywords  CPE - CPEB - bioinformatics - hidden Markov model - context free grammar - untranslated region

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