title: Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes.
abstract: Messenger ribonucleic acids (RNAs) contain a large number of cis-regulatory RNA elements that function in many types of post-transcriptional regulation. These cis-regulatory elements are often characterized by conserved structures and/or sequences. Although some classes are well known, given the wide range of RNA-interacting proteins in eukaryotes, it is likely that many new classes of cis-regulatory elements are yet to be discovered. An approach to this is to use computational methods that have the advantage of analysing genomic data, particularly comparative data on a large scale. In this study, a set of structural discovery algorithms was applied followed by support vector machine (SVM) classification. We trained a new classification model (CisRNA-SVM) on a set of known structured cis-regulatory elements from 3'-untranslated regions (UTRs) and successfully distinguished these and groups of cis-regulatory elements not been strained on from control genomic and shuffled sequences. The new method outperformed previous methods in classification of cis-regulatory RNA elements. This model was then used to predict new elements from cross-species conserved regions of human 3'-UTRs. Clustering of these elements identified new classes of potential cis-regulatory elements. The model, training and testing sets and novel human predictions are available at: http://mRNA.otago.ac.nz/CisRNA-SVM.
authors: Department of Biochemistry and Genetics Otago, University of Otago, Dunedin 9054, New Zealand. sylvia.x.chen@gmail.com
authors: Xiaowei Sylvia
authors: XS
authors: Chen
authors: Chris M
authors: CM
authors: Brown
mesh_terms: D020413:3' Untranslated Regions; D000465:Algorithms; D023281:Genomics / Q000379:methods*; D006801:Humans; D009690:Nucleic Acid Conformation; D011506:Proteins / Q000235:genetics; D012313:RNA / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid; D060388:Support Vector Machine
chemical_list: D020413:3' Untranslated Regions; D011506:Proteins; D038621:Regulatory Sequences, Ribonucleic Acid; D012313:RNA