Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes.
Nucleic Acids Res
; 40(18): 8862-73, 2012 Oct.
Article
em En
| MEDLINE
| ID: mdl-22821558
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.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Regiões 3' não Traduzidas
/
Genômica
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Sequências Reguladoras de Ácido Ribonucleico
Tipo de estudo:
Diagnostic_studies
/
Prognostic_studies
Limite:
Humans
Idioma:
En
Ano de publicação:
2012
Tipo de documento:
Article