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Bioinformatics. 2012 Mar 15;28(6):771-6. doi: 10.1093/bioinformatics/bts043. Epub 2012 Jan 27.

Functional microRNA targets in protein coding sequences.

Author information

1
Institute of Molecular Oncology, Biomedical Sciences Research Center, Vari, Greece. reczko@fleming.gr

Abstract

MOTIVATION:

Experimental evidence has accumulated showing that microRNA (miRNA) binding sites within protein coding sequences (CDSs) are functional in controlling gene expression.

RESULTS:

Here we report a computational analysis of such miRNA target sites, based on features extracted from existing mammalian high-throughput immunoprecipitation and sequencing data. The analysis is performed independently for the CDS and the 3(')-untranslated regions (3(')-UTRs) and reveals different sets of features and models for the two regions. The two models are combined into a novel computational model for miRNA target genes, DIANA-microT-CDS, which achieves higher sensitivity compared with other popular programs and the model that uses only the 3(')-UTR target sites. Further analysis indicates that genes with shorter 3(')-UTRs are preferentially targeted in the CDS, suggesting that evolutionary selection might favor additional sites on the CDS in cases where there is restricted space on the 3(')-UTR.

PMID:
22285563
DOI:
10.1093/bioinformatics/bts043
[Indexed for MEDLINE]

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