Functional microRNA targets in protein coding sequences
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TLDR
A computational analysis of miRNA target sites within protein coding sequences (CDSs) based on features extracted from existing mammalian high-throughput immunoprecipitation and sequencing data indicates that genes with shorter 3(')-UTRs are preferentially targeted in the CDS, suggesting that evolutionary selection might favor additional sites on the C DS in cases where there is restricted space on the 3 (')-UTR.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.
Availability: The results of DIANA-microT-CDS are available at www.microrna.gr/microT-CDS
Contact:hatzigeorgiou@fleming.gr; reczko@fleming.gr
Supplementary information:Supplementary data are available at Bioinformatics online.read more
Citations
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Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
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DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows
Maria D. Paraskevopoulou,Georgios Georgakilas,Nikos Kostoulas,Ioannis S. Vlachos,Thanasis Vergoulis,Martin Reczko,Christos Filippidis,Theodore Dalamagas,Artemis G. Hatzigeorgiou +8 more
TL;DR: DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA- microT-CDS, which has been updated to incorporate miRBase version 18 and Ensembl version 69.
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