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.
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.
Authors: Z Xu; D Nayak; W Yang; G Baskaran; S Ramachandran; N Sarma; A Aloush; E Trulock; R Hachem; G A Patterson; T Mohanakumar Journal: Am J Transplant Date: 2015-02-03 Impact factor: 8.086
Authors: Winston R Becker; Benjamin Ober-Reynolds; Karina Jouravleva; Samson M Jolly; Phillip D Zamore; William J Greenleaf Journal: Mol Cell Date: 2019-07-16 Impact factor: 17.970
Authors: Lili Zhou; Caitlyn Miller; Loren J Miraglia; Angelica Romero; Ludovic S Mure; Satchidananda Panda; Steve A Kay Journal: Proc Natl Acad Sci U S A Date: 2021-01-05 Impact factor: 11.205