Prediction of Altered 3'- UTR miRNA-Binding Sites from RNA-Seq Data

MicroRNAs (miRNAs) are small molecules that post-transcriptionally regulate the expression of a large number of protein-coding genes in metazoans, and are suggested to play important roles in fine-tuning immune mechanisms and disease responses. Polymorphisms in either miRNAs or their gene targets may have a significant impact on gene expression by abolishing, weakening or creating miRNA target sites, possibly leading to phenotypic variation.

A multi-national team led by researchers at INRA, Jouy-en-Josas, France has now explored the impact of variants in the 3′-UTR miRNA target sites of genes. They used combined predictions by TargetScan, PACMIT and TargetSpy, based on different biological parameters, for the identification of miRNA target sites and the discovery of polymorphic miRNA target sites (poly-miRTSs).

Predictions for three SLA genes (important determinants of immune, infectious disease and vaccine response in pigs) characterized by a different range of sequence variation provided proof of principle for the analysis of poly-miRTSs from a total of 144 M RNA-Seq reads collected from different porcine tissues….An inverse correlation in expression levels was demonstrated between miRNAs and co-expressed SLA targets by exploiting a published dataset (RNA-Seq and small RNA-Seq) of three porcine tissues. These results support the resource value of RNA-Seq collections to identify SNPs that may lead to altered miRNA regulation patterns.

  • Endale Ahanda ML, Fritz ER, Estellé J, Hu ZL, Madsen O, Groenen MA, Beraldi D, Kapetanovic R, Hume DA, Rowland RR, Lunney JK, Rogel-Gaillard C, Reecy JM, Giuffra E. (2012) Prediction of Altered 3′- UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region. PLoS One 7(11), e48607. [article]