microRNA Isoform Target Prediction by RNA-Seq

Computational prediction of microRNA targets remains a challenging problem. The existing rule-based, data-driven and expression profiling approaches to target prediction are mostly approached from the gene-level. The advent of next-generation sequencing technologies provides new opportunities to profile transcriptomes and microRNA targetomes at base-wise resolution and provides a new perspective for microRNA target prediction on the isoform-level.  We hypothesize that the splicing isoform is the ultimate effector in microRNA targeting and that with the use of gene-structure information derived from the RNA-seq data to assess isoform specific microRNA regulation it is possible to predict non-dominant isoform targets as well as their targeting regions that are otherwise invisible to many existing approaches.

Deng N, Puetter A, Zhang K, Johnson K, Zhao Z, Taylor C, Flemington EK, Zhu D. (2011) Isoform-level microRNA-155 target prediction using RNA-seq. Nucleic Acids Res {Epub ahead of print]. [article]