A guide through present computational approaches for the identification of mammalian microRNA targets

Abstract

Computational microRNA (miRNA) target prediction is a field in flux. Here we present a guide through five widely used mammalian target prediction programs. We include an analysis of the performance of these individual programs and of various combinations of these programs. For this analysis we compiled several benchmark data sets of experimentally supported miRNA-target gene interactions. Based on the results, we provide a discussion on the status of target prediction and also suggest a stepwise approach toward predicting and selecting miRNA targets for experimental testing.

Amyloid precursor protein regulates neurogenesis by antagonizing miR-574-5p in the developing cerebral cortex

“…Taken together, these results suggest that miR-574-5p serves as an important downstream effector of APP-mediated neuronal miR-574-5p regulates Sox12 expression in NPCs. Using bioinformatics approaches 16,17 , we identify the top five potential miR-574-5p targets based on their functional role in neuronal development, RNA hybrid scores and the presence of synergistic binding sites 18,19 . These candidates are identified as Sox12, Cend1, Olig3, Dedd2 and Traf7 (Supplementary Table 1).…”

A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss)

“…Regulation exhibited by miRNAs is mainly resulted from the interaction between miRNAs and their target genes via perfect or near-perfect complementation (Brown and Sanseau, 2005;Sethupathy et al, 2006). Therefore, it is of prime importance to identify the miRNA target genes to understand the miRNA regulatory function.…”

Phospho-ΔNp63α/microRNA network modulates epigenetic regulatory enzymes in squamous cell carcinomas

“…7,8 Primary microRNA transcripts are processed by the RNA-induced silencing complex to generate mature microRNAs; the latter form complexes with the specific sequences within mRNA targets based on complementarity. [7][8][9][10][11] The microRNA/mRNA complexes then cause an inhibition of protein translation and/or degradation of the mRNAs. A single microRNA could modulate several mRNAs, and a few microRNAs might regulate the expression of the same mRNA target.…”