Prediction of microRNAs affecting mRNA expression during retinal development

Microarray expression data from ciliary epithelial retinal stem cells (CE-RSCs), developing and adult mouse retina were generated or downloaded from public repositories. Analysis of gene expression profiles detected the effects of multiple miRNAs in CE-RSCs and retina. The expression of 20 selected miRNAs was confirmed by RT-PCR and the cellular distribution of representative candidates analyzed by in situ hybridization. The expression levels of miRNAs correlated with the significance of their predicted effects upon mRNA expression. Highly expressed miRNAs included miR-124, miR-125a, miR-125b, miR-204 and miR-9. Over-expression of three miRNAs with significant predicted effects upon global mRNA levels resulted in a decrease in mRNA expression of five out of six individual predicted target genes assayed.This study has detected the effect of miRNAs upon mRNA expression in immature and adult retinal tissue and cells. The validity of these observations is supported by the experimental confirmation of candidate miRNA expression and the regulation of predicted target genes following miRNA over-expression. Identified miRNAs are likely to be important in retinal development and function. Misregulation of these miRNAs might contribute to retinal degeneration and disease. Conversely, manipulation of their expression could potentially be used as a therapeutic tool in the future.miRNAs are small RNA molecules of 18-22 nucleotides in length which regulate gene expression. Precursor RNAs transcribed either as independent genes or within introns of coding genes are processed by the RNAseIII enzymes Drosha and Dicer to form the mature miRNAs [1]. The first miRNAs were discovered as a result of their role in the timing of adult cell fate determination in Caenorhabditis elegans. Both let-7 and lin-4 are temporally regulated and cause a decrease in expression of target proteins which control developmental stage-specific events [2-4]. The significance of miRNAs in developmental process