MicroRNA target prediction by expression analysis of host genes

Abstract

MicroRNAs (miRNAs) are small noncoding RNAs that control gene expression by inducing RNA cleavage or translational inhibition. Most human miRNAs are intragenic and are transcribed as part of their hosting transcription units. We hypothesized that the expression profiles of miRNA host genes and of their targets are inversely correlated and devised a novel procedure, HOCTAR (host gene oppositely correlated targets), which ranks predicted miRNA target genes based on their anti-correlated expression behavior relative to their respective miRNA host genes. HOCTAR is the first tool for systematic miRNA target prediction that utilizes the same set of microarray experiments to monitor the expression of both miRNAs (through their host genes) and candidate targets. We applied the procedure to 178 human intragenic miRNAs and found that it performs better than currently available prediction softwares in pinpointing previously validated miRNA targets. The high-scoring HOCTAR predicted targets were enriched in Gene Ontology categories, which were consistent with previously published data, as in the case of miR-106b and miR-93. By means of overexpression and loss-of-function assays, we also demonstrated that HOCTAR is efficient in predicting novel miRNA targets and we identified, by microarray and qRT-PCR procedures, 34 and 28 novel targets for miR-26b and miR-98, respectively. Overall, we believe that the use of HOCTAR significantly reduces the number of candidate miRNA targets to be tested compared to the procedures based solely on target sequence recognition. Finally, our data further confirm that miRNAs have a significant impact on the mRNA levels of most of their targets.

miR-204 is required for lens and retinal development via Meis2 targeting

“…Prediction of miRNA targets was performed using the Host gene Opposite Correlated TARgets (HOCTAR) tool (http://hoctar. tigem.it) (15).…”

“…Cells were transfected with either 50 nM miRIDIAN miRNA Mimics or 80 nM miRIDIAN miRNA Inhibitor (Dharmacon). Plasmids containing the 3′-UTR of the human MEIS2 gene and psiUx plasmid constructs containing the hsa-premiR-204 sequence were used in Luc assays, as described previously (15). Each assay was performed in duplicate, and all the results are shown as means ± SD of at least three independent assays.…”

“…The H36CE human lens epithelial cell line was grown as described (41). Cell transfections and qRT-PCR experiments were performed as described (15). Cells were transfected with either 50 nM miRIDIAN miRNA Mimics or 80 nM miRIDIAN miRNA Inhibitor (Dharmacon).…”

“…S1 and Tables S1 and S2). These included RNA in situ hybridization (ISH) using the miR-204-locked nucleic acid antisense probe and injections of 6-bp-mismatched Mo (mm-Mo-miR-204), which gave no aberrant phenotype at any concentration (Table S2) potential mRNA targets using the recently developed host-gene oppositely correlated target (HOCTAR) tool, which integrates expression profiling and sequence-based miRNA target recognition software (15). Among the predicted miR-204 targets, the homeobox transcription factors Meis1 and Meis2 appeared particularly attractive to explain the observed eye defects because they had been previously shown to regulate vertebrate eye development by modulating Pax6 expression (16).…”

The miRNA-kallikrein axis of interaction: a new dimension in the pathogenesis of prostate cancer

“…In addition, these interactions may be direct or indirect, which adds to the complexity. Although miRNAs act posttranscriptionally, recent evidence supports that they also usually interfere with the stability of their target mRNAs (Cheng and Li , 2008 ;Gennarino et al , 2009 ;Guimbellot et al , 2009 ) Moreover, KLKs may also contribute to miRNA regulation through transcriptional regulation of miRNA promoters as suggested by KLK nuclear localization (Korkmaz et al , 2001 ;Klokk et al , 2007 ).…”