MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence

Abstract

Regulation of post-transcriptional gene expression by microRNAs (miRNA) has so far been validated for only a few mRNA targets. Based on the large number of miRNA genes and the possibility that one miRNA might influence gene expression of several targets simultaneously, the quantity of ribo-regulated genes is expected to be much higher. Here, we describe the web tool MicroInspector that will analyse a user-defined RNA sequence, which is typically an mRNA or a part of an mRNA, for the occurrence of binding sites for known and registered miRNAs. The program allows variation of temperature, the setting of energy values as well as the selection of different miRNA databases to identify miRNA-binding sites of different strength. MicroInspector could spot the correct sites for miRNA-interaction in known target mRNAs. Using other mRNAs, for which such an interaction has not yet been described, we discovered frequently potential miRNA binding sites of similar quality, which can now be analysed experimentally. The MicroInspector program is easy to use and does not require specific computer skills. The service can be accessed via the MicroInspector web server at .

miRNAs Regulate miRNAs: Coordinated Transcriptional and Post-Transcriptional Regulation

“…It has been also recently demonstrated that miR-221/2 family interaction with c-Kit 3'UTR inhibits normal erythropoiesis and erythroleukemic cell growth. 36 It is notewhorthy that 3 out of 9 up-regulated miRNAs (33%) and 7 out of 23 down-regulated miRNAs (30%) are predicted to target c-Kit 3'UTR 5,[37][38][39] (Fig. 1B, dark grey bars): it seems that at least part of affected miRNAs could share a similar function to those initially variated, indicating that a connection among miRNAs with coordinated function exist.…”

miR-1247 Functions by Targeting Cartilage Transcription Factor SOX9

“…As expected, no changes in the luciferase activity were observed in the presence of the miR-1247 mimic, suggesting that miR-1247 does not, indeed, target the SOX9 3Ј-UTR. However, because miRNAs can, in many cases, target the coding sequences (CDS) of mRNAs (24), we screened for possible miR-1247 binding sites in the SOX9 CDS using MicroInspector (25) and RNAhybrid (26), and both programs detected overlapping putative binding sites in positions 525 and 540 of the CDS, respectively (Fig. 6E).…”

Modulation of microRNA processing by mismatch repair protein MutLα

“…Computational analysis using MicroInspector [30] identified a putative binding site for miR-422a in the MLH1 3′-UTR that is disrupted by the 3-nucleotide deletion, suggesting a possible role for miR422a in regulating expression of MLH1. To explore this possibility, HeLa cells were transfected with miR-422a precursor (pre-miR-422a) or anti-miR-422a, and the MLH1 protein level was quantified.…”