MicroRNAs (miRNAs) are a class of small single-stranded, endogenous 21-22 nt non-coding RNAs that regulate their target mRNA levels by causing either inactivation or degradation of the mRNAs. In recent years, miRNA genes have been identified from mammals, insects, worms, plants, and viruses. In this research, bioinformatics approaches were used to predict potential miRNAs and their targets in Nile tilapia from the expressed sequence tag (EST) and genomic survey sequence (GSS) database, respectively, based on the conservation of miRNAs in many animal species. A total of 19 potential miRNAs were detected following a range of strict filtering criteria. To test the validity of the bioinformatics method, seven predicted Nile tilapia miRNA genes were selected for further biological validation, and their mature miRNA transcripts were successfully detected by stem-loop RT-PCR experiments. Using these potential miRNAs, we found 56 potential targets in this species. Most of the target mRNAs appear to be involved in development, metabolism, signal transduction, transcription regulation and stress responses. Overall, our findings will provide an important foundation for further research on miRNAs function in the Nile tilapia.

MicroRNAs (miRNA) are non coding small RNA molecules consisting of 20-24 nucleotides (nt), which regulate gene expression negatively at the post transcriptional levels depending on the extent of com plementation between miRNA and mRNA in a variety of eukaryotic organisms. They have attracted increas ing attention recently. To date, a total of 1637 mature miRNAs from fishes have been deposited in the miR Base database (Release 21) and they are just a small portion of the miRNAs described in fish species. Espe cially in rainbow trout (Oncorhynchus mykiss) miRNAs, it is far from the numbers of miRNAs found in other fishes and many more miRNA remain to be discovered. In present study, we used known animal miRNAs to systematically search miRNA homologs in available expressed sequence tags (EST), genomic survey sequences (GSS), and transcript sequence assemblies (TSA) of O. mykiss based on the conservation of miRNA sequences. Following the filtering with a combination of stringent criteria, 39 miRNAs belonging to 25 independent families were identified, of which 14 are novel identified miRNAs firstly in O. mykiss. The randomly selected 13 miRNAs were verified by stem loop RT PCR indicating that the prediction method that we used to identify the miRNAs was effective. Furthermore, total of 94 target genes were predicted and their probable functions were illustrated. Their target genes are involved in transcription factors, develop ment, metabolism, signaling, immunity, and cell division. The current study has provided an update on O. mykiss miRNAs and their targets, which will be helpful for future research on miRNA mediated gene reg ulation in this important fish species.