Identification and characterization of microRNAs and their target genes from Nile tilapia (Oreochromis niloticus).
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.
Yong
Y
Huang
Xiu Ying
XY
Ma
You Bing
YB
Yang
Hong Tao
HT
Ren
Xi Hong
XH
Sun
Li Rui
LR
Wang
D000818:Animals; D001483:Base Sequence; D023681:Cichlids / Q000235:genetics*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D029941:Fish Proteins / Q000235:genetics*; D005786:Gene Expression Regulation; D035683:MicroRNAs / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012689:Sequence Homology, Nucleic Acid
D029941:Fish Proteins; D035683:MicroRNAs