Identification Of Novel MicroRNA Genes And Prediction Of Their Target Genes From Sea Squirt

MicroRNAs(miRNAs) are classes of small non-coding RNAs, about 20~22nt, which normally bind to 3'UTR of target gene to regulate expression. As a new kind of regulatory factors, in both animals and plants, miRNA play many important roles range over tissue differentiation, cell proliferation, embryonic development, signal transduction and diseases. In recent years, although many researches of miRNA in animal were reported, works of Ciona intestinalis were very limited. Research shows that approximate 0.5-1.5% of genome is made up of miRNA, but only 34 miRNA of Ciona intestinalis were reported on miRBase which means finding new miRNA is very important.As traditional experimental method was limited by the specific expression of miRNA, most researchers used bioinformatics to find new miRNA in the recent years and it largely improved the efficiency. Our research found new miRNAs by using homologous searching method to compared amphioxus, nematodes, fruit flies and human, miRNA probe with whole genome sequences of Ciona intestinalis combine with secondary structure of miRNA and SVM analysis. Through prediction of target gene and comparison of gene function to measure regulatory function of miRNA, our research also completed the evolutionary analysis of miRNA.The main results are as following:1. Ten new miRNA of Ciona intestinalis were found by homologous searching.2. The result of comparative analysis of new miRNA showed most of them located in intergenic gene and homogenous miRNA are very conserved in evolution.3. The secondary structure of miRNA shows the sites of miRNA in hairpin structure are diversified.4. The result of comparing miRNA with EST made our research more reliable.5. Our research used miRanda method to predict the target gene of new miRNA and the result showed the amount of miRNA target genes are largely distinguished.6. The predicted miRNA were classified to three group by GO function, and deeply research showed that miRNA target genes were regulated by miRNA in many fields as biological process, cellular component, molecular function and so forth.7. The evolutionary analysis between new miRNA and determined miRNA.