Identification of novel microRNA genes and prediction of their target genes from sea squirt(Ciona intestinalis)
MicroRNAs(miRNAs),a class of non-coding small RNAs with the length of approximately 22 nucleotides,have been shown to regulate gene expression by base pairing to target mRNA.In this study,BLAST was used to screen the Ciona intestinalis genome with miRNA probe from nematodes,fruit flies amphioxus and human,and combined with the secondary structure of miRNA and SVM analysis,a total of 10 novel miRNAs were found.Using the 10 miRNAs as queries,we predicted 225 potential target genes,which mainly involved in cell metabolism,regulation of transcription,binding activity and other functions.The identification of sea squirts novel miRNAs may provide important clues for the studies of miRNA.Furthermore,our works may provide a theoretical basis for the origin and evolution of vertebrate miRNAs.