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ISSN 1672-9145                                                Acta Biochim Biophys Sin 2005, 37(2): 75–87                                                   CN 31-1940/Q

Computational Identification of Novel Family Members of MicroRNA Genes in Arabidopsis thaliana and Oryza sativa

Yang LI, Wei LI, and You-Xin JIN*

 

State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences,

Chinese Academy of Sciences, Shanghai 200031, China

 

Abstract        MicroRNAs (miRNAs) are a class of endogenous small RNAs that play important regulatory roles in both animals and plants. miRNA genes have been intensively studied in animals, but not in plants. In this study, we adopted a homology search approach to identify homologs of previously validated plant miRNAs in Arabidopsis thaliana and Oryza sativa. We identified 20 potential miRNA genes in Arabidopsis and 40 in O. sativa, providing a relatively complete enumeration of family members for these miRNAs in plants. In addition, a greater number of Arabidopsis miRNAs (MIR168, MIR159 and MIR172) were found to be conserved in rice. With the novel homologs, most of the miRNAs have closely related fellow miRNAs and the number of paralogs varies in the different miRNA families. Moreover, a probable functional segment highly conserved on the elongated stem of pre-miRNA fold-backs of MIR319 and MIR159 family was identified. These results support a model of variegated miRNA regulation in plants, in which miRNAs with different functional elements on their pre-miRNA fold-backs can differ in their function or regulation, and closely related miRNAs can be diverse in their specificity or competence to downregulate target genes. It appears that the sophisticated regulation of miRNAs can achieve complex biological effects through qualitative and quantitative modulation of gene expression profiles in plants.

 

Key words        microRNA; post-transcriptional gene silencing; rice; Arabidopsis

 

 

 

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Received: September 8, 2004        Accepted: December 14, 2004

This work was supported by the grants from ­the National Natural Science Foundation of China (No. 30430210) and the Chinese Academy­ of Sciences (No. KSCX-2-2-04)

*Corresponding author: Tel, 86-21-54921222; Fax, 86-21-54921011; E-mail, [email protected]