Prediction of Mammalian MicroRNA Targets

04/06/2004

吳政道

Abstract

MicroRNAs (miRNAs) are endogenous ~22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression(Bartel, 2004). Recently, based on biochemical approaches and genome-wide, sequence-based computational predictions, more than 300 miRNAs have been reported by cloning endogenous RNAs and in silicon analysis(Ambros et al., 2003; Grad et al., 2003; Griffiths-Jones, 2004). However, no experimental or computational high-throughput method for target site identification in mammalian has been published yet. In this paper, based on genome-wide, sequence-based computational predictions, the authors developed informatics methods to predict more than 400 regulatory target genes, 11 out of 15 tested were validated experimentally using a HeLa cell reporter system. In addition, the authors also evaluated the frequency of specific gene ontology (GO) molecular function classification among the predicted targets of the miRNAs and suggested that the predicted regulatory targets were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions.

From: Cell. 2003 Dec 26;115(7):787-98.

References

Ambros,V., Bartel,B., Bartel,D.P., Burge,C.B., Carrington,J.C., Chen,X., Dreyfuss,G., Eddy,S.R., Griffiths-Jones,S., Marshall,M., Matzke,M., Ruvkun,G., and Tuschl,T. (2003). A uniform system for microRNA annotation. RNA. 9, 277-279.

Bartel,D.P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.

Grad,Y., Aach,J., Hayes,G.D., Reinhart,B.J., Church,G.M., Ruvkun,G., and Kim,J. (2003). Computational and experimental identification of C. elegans microRNAs. Mol. Cell 11, 1253-1263.

Griffiths-Jones,S. (2004). The microRNA Registry. Nucleic Acids Res. 32 Database issue, D109-D111.