Co-Authors:
German, M.A., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Pillay, M., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Jeong, D.-H., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Hetawal, A., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Luo, S., Illumina, Inc., 25861 Industrial Blvd., Hayward, CA 94545, United States
Janardhanan, P., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Kannan, V., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Rymarquis, L.A., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Nobuta, K., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
German, R., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
De Paoli, E., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Lu, C., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Schroth, G., Illumina, Inc., 25861 Industrial Blvd., Hayward, CA 94545, United States
Meyers, B.C., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Green, P.J., Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, United States
Abstract:
MicroRNAs (miRNAs) are important regulatory molecules in most eukaryotes and identification of their target mRNAs is essential for their functional analysis. Whereas conventional methods rely on computational prediction and subsequent experimental validation of target RNAs, we directly sequenced >28,000,000 signatures from the 5′ ends of polyadenylated products of miRNA-mediated mRNA decay, isolated from inflorescence tissue of Arabidopsis thaliana, to discover novel miRNA-target RNA pairs. Within the set of ∼27,000 transcripts included in the 8,000,000 nonredundant signatures, several previously predicted but nonvalidated targets of miRNAs were found. Like validated targets, most showed a single abundant signature at the miRNA cleavage site, particularly in libraries from a mutant deficient in the 5′-to-3′ exonuclease AtXRN4. Although miRNAs in Arabidopsis have been extensively investigated, working in reverse from the cleaved targets resulted in the identification and validation of novel miRNAs. This versatile approach will affect the study of other aspects of RNA processing beyond miRNA-target RNA pairs. © 2008 Nature Publishing Group.
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