Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome MicroRNAs (miRNAs) regulate the expression of target mRNAs in plants and animals (1) . Plant miRNA targets have been predicted on the basis of their extensive and often conserved complementarity to the miRNAs (2–4) , as well as on miRNA overexpression experiments (5) ; many of these target predictions have been confirmed by isolation of the products of miRNA-directed cleavage. Here, we present a transcriptome-wide experimental method, called “degradome sequencing,” to directly detect cleaved miRNA targets without relying on predictions or overexpression. The 5′ ends of polyadenylated, uncapped mRNAs from Arabidopsis were directly sampled, resulting in an empirical snapshot of the degradome. miRNA-mediated-cleavage products were easily discerned from an extensive background of degraded mRNAs, which collectively covered the majority of the annotated transcriptome. Many previously known Arabidopsis miRNA targets were confirmed, and several novel targets were also discovered. Quantification of cleavage fragments revealed that those derived from TAS transcripts, which are unusual in their production of abundant secondary small interfering RNAs (siRNAs), accumulated to very high levels. A subset of secondary siRNAs are also known to direct cleavage of targets in trans (6) ; degradome sequencing revealed many cleaved targets of these trans -acting siRNAs (ta-siRNAs). This empirical method is broadly applicable to the discovery and quantification of cleaved targets of small RNAs without a priori predictions. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Current Biology Elsevier

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

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Publisher
Elsevier
Copyright
Copyright © 2008 Elsevier Ltd
ISSN
0960-9822
D.O.I.
10.1016/j.cub.2008.04.042
Publisher site
See Article on Publisher Site

Abstract

MicroRNAs (miRNAs) regulate the expression of target mRNAs in plants and animals (1) . Plant miRNA targets have been predicted on the basis of their extensive and often conserved complementarity to the miRNAs (2–4) , as well as on miRNA overexpression experiments (5) ; many of these target predictions have been confirmed by isolation of the products of miRNA-directed cleavage. Here, we present a transcriptome-wide experimental method, called “degradome sequencing,” to directly detect cleaved miRNA targets without relying on predictions or overexpression. The 5′ ends of polyadenylated, uncapped mRNAs from Arabidopsis were directly sampled, resulting in an empirical snapshot of the degradome. miRNA-mediated-cleavage products were easily discerned from an extensive background of degraded mRNAs, which collectively covered the majority of the annotated transcriptome. Many previously known Arabidopsis miRNA targets were confirmed, and several novel targets were also discovered. Quantification of cleavage fragments revealed that those derived from TAS transcripts, which are unusual in their production of abundant secondary small interfering RNAs (siRNAs), accumulated to very high levels. A subset of secondary siRNAs are also known to direct cleavage of targets in trans (6) ; degradome sequencing revealed many cleaved targets of these trans -acting siRNAs (ta-siRNAs). This empirical method is broadly applicable to the discovery and quantification of cleaved targets of small RNAs without a priori predictions.

Journal

Current BiologyElsevier

Published: May 20, 2008

References

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