Cell
Volume 131, Issue 7, 28 December 2007, Pages 1340-1353
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Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome

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Summary

The exosome complex plays a central and essential role in RNA metabolism. However, comprehensive studies of exosome substrates and functional analyses of its subunits are lacking. Here, we demonstrate that as opposed to yeast and metazoans the plant exosome core possesses an unanticipated functional plasticity and present a genome-wide atlas of Arabidopsis exosome targets. Additionally, our study provides evidence for widespread polyadenylation- and exosome-mediated RNA quality control in plants, reveals unexpected aspects of stable structural RNA metabolism, and uncovers numerous novel exosome substrates. These include a select subset of mRNAs, miRNA processing intermediates, and hundreds of noncoding RNAs, the vast majority of which have not been previously described and belong to a layer of the transcriptome that can only be visualized upon inhibition of exosome activity. These first genome-wide maps of exosome substrates will aid in illuminating new fundamental components and regulatory mechanisms of eukaryotic transcriptomes.

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8

These authors contributed equally to this work.

9

Present address: Albert Eye Research Institute, Duke University Eye Center, Durham, NC 27710, USA.

10

Present address: Department of Molecular Biology, Cornell University, Ithaca, NY 14853.

11

Present address: Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA.

12

Present address: Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA.

13

Present address: School of Biological Sciences, University of Missouri—Kansas City, Kansas City, MO 64110, USA.