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Molecular and Cellular Biology, October 2003, p. 6982-6992, Vol. 23, No. 19
0270-7306/03/$08.00+0     DOI: 10.1128/MCB.23.19.6982-6992.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Rrp47p Is an Exosome-Associated Protein Required for the 3' Processing of Stable RNAs

Wellcome Trust Centre for Cell Biology, Institute for Cell and Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom,¹ Centre for Experimental Bioinformatics, University of Southern Denmark, DK-5230 Odense M, Denmark²

Received 7 April 2003/ Returned for modification 23 May 2003/ Accepted 3 July 2003

Related exosome complexes of 3'5' exonucleases are present in the nucleus and the cytoplasm. Purification of exosome complexes from whole-cell lysates identified a Mg²⁺-labile factor present in substoichiometric amounts. This protein was identified as the nuclear protein Yhr081p, the homologue of human C1D, which we have designated Rrp47p (for rRNA processing). Immunoprecipitation of epitope-tagged Rrp47p confirmed its interaction with the exosome and revealed its association with Rrp6p, a 3'5' exonuclease specific to the nuclear exosome fraction. Northern analyses demonstrated that Rrp47p is required for the exosome-dependent processing of rRNA and small nucleolar RNA (snoRNA) precursors. Rrp47p also participates in the 3' processing of U4 and U5 small nuclear RNAs (snRNAs). The defects in the processing of stable RNAs seen in rrp47- strains closely resemble those of strains lacking Rrp6p. In contrast, Rrp47p is not required for the Rrp6p-dependent degradation of 3'-extended nuclear pre-mRNAs or the cytoplasmic 3'5' mRNA decay pathway. We propose that Rrp47p functions as a substrate-specific nuclear cofactor for exosome activity in the processing of stable RNAs.

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