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J. Biol. Chem., Vol. 278, Issue 35, 33000-33010, August 29, 2003

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Organization and Function of APT, a Subcomplex of the Yeast Cleavage and Polyadenylation Factor Involved in the Formation of mRNA and Small Nucleolar RNA 3'-Ends^*

Eduard Nedea  , Xiaoyuan He ¶, Minkyu Kim ||, Jeff Pootoolal , Guoqing Zhong , Veronica Canadien **, Timothy Hughes , Stephen Buratowski || , Claire L. Moore ¶ and Jack Greenblatt  ** 

From the Banting and Best Department of Medical Research and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5G 1L6, Canada, the ^¶Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, the ^||Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, and ^**Affinium Pharmaceuticals, Toronto, Ontario M5J 1V6, Canada

Messenger RNA 3'-end formation is functionally coupled to transcription by RNA polymerase II. By tagging and purifying Ref2, a non-essential protein previously implicated in mRNA cleavage and termination, we isolated a multiprotein complex, holo-CPF, containing the yeast cleavage and polyadenylation factor (CPF) and six additional polypeptides. The latter can form a distinct complex, APT, in which Pti1, Swd2, a type I protein phosphatase (Glc7), Ssu72 (a TFIIB and RNA polymerase II-associated factor), Ref2, and Syc1 are associated with the Pta1 subunit of CPF. Systematic tagging and purification of holo-CPF subunits revealed that yeast extracts contain similar amounts of CPF and holo-CPF. By purifying holo-CPF from strains lacking Ref2 or containing truncated subunits, subcomplexes were isolated that revealed additional aspects of the architecture of APT and holo-CPF. Chromatin immunoprecipitation was used to localize Ref2, Ssu72, Pta1, and other APT subunits on small nucleolar RNA (snoRNA) genes and primarily near the polyadenylation signals of the constitutively expressed PYK1 and PMA1 genes. Use of mutant components of APT revealed that Ssu72 is important for preventing readthrough-dependent expression of downstream genes for both snoRNAs and polyadenylated transcripts. Ref2 and Pta1 similarly affect at least one snoRNA transcript.

Received for publication, April 29, 2003 , and in revised form, June 19, 2003.

^* This work was supported in part by grants from the Canadian Institutes of Health Research, the National Cancer Institute of Canada, the Canadian Cancer Society (to J. G.), by National Institutes of Health Grants GM41752 (to C. M.) and GM56663 (to S. B.), and by a Canadian Institutes of Health Research Operating Grant MOP 49451 (to T. H.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Supported by a C. H. Best doctoral fellowship.

Scholar of the Leukemia and Lymphoma Society.

To whom correspondence should be addressed: Banting and Best Dept. of Medical Research, University of Toronto, 112 College St., Rm. 210, Toronto, Ontario M5G 1L6, Canada. Tel.: 416-978-4141; Fax: 416-978-8528, E-mail: jack.greenblatt{at}utoronto.ca.

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