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Molecular and Cellular Biology, July 2004, p. 6241-6252, Vol. 24, No. 14
0270-7306/04/$08.00+0     DOI: 10.1128/MCB.24.14.6241-6252.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Identification of cis Elements Directing Termination of Yeast Nonpolyadenylated snoRNA Transcripts

Kristina L. Carroll,1 Dennis A. Pradhan,1 Josh A. Granek,2 Neil D. Clarke,2 and Jeffry L. Corden1*

Department of Molecular Biology and Genetics,1 Department of Biophysics and Biophysical Chemistry, School of Medicine, The Johns Hopkins University, Baltimore, Maryland 212052

Received 18 February 2004/ Returned for modification 22 March 2004/ Accepted 14 April 2004

RNA polymerase II (Pol II) termination is triggered by sequences present in the nascent transcript. Termination of pre-mRNA transcription is coupled to recognition of cis-acting sequences that direct cleavage and polyadenylation of the pre-mRNA. Termination of nonpolyadenylated [non-poly(A)] Pol II transcripts in Saccharomyces cerevisiae requires the RNA-binding proteins Nrd1 and Nab3. We have used a mutational strategy to characterize non-poly(A) termination elements downstream of the SNR13 and SNR47 snoRNA genes. This approach detected two common RNA sequence motifs, GUA[AG] and UCUU. The first motif corresponds to the known Nrd1-binding site, which we have verified here by gel mobility shift assays. We also show that Nab3 protein binds specifically to RNA containing the UCUU motif. Taken together, our data suggest that Nrd1 and Nab3 binding sites play a significant role in defining non-poly(A) terminators. As is the case with poly(A) terminators, there is no strong consensus for non-poly(A) terminators, and the arrangement of Nrd1p and Nab3p binding sites varies considerably. In addition, the organization of these sequences is not strongly conserved among even closely related yeasts. This indicates a large degree of genetic variability. Despite this variability, we were able to use a computational model to show that the binding sites for Nrd1 and Nab3 can identify genes for which transcription termination is mediated by these proteins.

* Corresponding author. Mailing address: Department of Molecular Biology and Genetics, Johns Hopkins Medical School, 725 N. Wolfe St., Baltimore, MD 21205. Phone: (410) 955-4719. Fax: (410) 502-6718. E-mail: jcorden{at}jhmi.edu.

Molecular and Cellular Biology, July 2004, p. 6241-6252, Vol. 24, No. 14
0022-538X/04/$08.00+0     DOI: 10.1128/MCB.24.14.6241-6252.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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