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Molecular and Cellular Biology, January 2007, p. 92-101, Vol. 27, No. 1
0270-7306/07/$08.00+0     doi:10.1128/MCB.01023-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Cytoplasmic Decay of Intergenic Transcripts in Saccharomyces cerevisiae

Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, Arizona 85721

Received 7 June 2006/ Returned for modification 11 October 2006/ Accepted 17 October 2006

Eukaryotes produce a number of noncoding transcripts from intergenic regions. In Saccharomyces cerevisiae, such cryptic unstable transcripts (CUTs) are thought to be degraded in the nucleus by a process involving polyadenylation and 3'-to-5' degradation by the nuclear exosome. In this work, we examine the degradation pathway of the RNA SRG1, which is produced from an intergenic region and contributes to the regulation of the SER3 gene by promoter occlusion during SRG1 transcription. Although there is some effect on SRG1 transcript levels when the nuclear exosome is compromised, the bulk of the SRG1 RNA is degraded in the cytoplasm by decapping and 5'-to-3' exonucleolytic digestion. Examination of other CUTs suggests that individual CUTs can be degraded by a variety of different mechanisms, including nuclear decay, cytoplasmic decapping and 5'-to-3' decay, and nonsense-mediated decay. Moreover, some CUTs appear to be associated with polyribosomes. These results indicate that some CUTs can be exported from the nucleus and enter translation before being degraded, identifying a potential mechanism for the evolution of new protein-encoding genes.

Published ahead of print on 30 October 2006.

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