This Article Full Text Full Text (PDF) Other Versions of this Article: MCB.00380-08v1 28/12/3883    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Google Scholar Articles by Jenks, M. H. Articles by Reines, D. PubMed PubMed Citation Articles by Jenks, M. H. Articles by Reines, D.

Next Article 

Molecular and Cellular Biology, June 2008, p. 3883-3893, Vol. 28, No. 12
0270-7306/08/$08.00+0     doi:10.1128/MCB.00380-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Properties of an Intergenic Terminator and Start Site Switch That Regulate IMD2 Transcription in Yeast

M. Harley Jenks, Thomas W. O'Rourke, and Daniel Reines^*

Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322

Received 5 March 2008/ Returned for modification 1 April 2008/ Accepted 8 April 2008

The IMD2 gene in Saccharomyces cerevisiae is regulated by intracellular guanine nucleotides. Regulation is exerted through the choice of alternative transcription start sites that results in synthesis of either an unstable short transcript terminating upstream of the start codon or a full-length productive IMD2 mRNA. Start site selection is dictated by the intracellular guanine nucleotide levels. Here we have mapped the polyadenylation sites of the upstream, unstable short transcripts that form a heterogeneous family of RNAs of 200 nucleotides. The switch from the upstream to downstream start sites required the Rpb9 subunit of RNA polymerase II. The enzyme's ability to locate the downstream initiation site decreased exponentially as the start was moved downstream from the TATA box. This suggests that RNA polymerase II's pincer grip is important as it slides on DNA in search of a start site. Exosome degradation of the upstream transcripts was highly dependent upon the distance between the terminator and promoter. Similarly, termination was dependent upon the Sen1 helicase when close to the promoter. These findings extend the emerging concept that distinct modes of termination by RNA polymerase II exist and that the distance of the terminator from the promoter, as well as its sequence, is important for the pathway chosen.

Published ahead of print on 21 April 2008.

These authors contributed equally to this work.