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Eukaryotic Cell, June 2008, p. 1009-1018, Vol. 7, No. 6
1535-9778/08/$08.00+0     doi:10.1128/EC.00057-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Genomewide Recruitment Analysis of Rpb4, a Subunit of Polymerase II in Saccharomyces cerevisiae, Reveals Its Involvement in Transcription Elongation ^,

Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India,¹ Genotypic Technology, Bangalore, India 560094,² Agilent Technologies, Tokyo, Japan 192-8510³

Received 13 February 2008/ Accepted 12 April 2008

The Rpb4/Rpb7 subcomplex of yeast RNA polymerase II (Pol II) has counterparts in all multisubunit RNA polymerases from archaebacteria to higher eukaryotes. The Rpb4/7 subcomplex in Saccharomyces cerevisiae is unique in that it easily dissociates from the core, unlike the case in other organisms. The relative levels of Rpb4 and Rpb7 in yeasts affect the differential gene expression and stress response. Rpb4 is nonessential in S. cerevisiae and affects expression of a small number of genes under normal growth conditions. Here, using a chromatin immunoprecipitation ("ChIP on-chip") technique, we compared genomewide binding of Rpb4 to that of a core Pol II subunit, Rpb3. Our results showed that in spite of being nonessential for survival, Rpb4 was recruited on coding regions of most transcriptionally active genes, similar to the case with the core Pol II subunit, Rpb3, albeit to a lesser extent. The extent of Rpb4 recruitment increased with increasing gene length. We also observed Pol II lacking Rpb4 to be defective in transcribing long, GC-rich transcription units, suggesting a role for Rpb4 in transcription elongation. This role in transcription elongation was supported by the observed 6-azauracil (6AU) sensitivity of the rpb4 mutant. Unlike most phenotypes of rpb4, the 6AU sensitivity of the rpb4 strain was not rescued by overexpression of RPB7. This report provides the first instance of a distinct role for Rpb4 in transcription, which is independent of its interacting partner, Rpb7.

Published ahead of print on 25 April 2008.

Supplemental material for this article may be found at http://ec.asm.org/.