Genome wide recruitment analysis of Rpb4, a subunit of Pol II in Saccharomyces cerevisiae reveals its involvement in transcription elongation

Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore, 560 012, India; Genotypic technology, Bangalore, India 560094; Agilent technologies, Japan 192-8510

^* To whom correspondence should be addressed. Email: pps{at}mcbl.iisc.ernet.in.

	Abstract

Rpb4/Rpb7 subcomplex of yeast RNA polymerase II has counterparts in all multi-subunit RNA polymerases from archaebacteria to higher eukaryotes. The Rpb4/7 subcomplex in S. cerevisiae is unique in that it easily dissociates from the core, unlike in other organisms. The relative levels of Rpb4 and Rpb7 in yeasts affect 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 ChIP on chip technique, we compared genome wide 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 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 sensitivity of rpb4 mutant. Unlike most phenotypes of rpb4, the 6AU sensitivity of rpb4 strain was not rescued by over expression of RPB7. This report provides the first instance of a distinct role for Rpb4 in transcription, which is independent of its interacting partner, Rpb7.