Yeast NC2 Associates with the RNA Polymerase II Preinitiation Complex and Selectively Affects Transcription In Vivo

Abstract

NC2 (Dr1-Drap1 or Bur6-Ydr1) has been characterized in vitro as a general negative regulator of RNA polymerase II (Pol II) transcription that interacts with TATA-binding protein (TBP) and inhibits its function. Here, we show that NC2 associates with promoters in vivo in a manner that correlates with transcriptional activity and with occupancy by basal transcription factors. NC2 rapidly associates with promoters in response to transcriptional activation, and it remains associated under conditions in which transcription is blocked after assembly of the Pol II preinitiation complex. NC2 positively and negatively affects approximately 17% of Saccharomyces cerevisiaegenes in a pattern that resembles the response to general environmental stress. Relative to TBP, NC2 occupancy is high at promoters where NC2 is positively required for normal levels of transcription. Thus, NC2 is associated with the Pol II preinitiation complex, and it can play a direct and positive role at certain promoters in vivo.

ACKNOWLEDGMENTS

We are particularly grateful to Danny Reinberg for providing the bur6 temperature-sensitive strain and for fruitful discussions on NC2 function. We also thank Jim Kadonaga for communicating unpublished information about positive and negative functions of NC2 in vitro and Laurent Kuras and Mario Mencia for advice and commentary throughout the course of the work.

This work was supported by research grants from the National Institutes of Health to K.S. (GM 30186 and GM 53720) and R.A.Y. (GM 34365).