Yeast NC2 associates with the RNA polymerase II preinitiation complex and selectively affects transcription in vivo

NC2 (Dr1-Drap1 or Bur6-Ydr1) has been characterized in vitro as a general n egative regulator of RNA polymerase II (Pol II) transcription that interact s 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 acti vation, and it remains associated under conditions in which transcription i s blocked after assembly of the Pol II preinitiation complex. NC2 positivel y and negatively affects approximately 17% of Saccharomyces cerevisiae gene s in a pattern that resembles the response to general environmental stress. Relative to TBP, NC2 occupancy is high at promoters where NC2 is positivel y required for normal levels of transcription. Thus, NC2 is associated with the Pol II preinitiation complex, and it can play a direct and positive ro le at certain promoters in vivo.