Transcription factor TFIIH is required for promoter melting in vivo

The Rad25 protein in yeast is a DNA helicase and a subunit of the general t ranscription factor TFIIH. While in vitro studies have led to the hypothesi s that TFIIH helicase activity plays a role in promoter melting, in vivo te sts are lacking. Using potassium permanganate, which preferentially modifie s single-stranded DNA, we show that a temperature-sensitive rad25(ts) mutan t severely reduces the normally extensive promoter melting observed in vivo on the highly expressed genes TDH2 and PDC1 and on the induced heat shock gene HSP82, Loss of promoter melting can be observed in as little as 30 s a fter a shift to the nonpermissive temperature and is accompanied by a drama tic reduction in transcription. These effects on the promoter are specific, since the mutation does not affect TATA box occupancy or, in the case of H SP82, recruitment of TATA-binding protein to the TATA element or that of he at shock factor to heat shock elements. Additionally, using the technique o f formaldehyde cross-linking coupled with restriction endonuclease cleavage and ligation-mediated PCR, we: were able to map the polymerase density on the promoter of HSP82, This high-resolution mapping allowed us to determine that the polymerase II (Pol II) density on the promoter is also dramatical ly reduced after inactivation of TFIIH. These data provide strong support f or the:hypothesis that TFIIH functions with Pol II in the transcriptionally required step of promoter melting and show, surprisingly, that the extent of TFIIH-dependent promoter melting observed in vivo is several times large r than that seen in vitro.