Our long-term objective is to understand molecular mechanisms of transcription modulation in eukaryotes. The promoters of the uninduced heat shock genes are primed for a rapid response to heat shock. This type of control is not heat shock specific, as we and others find paused Pol II associated with the 5' ends of other Drosophila and human genes.
Activation refers to the induced increase in the rate of transcription.
Heat shock triggers the trimerization and highly specific binding of HSF to heat shock gene promoters, resulting in a 200-fold increase in transcription. The mechanism by which HSF stimulates this dramatic and rapid increase in transcription is not understood, but it is clearly distinct from regulatory models in which activators recruit Pol II or general transcription factors to a promoter. Pol II is already recruited to promoters that display pausing, and this recruited Pol II encounters what appears to be a rate-limiting step early in its elongation. Fortunately, a large and growing repertoire of highly-specific antibodies to a variety of specific and general transcription factors are available for these CLIP assays, and we are using these to define when and where these proteins act in both the potentiation and activation of genes. We are using a variety of fast-acting conditional mutants in Drosophila proteins that we hypothesize are critical for both promoter potentiation and activation.