Heat shock rapidly activates expression of some genes and represses others. The kinetics of changes in RNA polymerase distribution on heat shock-modulated genes provides a framework for evaluating the mechanisms of activation and repression of transcription. Here, using two methods, we examined the changes in RNA polymerase II association on a set of Drosophila genes at 30-s intervals following an instantaneous heat shock. In the first method, Drosophila Schneider line 2 cells were quickly frozen to halt transcription, and polymerase distribution was analyzed by a nuclear run-on assay. RNA polymerase transcription at the 5' end of the hsp7O gene could be detected within 30 to 60 s of induction, and by 120 s the first wave of polymerase could already be detected near the 3' end of the gene. A similar rapid induction was found for the small heat shock genes (hsp22, hsp23, hsp26, and hsp27). In contrast to this rapid activation, transcription of the histone Hi gene was found to be rapidly repressed, with transcription reduced by -90%o within 300 s of heat shock. Similar results were obtained by an in vivo UV cross-linking assay. In this second method, cell samples removed at 30-s intervals were irradiated with 40-,us bursts of UV light from a Xenon flash lamp, and the distribution of polymerase was examined by precipitating UV cross-linked protein-DNA complexes with an antibody to RNA polymerase II. Both approaches also showed the in vivo rate of movement of the first wave of RNA polymerase through the hsp7O gene to be -1.2 kb/min.Transcriptional activation of Drosophila heat shock genes can occur within minutes of exposure to a heat shock stimulus. It was previously found that within 2 min of exposing Drosophila larvae to a temperature of 37°C a distinct puff could be seen at cytological position 63B (which contains the heat shock gene hsp83) and that this puff reached its maximum size within 5 min (1). Incorporation of [3H]uridine was also found at the 87A and 87C loci (which together contain five copies of the hsp70 gene) within 1 min of heat shock (1), suggesting a rapid transcriptional response. In support of this finding, mRNA transcribed from the hsp70 gene can be detected as early as 4 min after shifting Schneider line 2 (SL2) cells to the full heat shock temperature, and an increase in the level of HSP70 can be detected as early as 8 to 12 min after heat shock (19). 46 bases (9,26,28). This polymerase presumably resumes elongation into the body of the gene once the promoter becomes activated. Pausing of polymerase has also been detected at the 5' ends of the hsp26 (9, 26, 29), hsp23 (25), and hsp27 genes (26). A promoter that already contains an initiated polymerase could be capable of responding very rapidly to an increase in temperature. To measure the rapidity of this response, SL2 cells were exposed to an instantaneous heat shock (by adding an equal volume of 56°C tissue culture medium), samples were removed at 30-s intervals, and then they were rapidly frozen in liquid nitrogen. After isolation of the...