During productive infection by herpes simplex virus 1 (HSV-1), viral gene expression occurs in a temporally regulated cascade in which transcription of the viral immediate-early (IE) genes is strongly stimulated by the virion protein VP16. We have employed an oligonucleotide microarray to examine the effect of VP16 mutations on the overall pattern of viral gene expression following infection of HeLa cells. This microarray detects essentially all HSV-1 transcripts with relative and absolute levels correlating well with known kinetics of expression. This analysis revealed that deletion of the VP16 activation domain sharply reduced overall viral gene expression; moreover, the pattern of this reduced expression varied greatly from the pattern of a wild-type (wt) infection. However, when this mutant virus was delivered at a high multiplicity of infection or in the presence of the cellular stress inducer hexamethylene bisacetamide, expression was largely restored to the wt levels and pattern. Infection with virions that deliver wt VP16 protein at the start of infection but synthesize only truncated VP16 resulted in a normal kinetic cascade. This suggests that newly synthesized VP16 does not play a significant role in the expression of later classes of transcripts. The VP16 activation domain comprises two subregions. Deletion of the C-terminal subregion resulted in minimal changes in the level and profile of gene expression compared to a normal (wt) cascade. In contrast, deletion of the N-terminal subregion reduced the overall expression levels and skewed the relative levels of IE transcripts but did not significantly alter the kinetic pattern of early and late transcript expression. We conclude that the general activation of IE gene transcription by VP16, but not the specific ratios of IE transcripts, is necessary for the subsequent ordered expression of viral genes. Moreover, this report establishes the feasibility of microarray analysis for globally assessing viral gene expression programs as a function of the conditions of infection.During productive infection of mammalian cells by herpes simplex virus type 1 (HSV-1), transcription of the viral genes occurs in a coordinated cascade (11, 28; reviewed in references 34 and 37). The five viral immediate-early (IE) genes are transcribed rapidly upon viral entry and uncoating. Synthesis of the IE proteins peaks at approximately 2 to 4 h postinfection (hpi), but they continue to accumulate throughout the infection. The IE proteins stimulate the expression of the early (E) and late (L) genes and also have autoregulatory functions.The virion protein VP16 activates transcription of the IE genes through specific sequence elements in the IE promoters (reviewed in reference 19). VP16 interacts with the viral DNA template by associating with the cellular proteins Oct-1 and HCF-1 at promoter elements containing the sequence TAAT-GARAT (where R represents purine) (reviewed in reference 9). Activation by VP16 is also exerted through DNA sequences bound by the cellular protein GABP ...