The stress response in yeast cells is regulated by at least two classes of transcription activators-HSF and Msn2/4, which differentially affect promoter chromatin remodeling. We demonstrate that the deletion of SNF2, an ATPase activity-containing subunit of the chromatin remodeling SWI/SNF complex, eliminates histone displacement, RNA polymerase II recruitment, and heat shock factor (HSF) binding at the HSP12 promoter while delaying these processes at the HSP82 and SSA4 promoters. Out of the three promoters, the double deletion of MSN2 and MSN4 eliminates both chromatin remodeling and HSF binding only at the HSP12 promoter, suggesting that Msn2/4 activators are primary determinants of chromatin disassembly at the HSP12 promoter. Unexpectedly, during heat shock the level of Msn2/4 at the HSP12 promoter declines. This is likely a result of promoter-targeted Msn2/4 degradation associated with transcription complex assembly. While histone displacement kinetic profiles bear clear promoter specificity, the kinetic profiles of recovery from heat shock for all analyzed genes display an equal or even higher nucleosome return rate, which is to some extent delayed by the deletion of SNF2.The stress response in yeast cells is regulated by at least two types of transcriptional activators: heat shock factor (HSF) and the partially redundant Msn2 and Msn4 (Msn2/4) activators (7,19). The HSF system is highly conserved in its overall composition and function from yeast to humans (61). HSF binds to the major groove of DNA in heat shock promoter elements (HSEs), which are also conserved from yeast to humans (61). The activity of HSF is regulated via several distinct pathways. These include a monomer-trimer transition (45), phosphorylation, and other posttranslational modifications (30, 31, 54), as well as repression by molecular chaperones interacting with HSF, thus blocking their own production (45, 60) and forming a self-regulatory loop.The Msn2/4 system is more specific to Saccharomyces cerevisiae. The Msn2 and Msn4 factors recognize and bind stress response element (STRE) sequences (44) in promoter regions of a large array of genes partially overlapping the HSF-regulated array (3,7,22,46). The Msn2 factor seems to have a more pronounced role, since mutants lacking only Msn2 have an already distinct decrease in STRE-regulated transcription; however, only MSN2 and MSN4 double deletions exhibit pleiotropic stress sensitivity (19). Under stress, Msn2/4 accumulate in the nucleus within a few minutes (24, 32). The Msn2/4 factors are regulated by efficient and oscillatory nuclear transport (32), hyperphosphorylation upon stress (21, 24), and degradation associated with transcription initiation (37, 38). While the HSF system is actively involved in chromatin remodeling events at gene promoters, the role of the Msn2/4 system in these processes is poorly understood.Chromatin remodeling varies in intensity and intermediate states between genes. The most evident and intense examples of chromatin remodeling are the changes taking place at ...

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