Gene expression is controlled by a variety of proteins that interact with the genome. Their precise organization and mechanism of action at every promoter remains to be worked out. To better understand the physical interplay among genome-interacting proteins, we examined the temporal binding of a functionally diverse subset of these proteins: nucleosomes (H3), H2AZ (Htz1), SWR (Swr1), RSC (Rsc1, Rsc3, Rsc58, Rsc6, Rsc9, Sth1), SAGA (Spt3, Spt7, Ubp8, Sgf11), Hsf1, TFIID (Spt15/TBP and Taf1), TFIIB (Sua7), TFIIH (Ssl2), FACT (Spt16), Pol II (Rpb3), and Pol II carboxyl-terminal domain (CTD) phosphorylation at serines 2, 5, and 7. They were examined under normal and acute heat shock conditions, using the ultrahigh resolution genome-wide ChIP-exo assay in Saccharomyces cerevisiae. Our findings reveal a precise positional organization of proteins bound at most genes, some of which rapidly reorganize within minutes of heat shock. This includes more precise positional transitions of Pol II CTD phosphorylation along the 5′ ends of genes than previously seen. Reorganization upon heat shock includes colocalization of SAGA with promoter-bound Hsf1, a change in RSC subunit enrichment from gene bodies to promoters, and Pol II accumulation within promoter/+1 nucleosome regions. Most of these events are widespread and not necessarily coupled to changes in gene expression. Together, these findings reveal protein–genome interactions that are robustly reprogrammed in precise and uniform ways far beyond what is elicited by changes in gene expression.

基因表达由多种与基因组相互作用的蛋白质控制。他们在每个发起人身上的精确组织和行动机制仍有待制定。为了更好地了解基因组相互作用蛋白之间的物理相互作用，我们检查了这些蛋白的功能多样化子集的时间结合：核小体 (H3)、H2AZ (Htz1)、SWR (Swr1)、RSC (Rsc1、Rsc3、Rsc58、Rsc6) 、Rsc9、Sth1)、SAGA（Spt3、Spt7、Ubp8、Sgf11）、Hsf1、TFIID（Spt15/TBP 和 Taf1）、TFIIB（Sua7）、TFIIH（Ssl2）、FACT（Spt16）、Pol II（Rpb3）和Pol II 羧基末端结构域 (CTD) 在丝氨酸 2、5 和 7 处的磷酸化。在正常和急性热休克条件下，使用酿酒酵母中的超高分辨率全基因组 ChIP-exo 检测对它们进行了检查。我们的研究结果揭示了与大多数基因结合的蛋白质的精确位置组织，其中一些在热激后几分钟内迅速重组。这包括 Pol II CTD 磷酸化沿着基因 5' 末端比以前看到的更精确的位置转换。热激后的重组包括 SAGA 与启动子结合的 Hsf1 的共定位、RSC 亚基富集从基因体到启动子的变化以及启动子/+1 核小体区域内的 Pol II 积累。大多数这些事件是广泛存在的，并且不一定与基因表达的变化相关。总之，这些发现揭示了蛋白质与基因组的相互作用，这种相互作用以精确和统一的方式进行了强有力的重新编程，远远超出了基因表达变化引起的作用。