An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters [RNA-Seq]

Genome-wide, little is understood about how proteins organize at inducible promoters before and after in-duction, and to what extent inducible and constitutive architectures depend on cofactors. We report that se-quence-specific transcription factors and their tethered cofactors (e.g., SAGA, Mediator, TUP, NuA4, SWI/SNF, RPD3-L) are already bound to promoters prior to induction (“poised”), rather than recruited upon induction, whereas induction recruits the pre-initiation complex (PIC). Through depletion and/or deletion ex-periments we show that SAGA does not function at constitutive promoters, although a SAGA-independent Gcn5 does acetylate +1 nucleosomes there. At poised promoters, SAGA catalyzes +1 nucleosome acetylation but not PIC assembly. At induced promoters, SAGA catalyzes acetylation, deubiquitylation, and PIC assembly. Surprisingly, SAGA mediates induction by creating a PIC that allows TFIID to stably associate, rather than creating a TFIID-independent PIC, as is generally thought. These findings suggest that inducible systems, where present, evolved on top of constitutive systems.全基因组范围内，人们对蛋白质在诱导前后于诱导型启动子处的组织方式，以及诱导型与组成型启动子架构在多大程度上依赖辅因子，仍知之甚少。我们的研究表明，序列特异性转录因子及其锚定辅因子（例如SAGA、中介体复合物（Mediator）、TUP、NuA4、SWI/SNF、RPD3-L）在诱导启动前即已结合于启动子区域（处于“poised”预就绪状态），而非在诱导过程中被招募；与之相反，诱导过程会招募预起始复合物（pre-initiation complex，PIC）。 通过敲低和/或基因敲除实验，我们证实SAGA在组成型启动子处并不发挥功能，尽管不依赖SAGA的Gcn5可在该处对+1核小体进行乙酰化修饰。在处于“poised”预就绪状态的启动子处，SAGA可催化+1核小体的乙酰化修饰，但无法介导预起始复合物的组装。在诱导型启动子处，SAGA可同时催化乙酰化、去泛素化修饰以及预起始复合物的组装。 令人意外的是，SAGA并非如学界普遍认知的那样，构建出不依赖转录因子IID（TFIID）的预起始复合物；而是通过形成可使TFIID稳定结合的预起始复合物来介导诱导过程。上述研究结果表明，诱导型调控系统若存在，其通常是在组成型调控系统的基础上演化而来。