Large-scale reporter assay to assess expression and coactivator specificity of UAS-core promoter combinations (DNA)

Three general classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA and Mediator (MED) Tail, but little is known about whether this dependence is determined by the core promoter, Upstream activation sites (UAS), or other gene features. It is also unclear whether UASs can broadly activate transcription from the different promoter classes or whether efficient transcription requires matching UASs and promoters of similar gene class. Here we measure transcription and cofactor specificity for tens of thousands of UAS-core promoter combinations. We find that few UASs display strong core promoter specificity while most UASs can broadly activate promoters regardless of regulatory class. However, we find that matching UASs and promoters from the same gene class is generally important for optimal expression. We find that MED Tail and SAGA are dependent on the identity of both UAS and promoter while dependence on TFIID localizes to only the core promoter.本研究基于对转录辅因子TFIID、SAGA以及中介体尾部（Mediator (MED) Tail）的依赖性差异，区分出三类酵母蛋白编码基因。目前对于此类依赖性究竟由核心启动子（core promoter）、上游激活位点（Upstream activation sites, UAS）或是其他基因特征所决定，仍知之甚少。此外，目前尚不清楚UAS能否广泛激活不同启动子类别的转录，亦或是高效转录需要匹配同类基因的UAS与启动子。本研究针对数万个UAS-核心启动子组合，对转录活性与辅因子特异性进行了检测。研究发现，仅有极少数UAS表现出强烈的核心启动子特异性，而大多数UAS均可广泛激活各类启动子，不受其调控类别的限制。然而本研究同时发现，匹配同类基因的UAS与启动子，通常对于实现最佳表达水平至关重要。此外还观察到，中介体尾部（MED Tail）与SAGA的依赖性同时取决于UAS与启动子的特征，而对TFIID的依赖性则仅局限于核心启动子区域。