Transcription of nearly all yeast RNA Polymerase II-transcribed genes is dependent on transcription factor TFIID. Saccharomyces cerevisiae

Previous studies suggested that expression of most yeast mRNAs is dominated by either transcription factor TFIID or SAGA. We reexamined this longstanding problem by rapid depletion of TFIID subunits and measurement of changes in nascent transcription. We find that transcription of nearly all mRNAs is strongly dependent on TFIID function. Degron-dependent depletion of Tafs 1,2,7,11, and 13 showed similar transcription decreases for genes in the Taf1-depleted, Taf1-enriched, TATA-containing and TATA-less gene classes. The magnitude of TFIID-dependence varies with growth conditions, although this variation is similar at all gene classes. Many studies have suggested differences in gene regulatory mechanisms between TATA and TATA-less genes and these differences have been attributed in part to differential dependence on SAGA or TFIID. Our work indicates that TFIID contributes significantly to expression of nearly all yeast mRNAs and that differences in regulation between these two gene classes is due to other properties. Overall design: We used the auxin-inducible degron system to rapidly deplete selected TFIID subunits and Med14 subunit of Mediator. We then monitored genome-wide nascent transcription using native Pol II ChIP to analyze the position of Pol II elongation complexes before and after auxin-induced depletion of selected TFIID subunits and Med14 subunit of Mediator.

既往研究表明，大多数酵母mRNA的表达由转录因子TFIID或SAGA主导。本研究通过快速降解TFIID亚基并检测新生转录变化，重新审视了这一长期存在的学术问题。我们发现，几乎所有mRNA的转录均强烈依赖TFIID的功能。针对Taf1、2、7、11及13亚基的降解标签（degron）依赖性降解实验显示，在Taf1耗竭型、Taf1富集型、含TATA盒及不含TATA盒这四类基因中，转录水平的下降幅度均相似。TFIID的依赖程度随生长条件不同而变化，但该变化在所有基因类别中均保持一致。多项研究指出，含TATA盒与不含TATA盒的基因在基因调控机制上存在差异，且这类差异部分归因于二者对SAGA或TFIID的依赖程度不同。我们的研究表明，TFIID对几乎所有酵母mRNA的表达均有显著贡献，且这两类基因的调控差异源于其他分子特性。实验设计：本研究采用生长素诱导型降解标签系统，快速降解指定的TFIID亚基与中介体复合物（Mediator）的Med14亚基。随后通过天然Pol II染色质免疫沉淀（ChIP）检测全基因组新生转录水平，分析生长素诱导降解指定TFIID亚基及Med14亚基前后，RNA聚合酶II（Pol II）延伸复合物的定位变化。