Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA.
Present Address: Department of Medicine, Division of Translational Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
Genome Biol. 2020 Jun 2;21(1):132. doi: 10.1186/s13059-020-02040-0.
The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a pre-initiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function.
To determine the extent of promoter scanning across promoter classes in S. cerevisiae, we perturb Pol II catalytic activity and GTF function and analyze their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine the extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model.
Our observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast, which we term the shooting gallery. In this model, Pol II catalytic activity and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.
大多数真核生物启动子利用多个转录起始位点（TSS）。对于大多数物种来说，还不了解如何在真核生物的单个启动子上指定多个 TSS。在酿酒酵母中，由 Pol II 和保守的通用转录因子（GTFs）组成的起始前复合物（PIC）组装并打开 TSS 上游的 DNA。来自模型启动子的证据表明，PIC 从上游到下游扫描以识别 TSS。先前的结果表明，在 Pol II 催化活性或 GTF 功能改变时，发生扫描的启动子上的 TSS 分布以极性方式发生变化。
为了确定酿酒酵母中不同启动子类别之间的启动子扫描程度，我们扰乱了 Pol II 催化活性和 GTF 功能，并分析了它们对全基因组 TSS 使用的影响。我们发现，Pol II、TFIIB 或 TFIIF 功能的改变广泛改变了起始景观，这与所有酵母启动子都存在启动子扫描一致，无论启动子类别如何。然而，启动子结构可以以一种可以通过扫描模型预测的方式，决定启动子对改变的 Pol II 活性的敏感性程度。
我们的观察结果加上以前的数据，验证了酿酒酵母中 Pol II 起始的扫描模型的关键预测，我们称之为射击场。在这个模型中，Pol II 催化活性以及 Pol II 扫描的速率和连续性，以及启动子序列共同决定了 TSS 的分布及其使用。
