The molecular process of transcription by RNA Polymerase II is highly conserved among eukaryotes (“classic model”). A distinct way of locating transcription start sites (TSSs) has been identified in a budding yeast Saccharomyces cerevisiae (“scanning model”). Herein, we applied genomic approaches to elucidate the origin of the scanning model and its underlying genetic mechanisms. We first identified TSSs at single-nucleotide resolution for 12 yeast species using the nAnT-iCAGE technique, which significantly improved the annotations of these genomes by providing accurate 5′ boundaries for protein-coding genes. We then inferred the initiation mechanism of each species based on its TSS maps and genome sequences. We discovered that the scanning model likely originated after the split of Yarrowia lipolytica and the other budding yeasts. Species that use the scanning model showed an adenine-rich region immediately upstream of the TSS that might facilitate TSS selection. Both initiation mechanisms share a strong preference for pyrimidine–purine dinucleotides surrounding the TSS. Our results suggest that the purine is required to accurately recruit the first nucleotide, thereby increasing the chances of a messenger RNA of being capped during mRNA maturation, which is critical for efficient translation initiation during protein biosynthesis. Based on our findings, we propose a model for TSS selection in the scanning-model species, as well as a model for the stepwise process responsible for the origin and evolution of the scanning model.

中文翻译：

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酵母中一种独特的转录起始机制的起源和进化

RNA 聚合酶 II 的分子转录过程在真核生物中是高度保守的（“经典模型”）。已在出芽酵母酿酒酵母（“扫描模型”）中确定了一种定位转录起始位点 (TSS) 的独特方式。在这里，我们应用基因组方法来阐明扫描模型的起源及其潜在的遗传机制。我们首先使用 nAnT-iCAGE 技术以单核苷酸分辨率鉴定了 12 个酵母物种的 TSS，该技术通过为蛋白质编码基因提供准确的 5' 边界显着改善了这些基因组的注释。然后我们根据每个物种的 TSS 图和基因组序列推断出每个物种的起始机制。我们发现扫描模型很可能起源于Yarrowia lipolytica和其他芽殖酵母。使用扫描模型的物种在 TSS 的上游显示了一个富含腺嘌呤的区域，这可能有助于 TSS 的选择。两种起始机制都强烈偏好围绕 TSS 的嘧啶-嘌呤二核苷酸。我们的结果表明，嘌呤需要准确地募集第一个核苷酸，从而增加信使 RNA 在 mRNA 成熟过程中被加帽的机会，这对于蛋白质生物合成过程中的有效翻译起始至关重要。基于我们的发现，我们提出了一个用于扫描模型物种中 TSS 选择的模型，以及一个负责扫描模型起源和演化的逐步过程模型。