The evolution of transcription initiation mechanisms and its genetic basis

基因的DNA序列需要复制到信使核糖核酸分子中以实现其功能，这一过程被称为转录。细胞在基因转录的起始位置有很高的选择性。大多数真核生物，如人类、植物和真菌，都有定位转录起始位置的机制。然而，在包括贝克酵母在内的一些真菌物种中已经发现了一种独特的转录启动方式。该项目旨在确定转录启动的机制何时以及如何发生分歧。该项目的成功将促进对转录启动的进化和遗传机制的基本理解，这是利用生物学的力量促进生物经济的第一步。该项目还开发了新的软件并生成了大量的信使核糖核酸序列，这将使研究界受益。此外，该项目将建立一个用户友好的数据库，作为提高公众基因组学素养的门户，并促进K-12学校和大学的教学。该项目还通过培养博士后学者、研究生、本科生和高中生，为培养具有全球竞争力的STEM劳动力做出贡献。在大多数真核生物中，转录是由一个位于短序列元件TATA盒下游约30个核苷酸的大酶预起始复合体启动的，预起始复合体在那里组装。相反，预引发复合体扫描TATA盒下游的DNA序列，寻找酿酒酵母中有利的转录起始点。该项目旨在阐明转录启动机制何时出现分歧，并确定与这一过程相关的关键基因变化。该项目采用计算和实验相结合的方法来确定68种真菌的启动机制。该项目的目标1将开发新的生物信息学工具，用于基于高通量测序数据准确绘制转录起始点。在目标2中，该项目将捕获RNA分子的第一个核苷酸，并对这些转录本进行测序，以生成代表所有主要真菌谱系的68个物种的转录起始点图。每个物种的启动机制将根据TATA盒在基因组规模上相对于转录起始点的分布来确定。详细的启动机制演化史将被描绘出来，以准确地指出分歧的发生。第三个项目的目标是根据进化历史和表达谱识别与转录启动机制差异相关的关键基因。这些基因中的重要遗传变化也有望通过比较序列分析来确定。这些结果将为未来询问转录启动中启动前复杂组件的特定功能奠定坚实的基础。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

The DNA sequence of a gene needs to be copied into mRNA molecules to carry out its function, a process called transcription. Cells are highly selective in where they begin (initiate) transcription of their genes. The mechanism of locating the starting positions of transcription is shared by most eukaryotic organisms such as humans, plants, and fungi. Yet, a distinct way of transcription initiation has been found in a few fungal species including Baker’s yeast. This project aims to determine when and how the mechanisms of transcription initiation have diverged. Success of this project will advance basic understandings of the evolution and genetic mechanisms of transcription initiation, a first step in harnessing the power of biology for the bioeconomy. This project also develops new software and generates a large collection of mRNA sequences, which will benefit the research community. In addition, this project will build a user-friendly database that can serve as a portal for improving public literacy in genomics and facilitate teaching in K-12 schools and colleges. This project also contributes to the development of a globally competitive STEM workforce by training a postdoctoral scholar, graduate, undergraduate, and high school students.In most eukaryotes, transcription is initiated by a large enzyme preinitiation complex at about 30 nucleotides downstream of a short sequence element known as the TATA box, where the preinitiation complex is assembled. In contrast, the preinitiation complex scans DNA sequences further downstream of the TATA box for favorable transcription start sites in Saccharomyces cerevisiae. This project aims to elucidate when the transcription initiation mechanisms have diverged and to identify key genetic changes associated with this process. This project applies a combination of computational and experimental approaches to determine the initiation mechanism of 68 fungal species. Aim 1 of this project will develop novel bioinformatics tools for accurate mapping of transcription start sites based on high throughput sequencing data. In Aim 2, this project will capture the first nucleotide of RNA molecules and sequence these transcripts to generate transcription start site maps for 68 species representing all major fungal lineages. The initiation mechanism for each species will be determined based on the distribution of the TATA box relative to the transcription start site on a genomic scale. A detailed evolutionary history of initiation mechanisms will be depicted to pinpoint the occurrence of divergence. The third project aim will identify the key genes associated with the divergence of transcription initiation mechanisms based on their evolutionary history and expression profiles. Important genetic changes in these genes are also expected to be determined through comparative sequence analyses. These results will lay a solid foundation for future interrogation of the specific functions of preinitiation complex components in transcription initiation.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.