Investigating the role of prion-mediated epigenetic regulation in yeast using an integrative approach of multi-omics

酵母朊病毒是芽殖酵母（酿酒酵母）中不常见的遗传因子，以遗传蛋白构象的形式传播。酵母由于其简单和适应性，已成为研究朊病毒生物学的一个强有力的模型系统。多个朊病毒元素可以在单个酵母细胞中共存，这使得了解它们如何相互作用以及它们的相互作用如何影响酵母细胞生物学变得至关重要。该项目旨在研究Swi1朊病毒如何与另一个酵母朊病毒Mot3相互作用，以及这种朊病毒-朊病毒相互作用如何影响酵母的全局转录和蛋白质稳态。拟议的研究项目将作为培训研究生和暑期本科生实习生的平台。将建立一个外展项目，将芝加哥地区伊利诺斯州数学与科学学院代表性不足的高中生与西北大学范伯格医学院的李氏研究实验室联系起来。这包括学年期间每周一天的实验室活动和为期八周的暑期课程。最终更广泛的影响是推动芝加哥地区的弱势青年接受进一步的科学教育，并有可能从事以科学为导向的职业。[SWI+]朊病毒的蛋白决定因子是SWI/SNF染色质重塑复合体的亚基Swi1， [MOT3+]朊病毒的蛋白决定因子是转录抑制因子MOT3。Swi1和Mot3都是影响酵母多细胞性的转录调节因子。单个酵母细胞可以同时携带[SWI+]和[MOT3+]，为研究朊病毒-朊病毒相互作用提供了良好的平台。该项目的具体目标包括：1)利用高通量单细胞rna测序技术鉴定朊病毒特异性转录组变化和细胞间异质性。2)通过CUT&amp；RUN-sequencing方法检查与[SWI+]和/或[MOT3+]功能相关的重要转录调节因子和表观遗传标记的基因组占有率。3)利用多重标记蛋白质组学研究朊病毒特异性的蛋白质组学变化和翻译后修饰。这项研究的结果将为[SWI+]和[MOT3+]朊病毒之间的相互作用及其对全球转录和蛋白质静止的影响提供有价值的见解。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Yeast prions are unusual genetic elements in the budding yeast, S. cerevisiae, transmitted as inheritable protein conformations. Due to its simplicity and amenability, yeast has become a powerful model system for studying prion biology. Multiple prion elements can co-exist in a single yeast cell, making it crucial to understand how they interact and how their interactions affect yeast cell biology. This project aims to examine how the Swi1 prion interacts with another yeast prion, Mot3, and how such prion-prion interactions affect yeast global transcription and protein-homeostasis. The proposed research program will serve as a platform to train graduate students and summer undergraduate interns. An outreach program will be established to connect Chicago-area underrepresented high school students at the Illinois Math and Science Academy with the Li research laboratory at the Feinberg School of Medicine, Northwestern University. This includes a one-day per week lab activity during the academic year and an eight-week long summer program. The ultimate broader impact is to propel disadvantaged youth in the Chicago area towards further science education and potentially to a science-oriented career.The protein determinant of the [SWI+] prion is Swi1, a subunit of the SWI/SNF chromatin remodeling complex, and the protein determinant of the [MOT3+] prion is Mot3, a transcription repressor. Both Swi1 and Mot3 are transcriptional modulators affecting yeast multicellularity. A single yeast cell can harbor both [SWI+] and [MOT3+], providing an excellent platform to study prion-prion interactions. The specific objectives of this project include: 1) Identify prion-specific changes in transcriptome and cell-to-cell heterogeneity using the technology of high-throughput single-cell RNA-sequencing. 2) Examine the genomic occupancies of important transcriptional modulators and epigenetic marks that are functionally linked to [SWI+] and/or [MOT3+] through the CUT&RUN-sequencing methodology. 3) Investigate prion-specific changes in proteomics and post-translational modifications using multiplex-labeling proteomics. The results from the proposed study will provide valuable insights into the interaction between the [SWI+] and [MOT3+] prions and their impact on global transcription and proteostasis.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.