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S.酿酒酵母，作为可遗传的蛋白质构象传递。由于其简单易行，酵母已成为研究朊病毒生物学的一个强有力的模型系统。多个朊病毒元件可以共存于单个酵母细胞中，因此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至关重要。该项目旨在研究Swi 1朊病毒如何与另一种酵母朊病毒Mot 3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整体转录和蛋白质稳态。拟议的研究计划将作为一个平台，培养研究生和暑期本科实习生。将建立一个外展计划，将芝加哥地区代表性不足的高中学生在伊利诺伊州数学和科学学院与李研究实验室在范伯格医学院，西北大学。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弱势青年在芝加哥地区进一步科学教育和潜在的科学为导向的career.The蛋白质决定簇的[SWI+]朊病毒是Swi 1，一个亚基的SWI/SNF染色质重塑复合物，和蛋白质决定簇的[MOT 3 +]朊病毒是Mot 3，转录抑制子。Swi 1和Mot 3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含有[SWI+]和[MOT 3 +]，为研究朊病毒-朊病毒相互作用提供了一个很好的平台。 本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 RUN测序方法，检查与[SWI+]和/或[MOT 3 +]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位。3)利用多重标记蛋白质组学研究朊病毒在蛋白质组学和翻译后修饰中的特异性变化。从拟议的研究结果将提供有价值的见解之间的相互作用[SWI+]和[MOT 3 +]朊病毒和它们的影响，全球转录和proteostasis.This奖项反映了NSF的法定使命，并已被认为是值得的支持，通过评估使用基金会的智力价值和更广泛的影响审查标准。

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.