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

酵母蛋白是一种特殊的遗传元件，在萌芽酵母中以可遗传的蛋白质构象传递。由于其简单性和亲和性，酵母已成为研究Pron生物学的一个强大的模型系统。在一个酵母细胞中可以共存多个Pron元素，这使得了解它们是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是至关重要的。该项目旨在研究Swi1蛋白如何与另一种酵母蛋白基因mot3相互作用，以及这种蛋白与蛋白的相互作用如何影响酵母的整体转录和蛋白质平衡。拟议的研究计划将作为培训研究生和暑期本科生实习生的平台。将建立一个外联计划，将伊利诺伊州数学与科学学院芝加哥地区代表性不足的高中生与西北大学范伯格医学院的李研究实验室联系起来。这包括学年期间每周一天的实验活动和为期八周的暑期计划。最终的更广泛的影响是推动芝加哥地区的贫困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+]Prion的蛋白质决定因素是Swi1，它是SWI/SNF染色质重塑复合体的一个亚单位，而[MOT3+]Prion的蛋白质决定因素是转录抑制因子mot3。Swi1和mot3都是影响酵母多细胞特性的转录调控因子。一个酵母细胞可以同时含有[SWI+]和[MOT3+]，这为研究Pron-Prion相互作用提供了一个很好的平台。该项目的具体目标包括：1)利用高通量单细胞RNA测序技术，确定转录组蛋白特异性的变化和细胞间的异质性。2)通过CUT&AMP；Run-Sequence方法检查与[SWI+]和/或[MOT3+]在功能上相关联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蛋白质组学中的蛋白特异性变化和翻译后修饰。这项拟议研究的结果将为[SWI+]和[MOT3+]蛋白之间的相互作用及其对全球转录和蛋白质组学的影响提供有价值的见解。这一奖项反映了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。

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.