CAREER: Learning from NMD evasion by endogenous and viral transcripts

职业：从内源性和病毒转录本的 NMD 逃避中学习

• 批准号: 2338218
• 负责人: Sujatha Jagannathan
• 金额: $ 130万
• 依托单位: University of Colorado at Denver
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2024
• 资助国家: 美国
• 起止时间: 2024-03-01 至 2029-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2338218&HistoricalAwards=false
• 关键词: CAREER; Learning; NMD; evasion; endogenous

Robustness in biological systems relies on quality control. An important quality control step in the flow of genetic information is to eliminate faulty and/or foreign messenger RNA (mRNA) molecules so that proteins that may be harmful to the cell are not produced. One of the ways that cells can identify faulty RNAs is by sensing the length of the sequence within an RNA that encodes for a protein versus not. While this mechanism works well in simple organisms such as yeast, the human genome has evolved to have naturally long regions of mRNAs that do not encode for a protein but serve regulatory purposes. How then does the cell know to not degrade such normal transcripts and yet identify potentially toxic RNAs that arise from mutated genes or viral genomes? This project will leverage evolutionary analysis, molecular biology, and genomics tools to identify and understand signals that could allow physiological RNAs that resemble aberrant RNAs to escape quality control. The project will also promote broader societal impacts by engaging 8th- and 9th-grade students in Aurora Science and Tech, a local school that primarily serves underprivileged and low-income populations in Aurora, CO, in hands-on research to facilitate their training and exposure to scientific research. Nonsense-mediated RNA decay (NMD) is a quality control process that degrades transcripts containing premature termination codons (PTC) to prevent the production of toxic truncated proteins. NMD senses aberrant transcripts either via the presence of exon junction complexes (EJCs) downstream of the terminating ribosome or via the long 3’ untranslated region (UTR) generated by premature termination. Many non-aberrant endogenous transcripts and certain viral transcripts also mimic PTC-containing transcripts by virtue of possessing long 3’ UTRs and are also targeted by NMD. However, through the course of evolution, several transcripts with long UTRs, both viral and endogenous, have evolved mechanisms to bypass NMD by antagonizing the central NMD factor, UPF1. In this project, natural NMD evasion mechanisms will be investigated for novel insights into this fundamental quality control mechanism. The goals are to identify mechanisms of endogenous and viral bypass of long UTR NMD (Aim 1), determine the role of a mammal-specific UPF1 isoform in the arms race between NMD and its targets through experimental evolution in human and drosophila cells (Aim 2), and engage 8th-9th grade students from a local high-needs school in investigating the cross-regulation of different UPF1 paralogs and viral antagonists in yeast (Aim 3).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.

生物系统的鲁棒性依赖于质量控制。遗传信息流的一个重要质量控制步骤是消除故障和/或外国信使RNA（mRNA）分子，以便不会产生可能对细胞有害的蛋白质。细胞可以识别错误的RNA的一种方法是感应编码蛋白质而不是不编码的RNA内的序列的长度。尽管这种机制在诸如酵母这样的简单生物中效果很好，但人类基因组已经演变为自然而然的mRNA区域，这些区域不编码蛋白质，而是提供调节目的。那么细胞如何知道不降解这种正常转录本，而是识别出突变基因或病毒基因组引起的潜在有毒的RNA呢？该项目将利用进化分析，分子生物学和基因组学工具来识别和理解可以允许类似于异常RNA的物理RNA逃避质量控制的信号。该项目还将通过吸引8年级和9年级学生参加Aurora Science and Tech，这是一所本地学校，在CO的Aurora中为贫困和低收入人群提供动手研究，以促进他们的培训并接触科学研究。废话介导的RNA衰变（NMD）是一个质量控制过程，它降低了包含过早终止密码子（PTC）的转录本，以防止产生有毒截短的蛋白质。 NMD感觉通过终端核糖体下游的外显子连接复合物（EJC）或通过早产终止产生的长3'未翻译区（UTR）而异常。许多非常见的内源转录本和某些病毒转录本也通过拥有长3'UTR来模仿含PTC的转录本，并且也是NMD的靶向。但是，通过进化的过程，几个具有长长的UTR的转录本，包括病毒和内源性，通过拮抗中央NMD因子UPF1来绕开NMD的发展机制。在该项目中，将研究自然的NMD进化机制，以了解这种基本质量控制机制的新见解。目标是确定长UTR NMD的内源性和病毒旁路的机制（AIM 1），确定哺乳动物特异性的UPF1同工型在NMD及其目标之间通过人类和果蝇细胞的实验进化来确定在ARMD之间的竞赛中的作用（AIM 2），并与当地的高年级学生互动，从而在8至9年级的学生中互动。在酵母中（AIM 3）。该奖项反映了NSF的法定任务，并通过使用基金会的知识分子优点和更广泛的影响审查标准来评估，被认为是珍贵的支持。