CAREER: Learning from NMD evasion by endogenous and viral transcripts

生物系统的稳健性依赖于质量控制。遗传信息流中的一个重要质量控制步骤是消除有缺陷的和/或外来的信使RNA（mRNA）分子，以便不产生可能对细胞有害的蛋白质。细胞识别错误RNA的方法之一是通过感知RNA中编码蛋白质的序列的长度。虽然这种机制在酵母等简单生物体中运作良好，但人类基因组已经进化为具有天然的长区域mRNA，这些mRNA不编码蛋白质，但用于调节目的。那么，细胞是如何知道不降解这些正常的转录本，同时又能识别出来自突变基因或病毒基因组的潜在毒性RNA的呢？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能允许类似异常RNA的生理RNA逃避质量控制的信号。该项目还将促进更广泛的社会影响，让Aurora Science and Tech的8年级和9年级学生参与，Aurora Science and Tech是一所当地学校，主要为Aurora的贫困和低收入人群提供服务，CO，实践研究，以促进他们的培训和接触科学研究。无义介导的RNA衰变（NMD）是一种质量控制过程，其降解含有提前终止密码子（PTC）的转录物以防止有毒截短蛋白的产生。NMD通过终止核糖体下游外显子连接复合物（EJC）的存在或通过过早终止产生的长3'非翻译区（UTR）来感测异常转录物。许多非异常内源性转录物和某些病毒转录物也通过具有长3'UTR而模拟含PTC的转录物，并且也被NMD靶向。然而，在进化过程中，几种具有长UTR的转录物，包括病毒和内源性的，已经进化出通过拮抗中心NMD因子UPF 1来绕过NMD的机制。在这个项目中，自然的NMD规避机制将调查新的见解，这一基本的质量控制机制。目标是鉴定长UTR NMD的内源性和病毒旁路机制（Aim 1），通过在人类和果蝇细胞中的实验进化确定哺乳动物特异性UPF 1同种型在NMD及其靶标之间的军备竞赛中的作用（Aim 2），并让当地一所高需求学校的8 - 9年级学生参与调查酵母中不同UPF 1旁系同源物和病毒拮抗剂的交叉调节（该奖项反映了NSF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。

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.