The Role of alternative mRNA polyadenylation in SARS-CoV-2 replication & the host response

SARS-CoV-2复制和宿主中选择性mRNA多聚腺苷化作用的研究 先天免疫反应 非典-冠状病毒-2感染已导致新冠肺炎大流行，并了解 导致其病理生理学的机制是生物医学的首要任务。尽管对这个问题进行了密集的研究 去年，我们仍然有很多关于促进或限制SARS-CoV-2感染的宿主因素和 操纵它们可能会带来新的抗病毒治疗。受感染细胞内的变化通常是 由信使核糖核酸合成的变化调节，不仅影响转录，而且影响信使核糖核酸的加工。 MRNA前体在其3‘端被切割，并在被称为切割和切割的过程中加入聚(A)尾 多聚腺苷(C/P)。如果C/P受阻，则信使核糖核酸降解，核输出不佳，也就不好 翻译过来的。改变聚(A)位位置或替代聚腺苷酸化(APA)，会影响类型和 从一个信使核糖核酸产生的蛋白质的量。许多病毒已经找到了操纵C/P和APA的方法 促进病毒复制，干扰宿主的抗病毒反应，或劫持C/P蛋白以增强 病毒活动。几种筛选表明C/P蛋白与SARS-Cov2蛋白相互作用 和RNA，并鉴定了一些C/P蛋白为抗病毒因子。然而，目前还不清楚是否 SARS-CoV-2导致Poly(A)站点使用的变化，从而支持其复制和/或导致 先天免疫失调，可能导致致病性炎症反应 严重的新冠肺炎案例。 通过使用已公布的mRNA-seq数据分析感染SARS-CoV-2的细胞中全球PA位点的使用情况，我们 发现SARS-CoV-2感染改变了免疫、细胞凋亡、囊泡运输、 新陈代谢和细胞周期。基于这一初步观察，我们假设 SARS-CoV-2感染引起的C/P影响病毒复制和宿主抗病毒反应。至 研究SARS-CoV-2如何影响宿主细胞中的C/P以及靶向C/P蛋白是否会改变 病毒感染的进展，我们将1)确定在SARS期间C/P是否在整个基因组中被抑制- CoV-2感染，2)确定调节APA的C/P蛋白过度表达或耗尽的影响， 以及3)确定已知与C/P蛋白相互作用的特定病毒蛋白是否影响3‘末端加工。 这项研究的成功完成将决定C/P操纵是否有潜力成为一种新的 新冠肺炎的治疗靶点。

Determining the role of alternative mRNA polyadenylation in SARS-Cov-2 replication and the host innate immune response SARS-CoV-2 infection has caused the COVID-19 pandemic, and understanding the molecular mechanisms leading to its pathophysiology is a top biomedical priority. In spite of intense research over the last year, we still have much to learn about host factors that promote or restrict SARS-CoV-2 infection and how manipulating them might enable new antiviral treatments. Changes within the infected cell are often mediated by changes in mRNA synthesis that affect not only transcription but also mRNA processing. mRNA precursor is cleaved at its 3’ end and a poly(A) tail added in a process called cleavage and polyadenylation (C/P). If C/P is blocked, mRNA is degraded, poorly exported from the nucleus, and poorly translated. Changing the poly(A) site position, or alternative polyadenylation (APA), affects the type and amount of protein produced from an mRNA. Many viruses have found ways to manipulate C/P and APA to promote viral replication, to interfere with the host antiviral response, or to hijack C/P proteins to augment viral activities. Several screens have demonstrated interaction of C/P proteins with SARS-Cov2 proteins and RNA and identified some C/P proteins as antiviral factors. However, it remains unknown whether SARS-CoV-2 causes changes in poly(A) site usage that support its replication and/or lead to the dysregulation of innate immunity that might contribute to the pathogenic inflammatory response seen in severe COVID-19 cases. By analyzing global pA site usage in cells infected with SARS-CoV-2 using published mRNA-seq data, we found that SARS-CoV-2 infection changes APA of genes involved in immunity, apoptosis, vesicle transport, metabolism, and cell cycle. Based on this preliminary observation, we hypothesize that alterations in C/P caused by SARS-CoV-2 infection influence viral replication and the host antiviral response. To investigate how SARS-CoV-2 affects C/P in host cells and whether targeting the C/P proteins might alter the progression of viral infection, we will 1) determine if C/P is inhibited across the genome during SARS- CoV-2 infection, 2) determine the effects of overexpressing or depleting C/P proteins that regulate APA, and 3) determine if specific viral proteins known to interact with C/P proteins affect 3' end processing. Successful completion of this study will determine if manipulation of C/P has potential as a novel therapeutic target for COVID-19.