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

确定交替mRNA多聚腺苷酸化在SARS-Cov-2复制和宿主中的作用 先天免疫应答 SARS-CoV-2感染引起了COVID-19大流行，了解其分子机制 导致其病理生理学的机制是生物医学的首要任务。尽管有大量的研究， 去年，我们仍然有很多关于促进或限制SARS-CoV-2感染宿主因素的知识， 如何操纵它们可能使新的抗病毒治疗成为可能。受感染细胞内的变化通常 由mRNA合成的变化介导，不仅影响转录，而且影响mRNA加工。 mRNA前体在其3'端被切割，并在称为切割的过程中添加聚（A）尾， 多聚腺苷酸化（C/P）。如果C/P被阻断，mRNA被降解，从细胞核中输出的很少， は自动的改变多聚腺苷酸位点的位置，或选择性多聚腺苷酸化（阿帕），会影响其类型和功能。 从mRNA产生的蛋白质的量。许多病毒已经找到了操纵C/P和阿帕的方法， 促进病毒复制，干扰宿主的抗病毒反应，或劫持C/P蛋白，以增加 病毒活动。几个筛选已经证明C/P蛋白与SARS-Cov 2蛋白的相互作用 和RNA，并鉴定了一些C/P蛋白作为抗病毒因子。然而，目前尚不清楚是否 SARS-CoV-2引起poly（A）位点使用的变化，这些变化支持其复制和/或导致 先天性免疫失调可能导致致病性炎症反应， 严重的COVID-19病例。 通过使用已发表的mRNA-seq数据分析SARS-CoV-2感染细胞中的全局pA位点使用，我们 发现SARS-CoV-2感染改变了免疫、凋亡、囊泡转运等基因的阿帕， 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。到 研究SARS-CoV-2如何影响宿主细胞中的C/P，以及靶向C/P蛋白是否可能改变 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受到抑制- CoV-2感染，2）确定过表达或耗尽调节阿帕的C/P蛋白的影响， 和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。 本研究的成功完成将决定C/P操作是否有潜力作为一种新的 COVID-19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.