Molecular recognition by ADAR1 of Z-RNA within transcriptomes

ADAR1 对转录组中 Z-RNA 的分子识别

• 批准号: 10712207
• 负责人: Quentin Vicens
• 金额: $ 30.26万
• 依托单位: UNIVERSITY OF HOUSTON
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-26 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10712207
• 关键词: Address; Adenosine; Adopted; Adoption; Affect; Alu Elements; Autoimmune; Autoimmune Diseases; Base Sequence; Binding; Binding Sites; Biological Process; Biophysics; Brain Diseases; Cells; Contracts; Cytoplasm; Cytosine; DNA Transposable Elements; Disease; Enzymes; Event; Gene Expression Regulation; Geography; Goals; Guanosine; Human; Immune response; Immune system; Infection; Infectious Agent; Innate Immune Response; Inosine; Interferons; Joints; Knowledge; Lead; Left; Malignant Neoplasms; Mediating; Methods; Molecular Conformation; Names; Nuclear; Play; Point Mutation; Population; Prevalence; Process; Protein Isoforms; Proteins; Publishing; RNA; RNA Conformation; RNA Editing; RNA Recognition Motif; RNA Viruses; Regulation; Role; Sampling; Site; Specificity; Structure; Techniques; Work; Z-Form DNA; dsRNA adenosine deaminase; in vivo; molecular recognition; mutant; nervous system disorder; next generation sequencing; plasma protein Z; pseudotoxoplasmosis syndrome; response; restraint; three dimensional structure; transcriptome; transcriptome sequencing; tumor; tumor progression

Project Summary RNA editing of cellular RNAs helps the cell distinguish between self and non-self RNAs. This editing of adenosines into inosines is generally catalyzed by the `adenosine deaminase acting on RNA-1' protein (ADAR1). A>I editing is augmented in tumors and upon infection, primarily through the interferon-induced longer isoform of ADAR1 that comprises a Z-DNA/Z-RNA binding domain named ‘Zα’ at its N-terminus. Misediting is implicated in neurological diseases such as Aicardi-Goutières syndrome. Z-RNA in the form of repeats of cytosine and guanosine (CpG) in a left-handed double-helical conformation has been proposed in cells, but the prevalence of such structures and their exact role are unknown. In addition, many —if not most— regions proposed to adopt a Z conformation do not resemble regular (CpG)n. How these local Z-RNA conformations are generated within A-form helices, stabilized and regulated by Zα of ADAR1, as well as their exact role in the function of these RNAs, remain unknown. Our hypothesis is that the binding of Zα to Z-RNA plays an essential role during the editing process. Here, we propose to answer the following questions: What is the mechanism for Z-RNA formation at CpG but also non-CpG sequences? How widespread are transitions to Z-RNA across transcriptomes? Is Z- RNA sampled in the free form or only adopted upon binding by Zα? What are the structural features of Z-RNA recognition by Zα at non CpG sequences? We will first dynamically characterize the propensity of various sequence contexts to adopt Z-RNA conformations. This aim will use advanced NMR methods to characterize the sequence of events that lead an RNA region from A-form to Z-form. Second, we will determine the unbiased 3D structure of RNA fragments bound to Zα in solution. Finally, we will identify and localize Zα binding sites and Zα-dependent A>I editing events. This aim will take advantage of the robust expertise and support for next-generation sequencing on our campus and at a contracted company. Overall, our joint work as co-PIs will provide a structural rationale for the formation of Z-RNA and the resulting formation of A-Z junctions across a variety of RNAs. We ultimately aim to explain how the Z-RNA binding domain of ADAR1 increases the specificity and activity of ADAR1. Our findings will help beyond this application with proposing a comprehensive mechanism for ADAR1 editing and its RNA-mediated transcriptome-wide regulation, and contribute to understanding disease such as cancer or auto-immune deficiencies.

项目摘要 细胞RNA的RNA编辑有助于细胞区分自我和非自我RNA。这 将腺苷编辑成肌苷通常由作用于腺苷的腺苷脱氨酶催化， RNA-1'蛋白（ADAR 1）。A>I编辑在肿瘤中和感染后增强，主要是 通过干扰素诱导的更长的ADAR 1亚型，包括Z-DNA/Z-RNA结合 在其N-末端命名为“Zα”的结构域。错坐与神经系统疾病有关， 艾-古二氏综合征Z-RNA以胞嘧啶和鸟苷（CpG）的重复形式存在于细胞中， 在细胞中已经提出了左旋双螺旋构象，但是这种构象的普遍性是不确定的。 其结构及其确切作用尚不清楚。此外，许多-如果不是大多数-区域建议 采用Z构象不类似于常规（CpG）n。这些局部的Z-RNA构象 在A型螺旋内产生，由ADAR 1的Zα稳定和调节，以及它们的 在这些RNA的功能中的确切作用仍然未知。我们的假设是 在Z-RNA的编辑过程中，Zα到Z-RNA的转化起着至关重要的作用。在此，我们建议 回答以下问题：Z-RNA在CpG上形成的机制是什么， 非CpG序列在转录组中向Z-RNA的转变有多普遍？是Z- RNA以游离形式取样或仅在与Zα结合时采用？什么是结构 非CpG序列上Zα识别Z-RNA的特征？我们将首先动态地 表征各种序列背景采用Z-RNA构象的倾向。 这一目标将使用先进的核磁共振方法来表征事件的顺序，导致一个 RNA区域从A型到Z型。其次，我们将确定无偏的3D结构， RNA片段在溶液中与Zα结合。最后，我们将识别和定位Zα结合 位点和Zα依赖性A>I编辑事件。这一目标将利用强大的 专业知识和支持下一代测序在我们的校园和合同 公司总的来说，我们作为共同参与者的联合工作将为形成 Z-RNA和由此形成的跨各种RNA的A-Z连接。我们最终的目标是 为了解释ADAR 1的Z-RNA结合结构域如何增加ADAR的特异性和活性， ADAR 1.我们的研究结果将有助于超越这一应用，提出一个全面的 ADAR 1编辑机制及其RNA介导的全转录组调控，以及 有助于了解癌症或自身免疫缺陷等疾病。