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.

项目概要 细胞 RNA 的 RNA 编辑有助于细胞区分自身 RNA 和非自身 RNA。这 将腺苷编辑成肌苷通常由作用于的“腺苷脱氨酶”催化 RNA-1' 蛋白 (ADAR1)。 A>I 编辑在肿瘤和感染时增强，主要是 通过干扰素诱导的 ADAR1 较长亚型，其中包含 Z-DNA/Z-RNA 结合 在其 N 末端命名为“Zα”的结构域。错误编辑与神经系统疾病有关，例如 艾卡迪-古蒂埃综合征。 Z-RNA 以胞嘧啶和鸟苷 (CpG) 重复形式存在 已提出细胞中存在左手双螺旋构象，但这种现象的普遍存在 结构及其确切作用尚不清楚。此外，许多（如果不是大多数）地区建议 采用 Z 构象与常规 (CpG)n 不同。这些局部 Z-RNA 构象如何 在 A 型螺旋内生成，并由 ADAR1 的 Zα 稳定和调节，以及它们的 这些 RNA 的功能中的确切作用仍然未知。我们的假设是，结合 Zα 到 Z-RNA 在编辑过程中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 处形成的机制是什么？ 非 CpG 序列？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 结合后才采用？结构有哪些 Zα 在非 CpG 序列上识别 Z-RNA 的特征？我们首先会动态地 表征不同序列背景采用 Z-RNA 构象的倾向。 这一目标将使用先进的核磁共振方法来描述导致事件发生的顺序。 RNA区域从A型到Z型。其次，我们将确定无偏 3D 结构 RNA 片段在溶液中与 Zα 结合。最后，我们将识别并定位 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优势 我们校园和签约的下一代测序的专业知识和支持 公司。总体而言，我们作为共同PI的共同工作将为形成 Z-RNA 以及由此形成的各种 RNA 之间的 A-Z 连接。我们的最终目标是 解释 ADAR1 的 Z-RNA 结合域如何提高 ADAR1。我们的研究结果将有助于超越这一应用，提出全面的 ADAR1 编辑机制及其 RNA 介导的转录组范围调控，以及 有助于了解癌症或自身免疫缺陷等疾病。