Müller-Hermes Christoph, Piomponi Valerio, Hilber Stefan, Asami Sam, Kreutz Christoph, Bussi Giovanni, Sattler Michael
Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Garching, 85748, Germany.
Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany.
Nucleic Acids Res. 2025 Jun 20;53(12). doi: 10.1093/nar/gkaf550.
Adenosine-to-inosine (A-to-I) editing is a highly abundant modification of double-stranded RNA (dsRNA) and plays an important role in posttranscriptional gene regulation. Editing of multiple inosines by the ADAR1 enzyme leads to A-to-I hyper-editing of non-coding dsRNA, such as 3'UTRs, transposable elements, or foreign pathogenic RNAs, and is implicated in immune response and human diseases including cancer. The structural consequences of hyper-editing and its role in protein binding are poorly understood. Here, we combine solution nuclear magnetic resonance spectroscopy (NMR), biophysical methods such as small-angle X-ray scattering, and molecular dynamics simulations to study the sequence-dependent effects on conformation and dynamics of A-to-I hyper-editing for a 20-mer dsRNA and recognition of such RNAs by Endonuclease V. By comparing non-edited, single-edited, and hyper-edited dsRNA, we identify unique conformational features and extensive dynamics associated with hyper-editing, resulting in significantly increased base-pair opening. Hyper-edited dsRNA is more extended and adopts a highly dynamic ensemble of canonical and non-canonical conformations, which lead to preferential binding by Endonuclease V. Our integrated experimental and computational analysis identifies unique structural and dynamic features that are likely linked to specific protein recognition and the unique biological consequences of hyper-editing.
腺苷到肌苷（A-to-I）编辑是双链RNA（dsRNA）中一种高度丰富的修饰，在转录后基因调控中发挥着重要作用。ADAR1酶对多个肌苷的编辑导致非编码dsRNA（如3'非翻译区、转座元件或外来致病RNA）的A-to-I超编辑，并与免疫反应和包括癌症在内的人类疾病有关。超编辑的结构后果及其在蛋白质结合中的作用尚不清楚。在这里，我们结合溶液核磁共振光谱（NMR）、小角X射线散射等生物物理方法以及分子动力学模拟，研究20聚体dsRNA的A-to-I超编辑对构象和动力学的序列依赖性影响，以及核酸内切酶V对这类RNA的识别。通过比较未编辑、单编辑和超编辑的dsRNA，我们确定了与超编辑相关的独特构象特征和广泛的动力学，导致碱基对打开显著增加。超编辑的dsRNA更加伸展，采用高度动态的典型和非典型构象集合，这导致核酸内切酶V的优先结合。我们综合的实验和计算分析确定了独特的结构和动力学特征，这些特征可能与特定的蛋白质识别以及超编辑的独特生物学后果有关。
