Structural transitions and RNA-mediated mechanisms of LSD1

LSD1的结构转变和RNA介导的机制

• 批准号: 10737398
• 负责人: Nicholas J Reiter
• 金额: $ 42.68万
• 依托单位: MARQUETTE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-15 至 2027-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10737398
• 关键词: Acids; Address; Affect; Aging; Allosteric Regulation; Architecture; Binding; Binding Proteins; Binding Sites; Biochemical; Biochemistry; Biology; Biophysics; Cell Differentiation process; Cell Nucleus; Cells; Cellular Stress; Cellular biology; Chromatin; Chromatin Remodeling Factor; Chromosomal Stability; Chromosomes; Complex; DNA; DNA Damage; Data; Degenerative Disorder; Disease; Environment; Enzymes; Epigenetic Process; Excision; G-Quartets; Gene Expression; Gene Expression Regulation; Genome; Genome Stability; Genomic approach; Goals; Guanosine; Heterochromatin; Higher Order Chromatin Structure; Histones; Homeostasis; Human; Hybrids; In Vitro; KDM1A gene; Knowledge; Link; Liquid substance; Lysine; Malignant Neoplasms; Mediating; Mediator; Methods; Methylation; Molecular Conformation; Monitor; Neoplasm Metastasis; Normal Cell; Nuclear Localization Signal; Nucleic Acids; Nucleosomes; Oncogenic; Pathway interactions; Phase; Phosphorylation; Physical condensation; Play; Process; Property; Protein Conformation; Protein Region; Proteins; RNA; RNA Sequences; Regulation; Role; Site; Structure; Telomerase; Telomere Maintenance; Transcript; Transcriptional Regulation; Untranslated RNA; X-Ray Crystallography; cancer cell; conformational conversion; demethylation; genetic architecture; genome-wide; human disease; insight; live cell imaging; live cell microscopy; neuron development; optogenetics; protein complex; protein kinase A kinase; recruit; response; scaffold; simulation; structural biology; telomere; therapeutic development; therapeutic target

Project Summary/Abstract This project is centered on the hypothesis that RNA structure and RNA-chromatin associated protein interactions play crucial roles in maintaining genome stability. It is known that non-coding RNAs (ncRNAs) interact with protein components of chromatin, thus altering the higher order genetic architecture and gene expression. A subset of these RNA-protein interactions are linked to ageing, cancer metastasis, and neuronal development. As genomic approaches begin to identify RNA-protein associations and their links to cancer, there remain key gaps in our knowledge regarding epigenetic-based RNA binding proteins. RNA can mimic DNA, form transient DNA/RNA hybrids under cell stress, and function as scaffolds to recruit protein complexes to chromatin. Further, these RNAs can interact with structured and disordered protein regions to form multivalent networks that can undergo liquid-liquid phase separation, or biomolecular condensates. Thus, examining RNA-protein assemblies in solution and in a condensed, clustered state akin to a compact cell environment can address fundamental questions: 1) What are the sequence requirements or structural features that drive formation of multivalent RNA-protein interactions? And 2) How do RNA-protein conformational changes impact the function and activity of chromatin associated proteins? In this proposal, we seek to understand how RNA interacts with the lysine specific demethylase-1 (LSD1) enzyme. LSD1 is an essential methylation regulator and has oncogenic properties in many cancers due to its vast interaction network and association with RNAs in cell differentiation and DNA damage response pathways. We will focus on the telomeric repeat containing RNA (TERRA) that interacts with LSD1 in response to DNA damage at the ends of chromosomes. These RNA-LSD1 interactions are involved in the regulation of heterochromatin at telomeres. The co-I (Zhang) has discovered that telomere clustering occurs in telomerase-free cancer cells and that this process is driven through RNA-mediated phase separation. We will use integrative structural and cell biology approaches to demonstrate how specific nuclei acid structures engage with LSD1 and how larger nucleic acids may serve as functional coregulators in telomere maintenance. We hypothesize that higher-order RNA topologies function as crucial mediators of chromatin-associated proteins. The specific aims of this proposal are thus 1) to define the structural mechanism and auto-regulatory role of an intrinsically disordered region of LSD1, 2) to identify the mechanism of action for LSD1-RNA assemblies involved in telomere maintenance, and 3) to determine the architecture and conformational rearrangements of a higher-order TERRA in solution and in a biomolecular condensate state. The long-term goal of this project is to understand how RNA structure and conformational dynamics influence LSD1-mediated regulatory networks. Results from these studies will provide new mechanistic insight into RNA-based chromatin biology and serve as a starting point in the development of therapeutics that target LSD1 and RNA in a context-specific manner.

项目摘要/摘要 该项目以RNA结构和RNA染色质相关蛋白的假设为中心 相互作用在维持基因组稳定性方面起着至关重要的作用。众所周知，非编码RNA（NCRNA） 与染色质的蛋白质成分相互作用，从而改变了高阶遗传结构和基因 表达。这些RNA-蛋白质相互作用的子集与衰老，癌症转移和神经元有关 发展。随着基因组方法开始鉴定RNA蛋白缔合及其与癌症的联系， 关于基于表观遗传学的RNA结合蛋白的知识，我们的知识仍然存在关键差距。 RNA可以模仿 DNA，在细胞应激下形成瞬态DNA/RNA杂交，并充当支架，以募集蛋白质复合物 染色质。此外，这些RNA可以与结构化和无序的蛋白质区域相互作用以形成 可以进行液态液相分离或生物分子冷凝物的多价网络。因此， 检查溶液中的RNA-蛋白质组件，在类似于紧凑型细胞的凝结状态下 环境可以解决基本问题：1）序列要求或结构是什么 驱动多价RNA - 蛋白质相互作用的形成的特征？ 2）RNA-蛋白如何 构象变化会影响染色质蛋白的功能和活性？在这个建议中，我们 寻求了解RNA如何与赖氨酸特异性脱甲基酶-1（LSD1）酶相互作用。 LSD1是一个 必需的甲基化调节剂，并且由于其广泛的相互作用而在许多癌症中具有致癌特性 网络分化和DNA损伤反应途径的网络和与RNA的关联。我们将集中精力 在包含与LSD1相互作用的RNA（Terra）的端粒重复响应于DNA损伤时相互作用 染色体的末端。这些RNA-LSD1相互作用与异染色质的调节有关 端粒。 Co-I（Zhang）发现端粒聚类发生在无端粒酶细胞中 并且该过程通过RNA介导的相分离驱动。我们将使用综合结构和 细胞生物学方法证明特定核酸结构如何与LSD1互动以及如何更大 核酸可以用作端粒维持中的功能性核心节。我们假设高阶 RNA拓扑充当染色质相关蛋白的关键介质。这个特定的目的 因此，提案是1）定义本质上无序的结构机制和自动调节作用 LSD1的区域，2）确定与端粒有关的LSD1-RNA组件的作用机理 维护和3）确定高阶的结构和构象重排 溶液和生物分子冷凝物状态中的底田。该项目的长期目标是了解 RNA结构和构象动力学如何影响LSD1介导的调节网络。结果 这些研究将为基于RNA的染色质生物学提供新的机械洞察力，并作为开始 以特定方式靶向LSD1和RNA的治疗剂的开发。