Connecting perturbations of RNA binding proteins to their consequences

将 RNA 结合蛋白的扰动与其后果联系起来

• 批准号: 10388840
• 负责人: Michael P McGurk
• 金额: $ 6.76万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-12-01 至 2024-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10388840
• 关键词: Affect; Alternative Splicing; Back; Binding Proteins; Biological; Biology; Characteristics; Communities; Complex; Data; Data Set; Defect; Degenerative Disorder; Development; Disease; Doctor of Philosophy; Environment; Event; Exclusion; Exons; Family; Fibrinogen; Future; Generations; Genes; Genome; Genomics; Goals; Human; Individual; Institutes; Large-Scale Sequencing; Lead; Length; Light; Linear Models; Logic; Malignant Neoplasms; Maps; Massachusetts; Mentorship; Methodology; Mutation; Outcome; Pathology; Pattern; Point Mutation; Protein Splicing; RNA; RNA Processing; RNA Splicing; RNA-Binding Proteins; Regulation; Regulatory Element; Research; Role; Shapes; Short Tandem Repeat; Site; Source; Statistical Models; Stretching; Structure; Tandem Repeat Sequences; Technical Expertise; Technology; Tissues; Training; Transcript; Variant; Work; career; experience; experimental study; field study; flexibility; gene product; genetic regulatory protein; human disease; knock-down; preference; skills; tool; transcriptome; transcriptomics

PROJECT SUMMARY/ABSTRACT Alternative splicing allows multiple gene products to be generated from a single gene, and contributes to transcriptomic diversity across tissues, development, and individuals. Given that most genes undergo alternative splicing, the disruption of splicing is a common contributor to disease. Pathology can result through mutations affecting the splicing of particular genes as well as broad splicing defects that affect many genes. Advances in sequencing technology have greatly simplified the problem of identifying the splicing products present in a given tissue and determining how splicing is perturbed in diseases states. But the problem remains to extract actionable interpretations from the hundreds or thousands of splicing changes that even a single sequencing experiment might reveal. The goal of this project is to understand how perturbations of splicing regulators connect to the resulting changes in splicing. I will consider both variation at RNA-binding protein target sites and disruption of the RBPs themselves. I will first consider the connection between short tandem repeat (STR) variation and splicing. Given that many of the most abundant STRs in the genome match the sequence preferences of important splicing factors, I will leverage sequencing data spanning hundreds of individuals to determine whether these highly mutable sequences represent a frequently ignored source of splicing variation. I will then consider the regulatory characteristics of RBPs themselves. I will first reframe the approach commonly used to integrate RBP binding and splicing data as a flexible linear model which can incorporate additional information and confounders. I will then apply this to recent ENCODE panel of RBP binding and knockdown data to infer the networks of splicing events regulated by a given RBP. I will then seek to use these networks to interpret patterns of altered splicing in disease states. I will carry out this work under the mentorship of Christopher Burge at the Massachusetts Institute of Technology (MIT), a leader in the field of alternative splicing. Given the Burge lab’s long track record of strong computational and experimental work, this will provide an ideal environment for both carrying out this research and developing the skills I will need for an independent career as a computational biologist. The proposed training will involve frequent interaction with experts in the study of RNA binding proteins and splicing, including the research groups that generated many of the datasets I will study, such as the Graveley and Yeo labs. Through this work I will develop further technical expertise in a number statistical and computational approaches and be immersed in the biology of splicing. I will have access to the experience and expertise I will need to transition from the evolutionary genomics of my PhD to the study of RNA processing and its regulation

项目摘要/摘要 替代剪接允许从单个基因生成多个基因产物，并贡献 跨组织，发育和个体的转录组多样性。鉴于大多数基因经历了 替代剪接，剪接的破坏是疾病的共同贡献者。病理可以通过 影响特定基因剪接的突变以及影响许多基因的广泛剪接缺陷。 测序技术的进步大大简化了识别剪接产品的问题 存在于给定的组织中，并确定在疾病状态下剪接的干扰。但是问题 仍然要从数百或数千种拼接变化中提取可行的解释 单个测序实验可能会揭示。 该项目的目的是了解剪接调节器的扰动如何连接到由此产生的 剪接的变化。我将考虑RNA结合蛋白靶位点的变异和RBP的破坏 自己。我将首先考虑短串联重复（STR）变化和剪接之间的连接。 鉴于基因组中许多最丰富的str匹配重要的序列偏好 拼接因素，我将利用跨越数百个人的测序数据来确定这些是否是否 高度可变的序列代表了经常被忽略的剪接变化来源。然后我会考虑 RBP本身的监管特征。我将首先重新构架通常用于集成的方法 RBP绑定和拼接数据作为灵活的线性模型，可以包含其他信息，并且 混淆者。然后，我将将其应用于最新的RBP绑定和敲低数据的编码面板以推断 由给定的RBP调节的剪接事件网络。然后，我将寻求使用这些网络来解释 疾病状态中剪接改变的模式。 我将在马萨诸塞州学院的克里斯托弗·伯奇（Christopher Burge）的心态下进行这项工作 技术（麻省理工学院），替代剪接领域的领导者。鉴于Burge Lab的长期记录 计算和实验性工作，这将为进行这项研究提供理想的环境 并发展我作为计算生物学家独立职业所需的技能。提议 培训将涉及与专家进行RNA结合蛋白和剪接研究的经常互动，包括 我将研究许多数据集的研究小组，例如Graveley和Yeo Labs。 通过这项工作，我将在许多统计和计算方面发展进一步的技术专业知识 接近并沉浸在剪接生物学中。我将获得我将获得的经验和专业知识 需要从我的博士学位的进化基因组学到RNA处理的研究及其调节