Integrative analysis of tissue-specific alternative splicing regulation under adaptive selection

适应性选择下组织特异性选择性剪接调控的综合分析

• 批准号: 10402926
• 负责人: Chaolin Zhang
• 金额: $ 51.67万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-07 至 2023-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10402926
• 关键词: Adult; Affect; Alternative Splicing; Bioinformatics; Biological Assay; Biology; Brain; Cebidae; Code; Comparative Genomic Analysis; DNA; Data; Data Element; Development; Elements; Event; Evolution; Exons; Family; Frontotemporal Dementia; Genes; Genetic; Genetic Diseases; Goals; Human; In Vitro; Knowledge; Link; Malignant Neoplasms; Mammals; Maps; Methods; Modeling; Molecular; Monkeys; Motor Neurons; Mus; Mutate; Mutation; Neurons; Nucleic Acid Regulatory Sequences; Pan Genus; Phenotype; Phylogenetic Analysis; Phylogeny; Predisposition; Prevalence; Primates; Process; Protein Binding Domain; Protein Splicing; Proteins; RNA Splicing; RNA-Binding Proteins; RNA-Protein Interaction; Recording of previous events; Regulation; Regulatory Element; Reporter; Role; Series; Site; Source; Speed; Spinal; Statistical Models; Tissue Model; Tissues; Transcript; Untranslated RNA; Validation; axon growth; brain tissue; causal variant; cell type; comparative; driving force; experience; experimental study; fitness; genetic information; genomic signature; human disease; induced pluripotent stem cell; innovation; insight; interdisciplinary approach; mRNA Precursor; mammalian genome; nervous system disorder; species difference; trait; transcriptome sequencing

Integrative analysis of tissue-specific alternative splicing regulation under adaptive selection PROJECT SUMMARY Tissue-specific alternative splicing (AS) generates multiple transcripts from single genes and contributes critically to the cellular and phenotypic complexity of mammals. This process is tightly regulated by RNA-binding proteins (RBPs) which recognize specific regulatory elements in their target transcripts. A long-standing hypothesis from the evolutionary perspective is that changes of AS regulation due to mutations in cis-regulatory sequences provide a major driving force of speciation in mammals, including closely related species such as human and Chimpanzee. While recent studies convincingly demonstrated the pervasive species difference of AS in multiple tissues, two fundamental questions remain: 1) which evolutionary splicing changes are under adaptive selection in specific lineages because of acquired fitness advantages? 2) what are the underlying mutations that led to the shifted selective regimes? These challenges are associated with the intrinsic degeneracy of the splicing code and lack of effective computational and experimental approaches for direct comparative analysis. The primary goal of this project is to overcome these limitations, so that we can identify divergent AS events under adaptive selection and the causal mutations affecting important cis-regulatory elements. To achieve this overarching goal, we formulated three specific aims. In Aim 1, we will use phylogenetic genetic methods to detect lineage- specific changes in selection intensity and adaptive evolution of AS and map AS regulatory regions experiencing lineage-specific adaptive evolution. In Aim 2, to elucidate the underlying regulatory mechanisms that led to splicing divergence, we will systematically map divergent protein-RNA interactions and reconstruct the evolutionary history in the phylogeny through a combination of CLIP footprints, perturbation of RBPs and comparative genomic analysis. In Aim 3, we will focus on MAPT alternative exon 10, which is implicated in frontotemporal dementia (FTD), and perform detailed analysis to reveal the mechanism of its divergent splicing in primates and the associated functions at the cellular level. If successful, this study will advance our understanding of the contribution of AS evolution to potential phenotypic differences among different mammalian species and the underlying mechanisms. The strategy established in this study will also provide a new and generalizable paradigm to better understand the splicing code.

自适应选择下组织特异性替代剪接调节的综合分析 项目摘要 组织特异性的替代剪接（AS）产生来自单个基因的多个转录本，并至关重要 到哺乳动物的细胞和表型复杂性。该过程受RNA结合蛋白的严格调节 （RBP）识别其目标成绩单中特定的调节元素。一个长期的假设 进化的观点是，由于顺式调节序列突变引起的AS调节变化 在哺乳动物中提供主要的物种形成驱动力，包括与人类和人类相关的物种 黑猩猩。虽然最近的研究令人信服地证明了多种物种的普遍差异 组织，两个基本问题仍然存在：1）哪些进化剪接变化在自适应选择下 在特定的谱系中，由于获得了适应性的优势吗？ 2）导致什么的基础突变是什么 转移的选择性制度？这些挑战与剪接代码的内在变性有关 缺乏直接比较分析的有效计算和实验方法。主要 该项目的目标是克服这些限制，以便我们可以将不同的事件识别为自适应 选择和影响重要顺式调节元件的因果突变。实现这一总体 目标，我们提出了三个具体目标。在AIM 1中，我们将使用系统发育遗传学方法检测谱系 - 选择强度和AS和MAP的适应性演变的特定变化作为经历的监管区域 谱系特异性的自适应演化。在AIM 2中，阐明导致导致的基本调节机制 拼接差异，我们将系统地绘制发散蛋白-RNA相互作用并重建 通过剪辑足迹的组合，RBP和 比较基因组分析。在AIM 3中，我们将专注于MAPT替代外显子10，这与 额颞痴呆（FTD），并进行详细的分析以揭示其发散剪接的机制 在灵长类动物和细胞水平上的相关功能中。如果成功，这项研究将推动我们的 了解不同哺乳动物对潜在表型差异的进化的贡献 物种和基本机制。这项研究中制定的策略还将提供新的和 可以更好地理解剪接代码的可推广范式。