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

基本信息

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
项目类别：
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

项目摘要

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.

适应性选择下组织特异性选择性剪接调控的综合分析项目概要组织特异性选择性剪接 (AS) 从单个基因生成多个转录本，并发挥关键作用哺乳动物的细胞和表型复杂性。该过程受到 RNA 结合蛋白的严格调控（RBP）识别其目标转录本中的特定调控元件。一个长期存在的假设进化的观点是，由于顺式调控序列的突变，AS调控发生了变化提供哺乳动物物种形成的主要驱动力，包括密切相关的物种，例如人类和黑猩猩。虽然最近的研究令人信服地证明了 AS 在多个物种中普遍存在的物种差异对于组织，仍然存在两个基本问题：1）哪些进化剪接变化处于适应性选择之下由于获得的健身优势而在特定血统中？ 2）导致这种现象的潜在突变是什么？改变选择性制度？这些挑战与拼接代码的内在简并性有关缺乏有效的计算和实验方法进行直接比较分析。初级该项目的目标是克服这些限制，以便我们能够识别自适应下的不同 AS 事件选择和影响重要顺式调控元件的因果突变。为了实现这一总体目标目标，我们制定了三个具体目标。在目标1中，我们将使用系统发育遗传学方法来检测谱系- AS选择强度和适应性进化的具体变化以及地图AS监管区域经历的变化谱系特定的适应性进化。在目标 2 中，阐明导致剪接分歧，我们将系统地绘制不同的蛋白质-RNA 相互作用并重建通过 CLIP 足迹、RBP 扰动和比较基因组分析。在目标 3 中，我们将重点关注 MAPT 替代外显子 10，该外显子涉及额颞叶痴呆（FTD），并进行详细分析以揭示其发散剪接机制灵长类动物以及细胞水平的相关功能。如果成功的话，这项研究将推动我们了解 AS 进化对不同哺乳动物之间潜在表型差异的贡献物种和潜在机制。本研究中建立的策略也将提供一种新的、可推广的范式可以更好地理解拼接代码。