Evolution of Pre-mRNA Splicing in Primates

描述(申请人提供)：这个项目的目标是系统地调查灵长类动物中前-mRNA剪接的进化，并阐明产生物种特有外显子和剪接模式的分子机制。高等真核生物中的选择性剪接从有限的蛋白质编码基因库中产生了巨大的调控和功能多样性。它还允许基因进化出新的剪接异构体，同时仍然表达祖先的剪接异构体。许多基因都有物种特有的外显子和剪接模式，这些外显子和剪接模式要么是影响基本剪接信号的小规模序列变化，要么是大规模的插入或缺失。然而，尽管剪接在真核基因组进化中起着至关重要的作用，但关于剪接如何发生以及这种变化的进化意义的许多问题仍然在很大程度上没有被探索。我们建议结合基因组、计算和分子方法来研究灵长类和人类进化过程中的剪接变化。其具体目标是：1)利用脊椎动物物种的基因组比对、基于微阵列和测序技术产生的人类基因的广泛外显子水平转录组图谱以及人类和非人类灵长类动物新外显子的分子剪接分析，研究灵长类动物新外显子的诞生和进化。2)通过高密度外显子连接阵列和大量人类和灵长类组织的RNA-SEQ图谱，在全球范围内研究人类和非人类灵长类组织之间的剪接差异。3)通过剪接调控信号的比较分析和微基因实验，阐明灵长类剪接进化的机制。该项目将改进人类和灵长类基因组的注释，极大地扩展我们物种特有的新外显子和剪接模式的知识，并阐明真核基因组如何通过剪接的进化来扩展其功能谱系。这些研究的结果将阐明基因组序列的进化如何有助于物种之间的剪接差异。这将为剪接的调节以及基因变异如何破坏人类疾病中的剪接提供重要的洞察力。

DESCRIPTION (provided by applicant): The goal of this project is to systematically survey the evolution of pre-mRNA splicing in primates, and elucidate the molecular mechanisms that created species-specific exons and splicing patterns. Alternative splicing in higher eukaryotes generates an enormous regulatory and functional diversity from a limited repertoire of protein-coding genes. It also permits a gene to evolve a new spliced isoform, while still expressing the ancestral spliced isoform. Many genes have species-specific exons and splicing patterns that arose from either small-scale sequence changes that affected essential splicing signals, or large-scale insertions or deletions. However, despite the critical role of splicing during eukaryotic genome evolution, many questions regarding how splicing changes occurred and the evolutionary significance of such changes remain largely unexplored. We propose to combine genomic, computational, and molecular approaches to study splicing changes during primate and human evolution. The specific aims are: 1) To investigate the birth and evolution of new exons in primates, using genome alignments of vertebrate species, extensive exon-level transcriptome profiles of human genes generated by microarray and sequencing-based technologies, and molecular splicing analysis of new exons in humans and nonhuman primates. 2) To globally examine splicing differences between humans and nonhuman primates, by high-density exon junction array and RNA-seq profiling of a large panel of human and primate tissues. 3) To elucidate the mechanisms of splicing evolution in primates, via comparative analysis of splicing regulatory signals and minigene experiments. This project will improve the annotation of human and primate genomes, greatly expand the knowledge of new exons and splicing patterns that are unique to our species, and shed light on how eukaryotic genomes expand their functional repertoire via the evolution of splicing. The results of these studies will elucidate how the evolution of genomic sequences contributed to splicing differences among species. This will provide significant insight into the regulation of splicing, and how genetic variations disrupt splicing in human diseases.