Evolution of Pre-mRNA Splicing in Primates

描述（由申请人提供）：本项目的目标是系统地调查灵长类动物中前体mRNA剪接的进化，并阐明产生物种特异性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巨大的调节和功能多样性。它还允许基因进化新的剪接异构体，同时仍表达祖先的剪接异构体。许多基因具有物种特异性的外显子和剪接模式，其产生于影响基本剪接信号的小规模序列变化或大规模插入或缺失。然而，尽管剪接在真核生物基因组进化过程中发挥着关键作用，但关于剪接变化如何发生以及这种变化的进化意义的许多问题仍然没有得到很大程度的探索。我们建议结合联合收割机的基因组，计算和分子的方法来研究剪接的变化在灵长类动物和人类的进化。具体目标是：1）利用脊椎动物物种的基因组比对、通过微阵列和基于测序的技术产生的人类基因的广泛外显子水平转录组谱以及人类和非人类灵长类动物中新外显子的分子剪接分析，研究灵长类动物中新外显子的产生和进化。2)通过高密度外显子连接阵列和大量人类和灵长类动物组织的RNA-seq分析，全面检查人类和非人类灵长类动物之间的剪接差异。3)通过剪接调控信号的比较分析和小基因实验，阐明灵长类剪接进化的机制。该项目将改善人类和灵长类动物基因组的注释，大大扩展我们物种特有的新外显子和剪接模式的知识，并阐明真核生物基因组如何通过剪接的进化来扩展其功能库。这些研究的结果将阐明基因组序列的进化如何导致物种间的剪接差异。这将为剪接的调节以及遗传变异如何破坏人类疾病中的剪接提供重要的见解。 公共卫生相关性：许多人类疾病是由前体mRNA剪接的异常引起的。本计画将系统地研究灵长类剪接的演化，并阐明剪接模式如何随基因组序列演化而改变。这些研究将提供重要的见解剪接是如何调节的，以及遗传变异如何破坏人类疾病中的剪接。

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. PUBLIC HEALTH RELEVANCE: Many human diseases are caused by aberrations in pre-mRNA splicing. This project will systematically survey the evolution of splicing in primates, and elucidate how splicing patterns change as a result of genome sequence evolution. These studies will provide significant insight into how splicing is regulated, and how genetic variations disrupt splicing in human diseases.