Genetic and functional assessment of human-specific duplicated genes

项目总结 测序技术和生物信息学的最新进展创造了一幅新兴的图景 结构动态的人类和非人类灵长类基因组。除了单核苷酸变体，更大的 结构变异(SVS；例如，缺失、重复和倒置)在物种内和物种之间都很丰富 但更难研究。SV通常太大而不能可靠地识别短读(例如Illumina)数据 而且经常与重复的元素重合，使得这些基因座在历史上很难组装、注释、 并从功能上进行调查。尽管如此，已知与SV相关的重排会导致形态改变 和人类神经发育异常，以及少数人类特有的重复(HSD)基因 与创新的神经学特征有关。SVS的潜在功能影响是巨大的，因为 单个突变事件可以在整个基因组中重新排列基因和调控元件。然而， 虽然基因本身受到了越来越多的关注，但SVS的监管状况仍然很差 特色化的。众所周知，基因表达差异会导致多种人类疾病，而且 被认为是物种间表型差异的主要因素。因此，SVS代表一种 在这种情况下，研究不足且可能具有影响力的一组基因座。这在以下情况下尤其耐人寻味 HSD基因，尽管有几乎相同的序列，但表现出不同的表达模式。这项工作将 用基因组学技术研究进化上最新的SVS对基因表达的影响 人类和黑猩猩。这将通过三种方法实现：(1)高通量分析 人类复制的调节元件活性；(2)启动子-增强子差异的鉴定 跨SV断点的连接体；以及(3)测试候选监管机构之间的因果关系 具有功能意义的SV基因座的特征和基因表达。这项研究的发现将是第一个 同时描述数百个基因座的特征，并将提供对调控机制基础的洞察 灵长类物种之间的变化。

PROJECT SUMMARY Recent advances in sequencing technologies and bioinformatics have created an emerging picture of structurally dynamic human and non-human primate genomes. In addition to single-nucleotide variants, larger structural variants (SVs; e.g., deletions, duplications, and inversions) are prolific within and between species but are more difficult to study. SVs are often too large to reliably identify with short-read (e.g., Illumina) data and frequently coincide with repetitive elements, making these loci historically difficult to assemble, annotate, and functionally investigate. Despite this, SV-associated rearrangements are known to cause morphological and neurodevelopmental abnormalities in humans, and a handful of human-specific duplicated (HSD) genes have been linked to innovative neurological features. The potential functional impact of SVs is enormous, as single mutational events can rearrange genes and regulatory elements throughout the genome. However, while the genes themselves have received growing attention, the regulatory landscape of SVs remains poorly characterized. Gene expression differences are known to contribute to a variety of human diseases, and are thought to be a major contributor to phenotypic divergence between species. SVs thus represent an understudied and likely impactful set of loci to examine in this light. This is particularly intriguing in the case of HSD genes, which show distinct expression patterns despite having nearly identical sequences. This work will use genomic techniques to investigate the effect of evolutionarily recent SVs on gene expression between humans and chimpanzees. This will be accomplished via three approaches: (1) high-throughput assay of human-duplicated regulatory element activity; (2) identification of differences in the promoter-enhancer connectome across SV breakpoints; and (3) testing for causal relationships between candidate regulatory features and gene expression at SV loci of functional significance. The findings of this research will be the first to characterize hundreds of loci in parallel and will offer insight into the mechanistic basis for regulatory changes between primate species.