Genetic and functional assessment of human-specific duplicated genes

项目摘要 测序技术和生物信息学的最新进展已经创造了一个新兴的图景， 结构动态的人类和非人类灵长类动物基因组。除了单核苷酸变异， 结构变体（SV;例如，缺失、重复和倒位）在物种内和物种间大量发生 但更难研究。SV通常太大而不能用短读可靠地识别（例如，Illumina）数据 并且经常与重复的元素重合，使得这些位点在历史上难以组装，注释， 并进行功能性调查。尽管如此，已知SV相关的重排引起形态学改变， 和神经发育异常，以及少数人类特异性重复（HSD）基因 与创新的神经学特征有关。SV的潜在功能影响是巨大的， 单个突变事件可以在整个基因组中重新排列基因和调节元件。然而，在这方面， 虽然基因本身受到越来越多的关注，但SV的调控前景仍然很差 表征了已知基因表达差异导致多种人类疾病，并且 被认为是物种间表型差异的主要原因。因此，SV代表 研究不足，可能有影响力的一组基因座，以这种方式检查。这在以下情况下尤其有趣： HSD基因，尽管具有几乎相同的序列，但显示不同的表达模式。这项工作将 使用基因组技术研究进化上最近的SV对基因表达的影响， 人类和黑猩猩。这将通过三种方法来实现：（1）高通量测定 人复制的调节元件活性;（2）鉴定启动子-增强子的差异 SV断裂点上的连接体;和（3）测试候选调控基因之间的因果关系。 SV基因座的功能特征和基因表达。这项研究的结果将是第一个 同时表征数百个位点，并将提供对调控机制基础的深入了解。 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.