Discovering human divergent activity-regulated elements using comparative, computational, and functional approaches

项目摘要 新的经历会引起大脑活动的不同模式，导致基因表达、神经元和神经元的变化。 大脑可塑性的基础。在人类中， 与其他物种相比，大脑的发育特别漫长。然而，机制和程度 人类神经元发生了哪些变化以支持可塑性的增加仍然是未知的。此外，虽然 延长发育可塑性可能支持认知能力和行为灵活性的增加， 也增加了神经发育障碍的脆弱性。神经元可塑性依赖于活动调节 由活性响应基因组调控元件控制的基因表达变化。虽然 我们和其他人已经确定了调节元件作为人类特异性进化的重要底物， 变化，最近的人类和非人类灵长类动物死后大脑的地图集忽略了这种动态刺激- 反应性调节元件。如果不对上下文相关数据进行训练， 基于序列推断调节功能不能预测活性依赖性调节元件。我们 假设人类趋异活性调节元件（hDAREs）中存在遗传变化 我们可以利用全基因组技术来发现这些人类特有的可塑性遗传基础， 接近。我们将使用实验和计算的方法来预测和比较活性调节 人类神经元与恒河猴和黑猩猩神经元的反应。我们已经开发 创新的建模系统，使我们能够在以前无法达到的生理活动状态中刺激 灵长类神经元，机器学习模型来预测基于序列的调节功能， 平行的报告基因测定和CRISPRi测定将允许我们评估候选hDARE的功能。 通过这些研究的成功完成，我们将确定哪些基因组元件和遗传 这些变化是人类神经元活动依赖性反应的基础， 元件代表了人类谱系中进化选择的主要基质。这将奠定基础 用于进一步表征发育中的人脑中的细胞可塑性机制的表型。 此外，这些数据集将为解剖遗传机制提供有价值的资源。 神经发育障碍

PROJECT SUMMARY New experiences elicit distinct patterns of brain activity, leading to the changes in gene expression, neuronal properties, and connectivity that underlie brain plasticity. In humans, the period of enhanced plasticity during brain development is particularly protracted compared to other species. However, the mechanisms and extent to which human neurons have changed to support increased plasticity remain unknown. Furthermore, although prolonged developmental plasticity may support increased cognitive capabilities and behavioral flexibility, it may also increase vulnerability to neurodevelopmental disorders. Neuronal plasticity depends on activity-regulated changes in gene expression that are controlled by activity-responsive genomic regulatory elements. Although we and others have identified regulatory elements as prominent substrates of human-specific evolutionary change, recent atlases of postmortem human and non-human primate brains overlook such dynamic stimulus- responsive regulatory elements. Without training on context-dependent data, current computational models that infer regulatory function based on sequence fail to predict activity-dependent regulatory elements. We hypothesize that there have been genetic changes in human divergent activity-regulated elements (hDAREs) and that we can discover these human-specific genetic underpinnings of plasticity using genome-wide approaches. We will use experimental and computational methods to predict and compare the activity-regulated responses of human neurons versus neurons from rhesus macaque and chimpanzee. We have developed innovative model systems that will allow us to stimulate physiological activity states in previously inaccessible primate neurons, machine learning models to predict regulatory function based on sequence, and massively parallel reporter assays and CRISPRi assays that will allow us to assess the function of candidate hDAREs. Through the successful completion of these studies, we will determine which genomic elements and genetic changes underlie activity-dependent responses in human neurons and the extent to which changes in these elements represent a major substrate of evolutionary selection in the human lineage. This will lay the groundwork for further phenotypic characterization of cellular plasticity mechanisms in the developing human brain. Additionally, these datasets will provide a valuable resource for dissecting genetic mechanisms of neurodevelopmental disorders.