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

使用比较、计算和功能方法发现人类不同活动调节的元素

• 批准号: 10779701
• 负责人: KATHERINE S. POLLARD
• 金额: $ 83.21万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-15 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10779701
• 关键词: Address; Atlases; Autopsy; Behavioral; Biological Assay; Biological Models; Brain; CRISPR interference; Chromatin; Cognitive; Computer Models; Computing Methodologies; Data; Data Set; Development; Diploidy; Disease; Elements; Enhancers; Evolution; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Variation; Genetic study; Genome; Genomics; Human; In Vitro; Induced pluripotent stem cell derived neurons; Life Experience; Link; Location; Macaca; Macaca mulatta; Machine Learning; Mediator; Methods; Modeling; Molecular; Mutation; Neurodevelopmental Disorder; Neuronal Plasticity; Neurons; Pan Genus; Pattern; Phase; Phenotype; Phylogeny; Physiological; Prevalence; Primates; Property; Regulator Genes; Regulatory Element; Reporter; Resources; Sequence Analysis; Slice; Statistical Data Interpretation; Stimulus; Training; Variant; cognitive ability; comparative; convolutional neural network; developmental plasticity; experience; flexibility; genome-wide; innovation; machine learning model; nervous system disorder; nonhuman primate; response; sequence learning; single-cell RNA sequencing; species difference; stem cells

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.

项目总结 新的体验引发了大脑活动的不同模式，导致了基因表达、神经元 特性和连通性是大脑可塑性的基础。在人类中，可塑性增强的时期 与其他物种相比，大脑发育的时间特别长。然而，其机制和程度 人类神经元是否已经改变以支持更高的可塑性仍不清楚。此外，尽管 长期的发育可塑性可能支持认知能力和行为灵活性的增强，它可能 也会增加神经发育障碍的易感性。神经元的可塑性依赖于活动调节 由活性反应基因组调节元件控制的基因表达的变化。虽然 我们和其他人已经确定调控因素是人类特有的进化的显著底物 变化，最近的人类和非人类灵长类大脑的尸检图谱忽略了这种动态刺激- 反应灵敏的监管要素。如果不对上下文相关的数据进行训练，当前的计算模型 根据序列推断调控功能不能预测活动依赖的调控元件。我们 假设人类分化活性调节元件(HDARE)存在遗传变化 我们可以利用全基因组来发现这些人类特有的可塑性遗传基础 接近了。我们将使用实验和计算方法来预测和比较受活动调节的 人类神经元与恒河猴和黑猩猩神经元的反应。我们已经开发出 创新的模型系统将允许我们在以前无法访问的状态下刺激生理活动状态 灵长类神经元，基于序列和大规模预测调节功能的机器学习模型 平行的记者分析和CRISPRi分析将使我们能够评估候选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素和基因 变化是人类神经元活动依赖性反应的基础，以及这些反应的变化程度 元素代表了人类谱系中进化选择的主要底物。这将奠定基础 以进一步描述发育中的人脑细胞可塑性机制的表型特征。 此外，这些数据集将为剖析糖尿病的遗传机制提供宝贵的资源。 神经发育障碍。