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Elucidating the 3-D epigenetic determinants of activity-dependent gene expression in mammalian neurons

阐明哺乳动物神经元活动依赖性基因表达的 3-D 表观遗传决定因素

基本信息

批准号：
10545070
负责人：
Jennifer Elizabeth Phillips-Cremins
金额：
$ 50.77万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-02-01 至 2024-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10545070
关键词：
3-Dimensional Architecture Attention deficit hyperactivity disorder Bipolar Disorder Brain Brain Diseases CCCTC-binding factor CRISPR interference CRISPR-mediated transcriptional activation Cell Nucleus Chromatin Clustered Regularly Interspaced Short Palindromic Repeats Complex Computational Biology Defect Detection Dimensions Disease Electrophysiology (science)Elements Embryo Engineering Enhancers Environment Epigenetic Process FOS gene Foundations Gene Expression Gene Expression Regulation Genes Genetic Genetic Transcription Genome Genomics Guide RNA Hi-C Hippocampus Hour Immediate-Early Genes In Vitro Individual Kinetics Knowledge Link Mammalian Cell Maps Modeling Modification Molecular Mus Neurobiology Neurons Pathway interactions Process Protein Binding Domain Proteins Research Personnel Resolution Role Schizophrenia Single Nucleotide Polymorphism Slice Stimulus Structure Synapses Synaptic plasticity Testing Time Up-Regulation Work YY1 Transcription Factor addiction autism spectrum disorder cell type chromatin remodeling embryonic stem cell epigenome experience genome editing genome-wide genomic locus high dimensionality imaging study in vivo innovation interest long term memory mathematical model nervous system disorder neural neural circuit postmitotic predictive modeling public health relevance response spatiotemporal stem synaptogenesis ultra high resolution

项目摘要

Abstract Post-mitotic neurons in the mammalian brain form synapses that dynamically remodel throughout an individual’s lifetime to encode short- and long-term memories. Synaptic plasticity involves spatiotemporal fine- tuning of gene expression levels in response to environmental stimuli, including rapid transcription of immediate early genes on the time scale of minutes and longer-term global chromatin remodeling. The cis- acting genetic and epigenetic elements that govern activity-dependent expression are of outstanding interest toward understanding how experiences sculpt the brain. Here, we submit a proposal entitled ‘Elucidating the 3- D epigenetic determinants of activity-dependent gene expression in mammalian neurons’. We have assembled an interdisciplinary team with critical expertise in genome folding, epigenetics, chromatin engineering, neurobiology, synaptogenesis, electrophysiology, and computational biology. We aim to elucidate the causal link among long-range looping interactions, epigenetic modifications on the linear genome, expression of their spatial target genes, and the activity of mammalian neurons. We hypothesize that immediate early genes will functionally engage in singular short-range loops to rapidly activate expression on the time scale of seconds to minutes in response to the environmental stimulus of neuronal activation. By contrast, we posit that secondary response genes will spatially connect via architectural proteins into complex, long-range, pre-existing topological configurations to poise the genome for a second wave of expression on the order of hours to days in response to neuronal firing. To test our hypotheses, we will create high-resolution genome folding maps using the Hi-C during a time course of activation in mouse hippocampal neurons. We will identify activity- dependent enhancers and gene expression genome-wide and determine their temporal profile with respect pre-formed and activity-dependent loops. We will formulate mathematical models to predict activity-dependent expression of immediate early genes and secondary response genes from the timing of enhancer activation and looping contacts. By integrating single nucleotide variants linked to autism, schizophrenia, bipolar disorder, addiction, and attention-deficit/hyperactivity disorder with our models, we will predict the specific target genes and potential pathways involved in neurological disease. Finally, we will dissect the functional role for loops and enhancer activity in regulating the activity-dependent transcription of Bdnf and c-fos using CRISPR genome editing of architectural protein binding motifs and CRISPRi inhibition of specific enhancers. Our work will uncover the genome’s long-range interaction landscape in mammalian neurons and reveal the causal link between the 3-D Epigenome and the kinetics of transcriptional response to environmentally stimulated neuronal activation.

摘要：有丝分裂后的神经元参与哺乳动物的大脑，形成突触，在整个生命过程中动态地重塑神经元。个体的一生需要对短期记忆进行编码，而对长期记忆进行编码。突触的可塑性涉及时空和精细记忆。调节基因的表达水平以响应环境刺激，包括对基因的快速转录。即刻和早期的基因依赖于几分钟的时间和规模，而更长期的是全球细胞染色质的重塑。发挥作用的遗传基因和表观遗传基因元素可以管理依赖于活动的基因表达，这是一个悬而未决的利益所在。为了更好地理解我们的经历是如何塑造我们的大脑的。在这里，我们可以提交一份题为《阐明世界3--》的建议。 D-表观遗传学决定因素：在哺乳动物的神经元中，依赖于活性的基因表达。我们已经组装了。一个跨学科的研究团队在基因组折叠、表观遗传学、染色质和工程等方面拥有关键的专业知识。神经生物学、突触发生学、电生理学、计算机和计算生物学。我们的目标是进一步阐明其原因。在长程基因环路相互作用中，表观遗传修饰依赖于其线性基因组，以及它们的表达能力。空间研究的目标是基因，控制和控制哺乳动物神经细胞的早期活动。我们假设，即刻和早期的基因将会改变。在功能上，我可以参与到一个单一的、短距离的循环中，以在10秒的时间和尺度上快速激活表达能力。几分钟后，人们对神经元激活的主要环境刺激因素做出了反应。相比之下，我们假设这是继发性的。对基因的响应将不会在空间上将它们连接起来，通过它们的结构和蛋白质进入一个复杂的、远程的或预先存在的。拓扑学的配置使人类基因组研究从几个小时到几天的数量级上经历了第二波基因表达浪潮。为了回应神经元的激活。为了测试我们的假设，我们将不会创建一个高分辨率的基因组折叠图谱。在小鼠海马神经元激活过程中使用Hi-C技术，我们将无法确定其活动-- 依赖的基因增强子在全基因组范围内控制和控制基因的表达，并以不同的尊重决定他们的临时基因表达谱。预先形成的活动和依赖于活动的循环。我们将制定新的数学模型来预测依赖于活动的活动。即刻和早期基因的表达水平和次级免疫反应基因的表达水平来自于增强子基因激活的最佳时机。以及接触者之间的循环。通过整合与自闭症、精神分裂症和双相情感障碍相关的单核苷酸变异。成瘾、精神障碍和注意力缺陷/多动障碍与我们的新模型有关，但我们无法预测这些特定的目标基因。还有一些潜在的神经通路参与了神经系统疾病的发生。最后，我们将深入剖析这些回路的功能和作用。此外，增强子的活性也参与了使用CRISPR来调节bdnf基因和c-fos基因的转录活性。结构蛋白和结合基序的基因组编辑功能，以及特定基因增强子的抑制功能。这是我们的工作。我们将揭示基因组在哺乳动物大脑神经元中的远程相互作用和景观效应，并揭示两者之间的因果关系。在3-D和表观基因组之间，转录反应和对环境刺激的反应的主要动力学过程。神经元的激活。