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.

抽象的哺乳动物脑形成突触中的有丝分裂后神经元，在整个过程中动态重塑个人的一生，以编码短期和长期记忆。突触可塑性涉及时空精细 - 根据环境刺激对基因表达水平的调整，包括快速转录立即在几分钟和长期全球染色质重塑的时间范围内立即进行早期基因。顺式 - 控制活动依赖性表达的行动通用和表观遗传元素具有杰出的兴趣要了解体验如何雕刻大脑。在这里，我们提交了一个名为“阐明3-的提案” D活性依赖性基因表达在哺乳动物神经元中的表观遗传决定因素。我们已经组装了一个跨学科团队，在基因组折叠，表观遗传学，染色质工程方面具有关键专业知识，神经生物学，突触发生，电生理学和计算生物学。我们旨在阐明因果关系远程循环相互作用之间的联系，线性基因组的表观遗传修饰，其表达空间靶基因和哺乳动物神经元的活性。我们假设立即的早期基因将功能从功能上参与奇异的短距离环，以在秒的时间尺度上快速激活表达响应神经元激活的环境刺激的分钟。相比之下，我们认为那个次要响应基因将通过建筑蛋白在空间上连接成复杂的，远程，预先存在的拓扑配置可以使基因组在数小时至几天的数小时以上的第二波表达响应神经元的射击。为了检验我们的假设，我们将创建高分辨率的基因组折叠图在小鼠海马神经元中激活的时间过程中使用HI-C。我们将确定活动 - 依赖增强子和基因表达全基因组，并确定其临时概况预先形成和活性依赖性环。我们将构建数学模型以预测活动依赖性来自增强子激活的时间的直接早期基因和次级反应基因的表达和循环触点。通过整合与自闭症，精神分裂症，躁郁症相关的单核苷酸变体，成瘾和注意力缺陷/多动症与我们的模型，我们将预测特定的靶基因和神经疾病涉及的潜在途径。最后，我们将剖析循环的功能作用使用CRISPR控制BDNF和C-FOS的活动依赖性转录方面的增强剂活性建筑蛋白结合基序的基因组编辑和对特定增强子的CRISPRI抑制。我们的工作将发现基因组在哺乳动物神经元中的远程相互作用景观并揭示因果关系在3-D表观基因组和对环境刺激的转录反应的动力学之间神经元激活。