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.

抽象的哺乳动物大脑中的有丝分裂后神经元形成突触，在整个过程中动态重塑个人一生编码短期和长期记忆的突触可塑性涉及时空精细。调整基因表达水平以响应环境刺激，包括快速转录在几分钟的时间尺度上的早期基因和长期的整体染色质重塑。控制活性依赖性表达的作用遗传和表观遗传元件引起了人们的极大兴趣旨在理解经验如何塑造大脑。在这里，我们提交了一份题为“阐明 3- D 哺乳动物神经元活性依赖性基因表达的表观遗传决定因素。一个跨学科团队，在基因组折叠、表观遗传学、染色质工程、我们的目标是阐明神经生物学、突触发生、电生理学和计算生物学。长程循环相互作用、线性基因组表观遗传修饰、其表达之间的联系空间目标基因，以及哺乳动物神经元的活动。我们捕获立即的早期基因。功能性地参与单一短程循环，以秒为单位快速激活表达相比之下，我们认为次要的是对环境刺激的反应。反应基因将通过结构蛋白在空间上连接成复杂的、长距离的、预先存在的拓扑结构，使基因组在几小时到几天的时间内为第二波表达做好准备为了响应神经放电，我们将创建高分辨率的基因组折叠图。在小鼠海马神经元的激活过程中使用 Hi-C 我们将识别活动- 依赖增强子和全基因组基因表达，并确定它们的时间概况我们将制定数学模型来预测活动相关的循环。从增强子激活的时间开始立即早期基因和次级反应基因的表达通过整合与自闭症、精神分裂症、双相情感障碍相关的单核苷酸变异，成瘾，注意力缺陷/多动障碍与我们的模型，我们将预测特定的目标基因最后，我们将剖析循环的功能作用。使用 CRISPR 调节 Bdnf 和 c-fos 活性依赖性转录的增强子活性我们的工作是结构蛋白结合基序的基因组编辑和 CRISPRi 抑制。将揭示哺乳动物神经元基因组的远程相互作用景观并揭示因果关系 3-D 表观基因组与环境刺激转录反应动力学之间的关系神经激活。