From 3D genomes to neural connectomes: Higher-order chromatin mechanisms encoding long-term memory

从 3D 基因组到神经连接组：编码长期记忆的高阶染色质机制

• 批准号: 10674017
• 负责人: Jennifer Elizabeth Phillips-Cremins
• 金额: $ 113.75万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-15 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10674017
• 关键词: 3-Dimensional; Address; Architecture; Brain; CRISPR screen; Cell Reprogramming; Cells; Central Nervous System; Chromatin; Data Set; Defect; Development; Disease; Engineering; Epigenetic Process; Exhibits; Foundations; Fragile X Syndrome; Functional disorder; Future; Gene Expression; Genetic; Genetic Transcription; Genome; Genomics; Goals; Imaging technology; In Vitro; Individual; Knowledge; Length; Link; Maps; Memory; Modification; Molecular; Neurodegenerative Disorders; Neurodevelopmental Disorder; Neurons; Neurosciences; Pathologic; Pattern; Phenotype; Physiological; Proteins; RNA; Role; Somatic Cell; Structure-Activity Relationship; Synapses; Synaptic plasticity; Technology; Work; Writing; cell type; connectome; genome-wide; in vivo; in vivo Model; insight; long term memory; memory consolidation; memory encoding; nervous system disorder; neural; neural circuit; public health relevance; transcription factor

Title: From 3D genomes to neural connectomes: Higher-order chromatin mechanisms encoding long- term memory Summary The Cremins Lab focuses on higher-order genome folding and how classic epigenetic modifications work through long-range, spatial mechanisms to govern genome function in the developing brain. Much is already known regarding how transcription factors work in the context of the linear genome to regulate gene expression. Yet, severe limitations exist in our ability to engineer chromatin in neural circuits to correct synaptic defects in vivo. At the lab’s inception, it remained unclear whether and how genome folding would functionally influence cell type-specific gene expression. Thus far, we have developed and applied new molecular and computational technologies to discover that nested chromatin domains and long-range loops undergo marked reconfiguration during neural lineage commitment, somatic cell reprogramming, neuronal activity stimulation, and in repeat expansion disorders. We have demonstrated that loops induced by cortical neuron stimulation, engineered through synthetic architectural proteins, and miswired in fragile X syndrome were tightly connected to transcription, thus providing early insight into the genome’s structure-function relationship. We will now focus on a fundamental mystery in neuroscience: how memory is encoded over decades despite rapid turnover of synaptic proteins/RNAs. We hypothesize that the 3D genome integrates molecular traces of synaptic plasticity written on chromatin to store long-term memory in neural circuits. We will employ single-cell genomics and imaging technologies to dissect the extent to which individual synaptic inputs create 3D epigenetic traces. We will perform genome-wide CRISPR screens to identify specific loops and epigenetic modifications functionally important for synaptic plasticity. We will also re-direct technologies used for genome architecture mapping to create molecular activity-dependent connectome maps, and computationally integrate neuronal connectome maps across length scales with 3D epigenetic data sets. Successful completion of this work will shed new light on the genetic and epigenetic mechanisms governing structural and functional synaptic plasticity in physiologically relevant in vitro and in vivo models of memory encoding and consolidation. Many neurological disorders exhibit synaptic defects, and alterations in neuronal activity-dependent gene expression underlie pathological neural phenotypes. Addressing this knowledge gap will provide an essential foundation for our long-term goals to understand how, when, and why pathologic genome misfolding leads to synaptic dysfunction, and to engineer the 3D genome to reverse pathologic synaptic defects in debilitating neurological diseases.

标题：从3D基因组到神经连接：编码长染色体的高阶染色质机制 术语记忆 摘要 克雷姆斯实验室专注于高阶基因组折叠以及经典的表观遗传修饰如何起作用 通过远程、空间机制来控制发育中大脑中的基因组功能。很多事情都已经发生了 已知转录因子如何在线性基因组的背景下工作来调节基因 表情。然而，我们在神经回路中设计染色质以纠正突触的能力存在严重的局限性。 体内的缺陷。在实验室开始时，尚不清楚基因组折叠是否以及如何发挥作用 影响细胞类型特异性基因的表达。迄今为止，我们已经开发和应用了新的分子和 发现嵌套染色质结构域和长程环的计算技术经历了标记 神经谱系承诺，体细胞重新编程，神经元活动刺激， 以及重复扩张性疾病。我们已经证明了由大脑皮层神经元刺激诱导的环路， 通过人工合成的建筑蛋白进行工程设计，并在脆性X综合征中连接错误，紧密相连 到转录，从而提供对基因组的结构-功能关系的早期洞察。我们现在将集中精力 关于神经科学中的一个基本谜团：记忆是如何在几十年来编码的，尽管记忆的快速更替 突触蛋白/RNA。我们假设3D基因组整合了突触可塑性的分子痕迹 写在染色质上，用来存储神经回路中的长期记忆。我们将使用单细胞基因组学和 成像技术剖析了单个突触输入在多大程度上创造了3D表观遗传痕迹。我们 将进行全基因组CRISPR筛查，以确定特定的循环和表观遗传修饰的功能 对突触的可塑性很重要。我们还将把用于基因组结构映射的技术重新定向到 创建分子活性依赖的连接组图，并通过计算整合神经元连接组 利用3D表观遗传数据集绘制了长度范围的地图。这项工作的顺利完成将带来新的曙光。 大鼠突触结构和功能可塑性的遗传和表观遗传机制 与生理相关的记忆编码和巩固的体外和体内模型。许多神经科 疾病表现为突触缺陷，神经元活性依赖基因表达的改变是其基础 病理神经表型。解决这一知识差距将为我们的 理解病理性基因组错误折叠如何、何时以及为什么导致突触的长期目标 功能障碍，并设计3D基因组以逆转衰弱神经中的病理性突触缺陷 疾病。

项目成果

3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome.

• DOI: 10.1016/j.cell.2022.06.052
• 发表时间: 2022-07-21
• 期刊: CELL
• 影响因子: 64.5
• 作者: Haws, Spencer A.;Simandi, Zoltan;Barnett, R. Jordan;Phillips-Cremins, Jennifer E.
• 通讯作者: Phillips-Cremins, Jennifer E.

A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations.

多环染色质特征可预测患有家族性阿尔茨海默病突变的神经元中基因表达失调。

• DOI: 10.1101/2024.02.27.582395
• 发表时间: 2024
• 期刊: bioRxiv : the preprint server for biology
• 作者: Chandrashekar,Harshini;Simandi,Zoltan;Choi,Heesun;Ryu,Han-Seul;Waldman,AbrahamJ;Nikish,Alexandria;Muppidi,SrikarS;Gong,Wanfeng;Paquet,Dominik;Phillips-Cremins,JenniferE
• 通讯作者: Phillips-Cremins,JenniferE

Cohesin-dependence of neuronal gene expression relates to chromatin loop length.

• DOI: 10.7554/elife.76539
• 发表时间: 2022-04-26
• 期刊: eLife
• 影响因子: 7.7
• 作者: Calderon L;Weiss FD;Beagan JA;Oliveira MS;Georgieva R;Wang YF;Carroll TS;Dharmalingam G;Gong W;Tossell K;de Paola V;Whilding C;Ungless MA;Fisher AG;Phillips-Cremins JE;Merkenschlager M
• 通讯作者: Merkenschlager M