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 基因组到神经连接组：编码长链的高阶染色质机制 术语记忆 概括 Cremins 实验室专注于高阶基因组折叠以及经典表观遗传修饰的工作原理 通过远程空间机制来控制发育中的大脑中的基因组功能已经有很多工作。 已知转录因子如何在线性基因组背景下发挥作用来调节基因 然而，我们在神经回路中改造染色质以纠正突触的能力存在严重限制。 在实验室成立之初，尚不清楚基因组折叠是否以及如何发挥作用。 迄今为止，我们已经开发并应用了新的分子和技术。 计算技术发现嵌套染色质结构域和长程环经历了标记 神经谱系定向期间的重新配置、体细胞重新编程、神经活动刺激、 在重复扩张障碍中，我们已经证明了皮质神经元刺激引起的环路， 通过结构合成蛋白设计，与脆性 X 综合征中的错误接线紧密相连 转录，从而提供对基因组结构与功能关系的早期了解。 神经科学的一个基本谜团：尽管记忆快速更新，但几十年来记忆是如何编码的 我们发现 3D 基因组整合了突触可塑性的分子痕迹。 写在染色质上以在神经回路中存储长期记忆我们将采用单细胞基因组学和 我们使用成像技术来剖析单个突触输入产生 3D 表观遗传痕迹的程度。 将进行全基因组 CRISPR 筛选，以识别功能上的特定环和表观遗传修饰 对于突触可塑性很重要，我们还将重新定向用于基因组结构映射的技术。 创建分子活动依赖性连接组图，并通过计算整合神经连接组 利用 3D 表观遗传数据集绘制跨长度尺度的图谱，这项工作的成功完成将为我们带来新的启示。 控制结构和功能突触可塑性的遗传和表观遗传机制 记忆编码和巩固的生理相关的体外和体内模型。 疾病表现出突触缺陷，神经活动依赖性基因表达的改变是其背后的原因 解决这一知识差距将为我们提供重要的基础。 长期目标是了解病理性基因组错误折叠如何、何时以及为何导致突触 功能障碍，并设计 3D 基因组来逆转神经衰弱的病理性突触缺陷 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