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：编码长链DNA的高阶染色质机制 term内存 总结 Cremins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工作 通过长距离的空间机制来控制发育中大脑的基因组功能。很多已经 关于转录因子如何在线性基因组的背景下工作以调节基因表达， 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。 体内缺陷。在该实验室成立之初，人们还不清楚基因组折叠是否以及如何在功能上发挥作用。 影响细胞类型特异性基因表达。到目前为止，我们已经开发和应用了新的分子和 计算技术发现，嵌套的染色质结构域和长程环经历了显着的 神经谱系定型过程中的重构，体细胞重编程，神经元活性刺激， 和重复扩张障碍。我们已经证明了皮层神经元刺激引起的回路， 通过合成结构蛋白质进行工程改造，与脆性X综合征中的错误连接紧密相连， 转录，从而提供早期洞察基因组的结构功能关系。我们现在要集中精力 关于神经科学中的一个基本谜团：尽管大脑中的神经元迅速更替， 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，在神经回路中储存长期记忆。我们将采用单细胞基因组学， 成像技术来剖析单个突触输入创建3D表观遗传痕迹的程度。我们 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 对突触可塑性很重要我们还将重新指导用于基因组结构绘图的技术， 创建分子活性依赖的连接体图谱，并通过计算整合神经元连接体， 利用3D表观遗传学数据集绘制了不同长度尺度的地图。这项工作的成功完成将使人们对 关于控制结构和功能突触可塑性的遗传和表观遗传机制， 生理相关的体外和体内模型的记忆编码和巩固。许多神经 这些疾病表现出突触缺陷，神经元活性依赖性基因表达的改变是神经元功能障碍的基础。 病理性神经表型解决这一知识差距将为我们的 长期目标是了解病理性基因组错误折叠如何，何时以及为什么导致突触 功能障碍，并设计3D基因组来逆转衰弱神经系统中的病理性突触缺陷。 疾病

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.