Deciphering how 3D genome organization orchestrates cardiac cellular identity

项目摘要 在心脏发育期间，协调的基因表达变化促进了进行性谱系限制 将多能祖细胞转化为终极身份，并在其一生中保持不变。受到威胁 分化和/或细胞状态与多种疾病有关，包括先天性心脏病的某些方面 疾病和心力衰竭。因此，细胞识别的潜在机制引起了人们的浓厚兴趣。模型 潜在的命运决定和身份往往集中在转录因子和/或生态位信号上。当前 范式未能协调有限数量的形态起源和特定血统之间的相互作用 转录因子导致200+种细胞具有不同和稳定的特性。我假设核子武器 体系结构是实现对数百个基因的协调调控的关键机制 通过管理其可访问性或可用性来支持蜂窝身份。支持我们的假设，我们有 建立了一个强大的工作机构，证明了核结构调节心脏细胞的身份 发展和疾病。首先，我们发现了关键转录因子不仅通过其机制 控制转录，但也编排基因组折叠，以调节心脏神经峰命运的决定。 其次，我们的工作表明，染色质的空间位置保护了心脏细胞的特性，并可能 导致人类心脏病(即椎板病)。数十年的研究表明，基因表达 程序受激活蛋白和相反抑制蛋白的招募和活性调节。此外 为了彻底改变我们对转录的理解，这项工作导致了直接针对转录的治疗 各种因素。同样平衡核结构的形成、维持和解体的机制 人们对此了解甚少。在EIA应用程序中，我概述了一个跨学科的愿景，以揭示这些 控制心脏细胞特性的机制。在主题1中，我提出了确定和破译如何 指导基因组折叠冲击心肌细胞建立、维持和拆解的分子分子 州政府。在主题2中，我提出了一些策略来揭示表观遗传、转录和机械输入是如何 在生理和病理上调节基因组相对于核层的空间位置 条件。我们已经建立了一个多管齐下的计划，将使用高通量3D成像，遗传 具有精确时空分辨率的操作，可调节的心脏微组织，表观基因组工程， 超分辨率成像和最先进的基因组学，以解决拟议的研究，重点是 生理上的相关性。正交化方法促进了严密性，但需要灵活性。我出色的履历 建立一个有影响力的工作实体支持我们对这一范式转换工作的追求。建议进行的研究 有可能重塑我们对表观遗传学、转录和机械相关的理解 机制指导3D基因组组织和协调心脏细胞身份。通过查看心脏 通过基因组组织的棱镜，我们预测了大量未实现的治疗机会。

Project Summary During cardiac development, coordinate gene expression changes facilitate the progressive lineage restriction of multipotent progenitors into a terminal identity that is maintained over their lifespan. Compromised differentiation and/or cell state have been linked to multiple diseases, including aspects of congenital heart disease and heart failure. Thus, the mechanisms underlying cellular identity are of intense interest. Models underlying fate determination and the identity often focus on transcription factors and/or niche signals. Current paradigms fail to reconcile how the interplay between a finite number of morphogens and lineage specific transcription factors result in 200+ cell types with distinct and stable identities. I hypothesize that nuclear architecture represents a critical mechanism for achieving coordinated regulation of hundreds of genes underlying cellular identity by governing their accessibility or availability. Supporting our hypothesis, we have built a strong body of work demonstrating that nuclear architecture regulates cardiac cellular identity in development and disease. First, we discovered mechanisms by which critical transcription factors not only govern transcription, but also choreograph genome folding to regulate cardiac neural crest fate determination. Second, our work shows that spatial positioning of chromatin safeguards cardiac cellular identity and likely contributes to human cardiac disease (i.e. laminopathies). Decades of work have shown that gene expression programs are regulated by the recruitment and activity of activator and opposing repressor proteins. In addition to revolutionizing our understanding of transcription, this work has led to therapies directly targeting transcription factors. The mechanisms that similarly balance formation, maintenance and dissolution of nuclear architecture are poorly understood. In the EIA application I outline an interdisciplinary vision to uncover how these mechanisms control cardiac cellular identity. In Theme 1, I propose strategies to identify and decipher how molecular players guiding establishment, maintenance and disassembly of genome folding impact cardiac cell state. In Theme 2, I propose strategies to uncover how epigenetic, transcriptional, and mechanical inputs regulate spatial positioning of the genome in relation to the nuclear lamina in physiologic and pathologic conditions. We have established a multipronged program that will use high throughput 3D imaging, genetic manipulations with precise spatiotemporal resolution, tunable cardiac microtissues, epigenome engineering, super-resolution imaging and state-of-the-art genomics to tackle the propose studies, with a focus grounded in physiological relevance. The orthogonal approaches promote rigor, but require flexibility. My strong track record of building an impactful body of work support our pursuit of this paradigm shifting work. The proposed studies have the potential to reshape our understanding of how epigenetics, transcriptional, and mechano-related mechanisms direct 3D genome organization and orchestrate cardiac cellular identity. By viewing cardiac diseases through the prism of genome organization, we predict a wealth of unrealized therapeutic opportunities.