Folding, Misfolding, and Unfolding: How human 3D genome structure resists, adapts, or succumbs to physical stresses in health and disease

项目摘要/摘要： 人类染色体在细胞核内的3D折叠影响了许多基本的生物过程， 包括基因调控、DNA修复和复制，甚至细胞核的物理性质。近期 研究开始确定构成基因组结构的关键分子因素，但知之甚少 关于这种结构如何对细胞和细胞核经历的物理压力做出反应。3D基因组 健康细胞的结构必须经受住或对诸如物理力、核形状等扰动做出反应 变化，以及DNA破坏性的侮辱，比如辐射。基因组结构和核结构的破坏 会导致癌症或早衰等疾病，所以我们确定特征是很重要的， 3D基因组变化的原因和影响。通常，3D基因组组织中与疾病相关的变化是 孤立地考虑，即“这种变化发生在癌症中”，但这一观点可能会遗漏共同的潜在原因 在许多生物情况下管理3D基因组的机制。我的研究项目试图 对染色体在响应物理干扰时所经历的变化形成一个综合的观点 通过一系列相辅相成的项目。我们的首要目标是了解不同级别的3D 基因组结构对核形状变化和DNA损伤辐射的响应以及如何 基因组中的3D接触网络可以完成基因调节功能并有助于 原子核的必要物理性质。为此，我们将把显微镜、尖端技术 基于测序的技术，如染色体构象捕捉(Hi-C)和计算 在几个系统中研究3D基因组破坏的方法，包括：1)暴露于DNA的细胞 破坏性X射线照射，2)细胞核所需的3D基因组的初始状态和适应 在有限的迁徙过程中挤过狭窄的空间，以及3)基因组结构的方面 在层蛋白突变的早衰症细胞中，在细胞老化过程中被破坏和维持。我们的研究项目已经 产生了促进对这些系统的进一步研究的初步证据：我们已经确定细胞 在X射线损伤后主动保护其3D基因组结构以及3D基因组折叠状态影响 癌细胞核在转移过程中是否能挤过狭窄的空间。这些结果表明 对基因组结构变化的全面了解对于更好地了解疾病是必要的 开始和进展。分析跨系统的基因组结构变化将提供一个独特的， 哪种类型的基因组区域或结构是最健壮或最脆弱的，以及 不同长度尺度的基因组结构之间的依赖关系。所有这些结果将帮助我们建立一个 我们可以理解并最终预测某些治疗或状况的影响的框架 人类细胞类型，取决于它们最初的基因组折叠状态。这一框架将为 未来基于染色体结构的疾病诊断和治疗。

Project Summary/Abstract: The 3D folding of human chromosomes inside the nucleus affects numerous fundamental biological processes, including gene regulation, DNA repair and replication, and even the physical properties of the nucleus. Recent research is beginning to define the key molecular factors that build the genome structure, but little is known about how this structure responds to physical stresses experienced by cells and nuclei. The 3D genome structure in healthy cells must withstand or respond to perturbations such as physical forces, nuclear shape changes, and DNA damaging insults, like radiation. Disruptions in genome structure and nuclear architecture can lead to diseases such as cancer or premature aging, so it is important that we determine the characteristics, causes, and effects of 3D genome changes. Often, disease-related changes in 3D genome organization are considered in isolation, i.e. “this change occurs in cancer,” but this perspective may miss common underlying mechanisms that govern the 3D genome across many biological situations. My research program seeks to develop an integrative view of the changes that chromosomes experience in response to physical disruptions through a complementary set of projects. Our overarching goals are to understand how different levels of 3D genome structure change in response to nuclear shape changes and DNA damaging radiation and how the network of 3D contacts in the genome can accomplish both gene regulatory functions and contribute to necessary physical properties of the nucleus. To this end, we will integrate microscopy, cutting edge sequencing-based techniques such as chromosome conformation capture (Hi-C), and computational approaches to investigate 3D genome disruptions in several systems, including: 1) cells exposed to DNA damaging X-ray irradiation, 2) the initial states and adaptations of the 3D genome necessary for cell nuclei to squeeze through tight spaces during confined migration, and 3) the aspects of genome structure that are disrupted and maintained during cellular aging in a lamin-mutant progeria cell. Our research program has yielded preliminary evidence that motivates further study of these systems: we have determined that the cell actively protects its 3D genome structure after X-ray damage and that the 3D genome folding state influences whether cancer cell nuclei can squeeze through tight spaces during metastatic migration. These results show that a comprehensive understanding of genome structure changes is necessary to better understand disease initiation and progression. Analyzing genome structure changes across systems will provide a unique, integrated view of what types of genomic regions or structures are the most robust or fragile and the degree of dependence between genome structures at different length scales. All these results will help us build a framework in which we can understand, and eventually predict, the impact of certain treatments or conditions on human cell types, depending on their initial genome folding state. This framework will open avenues for future chromosome structure-based disease diagnosis and treatment.