Collaborative Research: URoL: Epigenetics 2: Phase separated genome compartments as drivers of epigenetic phenotypes

合作研究：URoL：表观遗传学 2：相分离的基因组区室作为表观遗传表型的驱动因素

• 批准号: 1921500
• 负责人: Stavros Lomvardas
• 金额: $ 100万
• 依托单位: Columbia University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1921500&HistoricalAwards=false
• 关键词: Collaborative; Research; URoL; Epigenetics; Phase

Different cell types in a given animal, such as heart cells and brain cells display different behaviors because they express different sets of genes. Yet, they all have DNA with essentially the same sequence and thus the same set of genes. How is it that the same DNA is used to generate different cell types? Which genes are on and which genes are off is controlled by how their underlying DNA sequences are packaged. DNA is packaged by wrapping it around specific proteins called histones to generate bead-like structures called nucleosomes. Strings of nucleosomes are then further folded to condense the underlying DNA and make it less accessible. Structures called heterochromatin are thought to be particularly effective at compacting strings of nucleosomes and turning off the underlying genes. A few years ago it was discovered that proteins named HP1 proteins, which are core components of heterochromatin, can sequester DNA into droplets that are separated from the surrounding solution in a different phase. This discovery provides a novel way to think about DNA packaging while also raising new fundamental questions such as: how are these droplet-based DNA compartments regulated by cellular signals and; how do changes in droplet mediated DNA organization impact biology at the level of a whole animal? To address these questions the PIs have assembled a multi-disciplinary team that brings together expertise in mouse biology, cutting-edge imaging technology and advanced biophysical methods. Another key goal of the project is to provide middle school students from underrepresented communities hands-on experience in carrying out experiments with packaged DNA. The research will: (i) shed light on how small collections of molecules can drive heritable changes at the level of a whole animal and; (ii) introduce middle-school students to the wonders of scientific discovery. A major form of heritable gene regulation is driven by heterochromatin, which silences specific subsets of genes and is essential for cellular differentiation, environmental adaptation and organismal physiology. The discovery that heterochromatin can form by phase-separation based mechanisms have led to a new paradigm for imagining genome organization, in which phase-separation enables genome sequestration. Given the novelty of the findings many fundamental questions remain unanswered such as: (i) what are the physico-chemical rules underlying phase-separation by heterochromatin; (ii) what types of emergent properties are conferred by phase-separation and; (iii) what are the physiological consequences? Addressing these questions requires working at the intersection of multiple disciplines. Therefore this project is organized within the physiological context of mouse olfactory receptor regulation as studied by Dr. Lomvardas and uses new imaging technologies pioneered by Dr. Larabell and biophysical tools developed by Dr. Narlikar. The project integrates experimental enquiry across multiple scales, from atomic-level studies of HP1 behavior to assessment of whole mouse phenotypes. Specifically the PIs will study olfactory receptor (OR) expression in mice, which is controlled by specialized heterochromatic compartments (ORH). ORH is spatially distinct from heterochromatin formed near centromeres (PH), strongly indicative of two different phase-separated states. ORH and PH are enriched for different HP1 paralogs, HP1 and HP1, respectively. Using a combination of mouse genetics, soft-Xray tomography and quantitative phase-separation methods the PIs will investigate (i) whether ORH and PH have different physico-chemical properties that prevent mixing and enable distinct physiological functions and, (ii) whether these different properties may arise from differences in the substructures formed within HP1 vs. HP1 phases. The PIs anticipate these studies will illuminate how atomic scale differences in sequence between HP1; and HP1; result in meso-scale differences in droplet structure, which in turn have a defined physiological impact. A key goal of the project is also to provide middle school students a hands-on experience in heterochromatin based phase-separation experiments through an annual summer workshop.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

特定动物的不同细胞类型，如心脏细胞和脑细胞，表现出不同的行为，因为它们表达不同的基因组。然而，它们都具有基本相同序列的DNA，因此具有相同的基因组。同样的DNA是如何产生不同类型的细胞的？哪些基因是开启的，哪些基因是关闭的，这取决于它们的基本DNA序列是如何包装的。DNA是通过将其包裹在称为组蛋白的特定蛋白质周围来包装的，以产生称为核小体的珠状结构。核小体串然后进一步折叠以浓缩底层DNA并使其不易接近。被称为异染色质的结构被认为在压缩核小体串和关闭潜在基因方面特别有效。几年前，人们发现名为HP 1蛋白的蛋白质是异染色质的核心成分，可以将DNA隔离到与周围溶液分离的液滴中。这一发现提供了一种新的方式来思考DNA包装，同时也提出了新的基本问题，如：这些基于液滴的DNA区室如何受到细胞信号的调节;液滴介导的DNA组织的变化如何影响整个动物水平的生物学？为了解决这些问题，PI组建了一个多学科团队，汇集了小鼠生物学，尖端成像技术和先进生物物理方法的专业知识。该项目的另一个关键目标是为来自代表性不足社区的中学生提供进行包装DNA实验的实践经验。该研究将：（i）阐明小分子集合如何在整个动物水平上驱动遗传变化;（ii）向中学生介绍科学发现的奇迹。 遗传基因调控的一种主要形式是由异染色质驱动的，异染色质沉默特定的基因子集，对细胞分化、环境适应和生物生理学至关重要。异染色质可以通过基于相分离的机制形成的发现已经导致了用于想象基因组组织的新范例，其中相分离使基因组隔离成为可能。鉴于这些发现的新奇，许多基本问题仍然没有得到解答，例如：（i）异染色质相分离的物理化学规则是什么;（ii）相分离赋予了什么样的紧急性质;（iii）生理后果是什么？解决这些问题需要在多个学科的交叉点工作。因此，该项目是在Lomvardas博士研究的小鼠嗅觉受体调节的生理背景下组织的，并使用Larabell博士开创的新成像技术和Narlikar博士开发的生物物理工具。该项目整合了多个尺度的实验研究，从原子水平的HP 1行为研究到整个小鼠表型的评估。具体而言，PI将研究小鼠的嗅觉受体（OR）表达，这是由专门的异染色质区室（ORH）控制的。ORH在空间上不同于着丝粒（PH）附近形成的异染色质，强烈指示两种不同的相分离状态。ORH和PH分别富集不同的HP 1旁系同源物HP 1和HP 1。使用小鼠遗传学，软X射线断层扫描和定量相分离方法的组合，PI将研究（i）ORH和PH是否具有不同的物理化学性质，以防止混合并实现不同的生理功能，以及（ii）这些不同的性质是否可能源于HP 1与HP 1相内形成的亚结构的差异。 PI预计这些研究将阐明HP 1和HP 1之间的原子尺度序列差异如何导致液滴结构的中尺度差异，这反过来又具有明确的生理影响。该项目的一个关键目标是通过每年的夏季研讨会为中学生提供基于异染色质的相分离实验的实践经验。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。