Collaborative Research: Interphase Chromatin as a Complex Active Fluid: Experiments and Microscopic to Mesoscopic Modeling

合作研究：间期染色质作为复杂的活性流体：实验和微观到介观建模

基本信息

批准号：
1762506
负责人：
Alexandra Zidovska
金额：
$ 39.89万
依托单位：
New York University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2018
资助国家：
美国
起止时间：
2018-06-01 至 2022-05-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1762506&HistoricalAwards=false
关键词：
Collaborative Research Interphase Chromatin Complex

项目摘要

Almost every human cell contains a copy of the 3-meters of genetic material (DNA) that makes us unique. In an amazing achievement, the genetic sequence of these enormous DNA molecules was decoded about twenty years ago. Despite knowing the sequence, it remains unclear how these enormous molecules are packed into a cell nucleus (approximately a six micrometer diameter sphere) in a way that the genetic information can be useful. Understanding how the information in DNA is made available for use by the cell is fundamental for advances in modern medicine and to advancing health. During one phase in the growth of cells, the molecules of the nucleus fill it in an uncondensed polymeric form that rapidly moves because of natural thermal agitation. The molecular motion is not fully understood, especially the coherent motions caused by the close packing in the nucleus where many parts of the molecules move together. The goal of this research is to determine the mechanisms of this dynamic self-organization using a powerful combination of experiments, simulations and modeling. By providing a microscopic description for the origin of coherent motions, the proposed research will transform our understanding of the mechanobiology of the nucleus. This project also will provide novel educational opportunities for graduate and undergraduate students, who will receive training in advanced imaging techniques and analysis, cellular biology, polymer dynamics, fluid mechanics, as well as mathematical and computational modeling. This collaborative project will combine high-resolution live cell imaging experiments with theoretical and computational models to probe and illuminate the microscopic origins of interphase chromatin dynamics and its effect on the spatiotemporal self-organization of DNA. To develop a close connection between experiments and models, we will perform experiments in several cell lines with different spatial distributions of chromatin. These experiments will provide exquisite measurements of correlated motions over a wide range of length and time scales, and will be used to decipher the contributions of internal active forces on chromatin organization. Moreover, these experiments will guide theoretical and computational models based on coarse-grained descriptions of the chromatin as a confined and hydrodynamically interacting flexible polymer chain driven internally by stochastic force dipoles representing active enzymes. We will test the hypothesis that chromatin dynamics is primarily the consequence of internal activity via hydrodynamic interactions, and use quantitative comparisons between experiments and models to elucidate the symmetries, frequencies, and intensities of active events responsible for coherent motion. Such knowledge is critical for understanding the physiology of the interphase chromatin dynamics in the cell nucleus.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.

几乎每个人体细胞都含有一份 3 米长的遗传物质 (DNA) 副本，这使我们独一无二。大约二十年前，这些巨大 DNA 分子的基因序列被破译，这是一项令人惊叹的成就。尽管知道序列，但仍不清楚这些巨大的分子如何以遗传信息有用的方式包装到细胞核（直径约六微米的球体）中。了解 DNA 中的信息如何供细胞使用对于现代医学的进步和促进健康至关重要。在细胞生长的一个阶段，细胞核分子以未缩合的聚合形式填充，由于自然热搅动，该形式快速移动。分子运动尚不完全清楚，特别是由分子的许多部分一起运动的原子核中的紧密堆积引起的相干运动。这项研究的目标是通过实验、模拟和建模的强大结合来确定这种动态自组织的机制。通过为相干运动的起源提供微观描述，拟议的研究将改变我们对原子核力学生物学的理解。该项目还将为研究生和本科生提供新颖的教育机会，他们将接受先进成像技术和分析、细胞生物学、聚合物动力学、流体力学以及数学和计算建模方面的培训。该合作项目将高分辨率活细胞成像实验与理论和计算模型相结合，探索和阐明间期染色质动力学的微观起源及其对 DNA 时空自组织的影响。为了建立实验和模型之间的紧密联系，我们将在具有不同染色质空间分布的几种细胞系中进行实验。这些实验将在广泛的长度和时间尺度上提供相关运动的精确测量，并将用于破译内部主动力对染色质组织的贡献。此外，这些实验将指导基于染色质粗粒度描述的理论和计算模型，染色质是由代表活性酶的随机力偶极子内部驱动的受限且流体动力学相互作用的柔性聚合物链。我们将测试染色质动力学主要是通过流体动力学相互作用进行内部活动的结果这一假设，并使用实验和模型之间的定量比较来阐明负责相干运动的活动事件的对称性、频率和强度。这些知识对于理解细胞核中间期染色质动力学的生理学至关重要。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。