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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.

几乎每个人类细胞都含有一份3米长的遗传物质(DNA)的副本，这使我们独一无二。大约20年前，这些巨大的DNA分子的基因序列被破译，这是一项令人惊叹的成就。尽管知道了序列，但目前还不清楚这些巨大的分子是如何以遗传信息有用的方式装入细胞核(直径约为6微米的球体)的。了解DNA中的信息是如何被细胞使用的，对于现代医学的进步和促进健康是至关重要的。在细胞生长的一个阶段，细胞核的分子以一种未浓缩的聚合物形式填充它，由于自然的热搅拌，这种聚合物迅速移动。对于分子的运动，尤其是由原子核中紧密堆积引起的相干运动，人们还没有完全了解，在原子核中，分子的许多部分一起运动。这项研究的目标是通过实验、模拟和建模的强大组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，拟议中的研究将改变我们对原子核机械生物学的理解。该项目还将为研究生和本科生提供新的教育机会，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。这个合作项目将结合高分辨率的活细胞成像实验与理论和计算模型来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，我们将在几个染色质空间分布不同的细胞系中进行实验。这些实验将在广泛的长度和时间范围内提供相关运动的精确测量，并将用于破译内部作用力对染色质组织的贡献。此外，这些实验将指导理论和计算模型，基于对染色质的粗粒度描述，将染色质描述为由代表活性酶的随机力偶极子内部驱动的受限和流体动力相互作用的柔性聚合物链。我们将检验染色质动力学主要是内部活动通过流体动力学相互作用的结果的假设，并使用实验和模型之间的定量比较来阐明导致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。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

期刊论文数量（11）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Symmetry-based classification of forces driving chromatin dynamics

基于对称性的染色质动力学驱动力分类

DOI：
10.1039/d2sm00840h
发表时间：
2022
期刊：
Soft Matter
影响因子：
3.4
作者：
Eshghi, Iraj;Zidovska, Alexandra;Grosberg, Alexander Y.
通讯作者：
Grosberg, Alexander Y.

Structural and Dynamical Signatures of Local DNA Damage in Live Cells

DOI：
10.1016/j.bpj.2019.10.042
发表时间：
2020-05-05
期刊：
BIOPHYSICAL JOURNAL
影响因子：
3.4
作者：
Eaton, Jonah A.;Zidovska, Alexandra
通讯作者：
Zidovska, Alexandra

Euchromatin Activity Enhances Segregation and Compaction of Heterochromatin in the Cell Nucleus

常染色质活性增强细胞核中异染色质的分离和压缩

DOI：
10.1103/physrevx.12.041033
发表时间：
2022
期刊：
Physical Review X
影响因子：
12.5
作者：
Mahajan, Achal;Yan, Wen;Zidovska, Alexandra;Saintillan, David;Shelley, Michael J.
通讯作者：
Shelley, Michael J.

Mechanical stress affects dynamics and rheology of the human genome

机械应力影响人类基因组的动力学和流变学