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

几乎每个人类细胞都包含一个3米长的遗传物质（DNA）的副本，使我们独一无二。 在一项惊人的成就中，这些巨大的DNA分子的基因序列在大约20年前被解码。 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（大约6微米直径的球体）中。了解DNA中的信息如何被细胞利用是现代医学进步和促进健康的基础。 在细胞生长的一个阶段，细胞核的分子以未凝聚的聚合物形式填充细胞核，由于自然的热搅动，这种聚合物形式迅速移动。分子的运动还没有完全弄清楚，特别是核中紧密堆积所引起的相干运动，在核中许多分子部分一起运动。本研究的目标是确定这种动态自组织的机制，使用一个强大的实验，模拟和建模相结合。 通过对相干运动起源的微观描述，这项研究将改变我们对细胞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的培训。这个合作项目将联合收割机高分辨率活细胞成像实验与理论和计算模型相结合，以探测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个细胞系中进行实验。这些实验将在很宽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，这些实验将指导理论和计算模型的基础上粗粒度的描述染色质作为一个封闭的和流体动力学相互作用的灵活的聚合物链驱动内部随机力偶极子代表活性酶。我们将测试的假设，染色质动力学主要是通过流体动力学相互作用的内部活动的后果，并使用实验和模型之间的定量比较，以阐明对称性，频率和强度的活动事件负责连贯的运动。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，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

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.