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CAREER: Physics of Chromatin: Micromechanics of Active Chromatin Dynamics in Interphase

职业：染色质物理学：间期活性染色质动力学的微观力学

基本信息

批准号：
1554880
负责人：
Alexandra Zidovska
金额：
$ 80万
依托单位：
New York University
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2016
资助国家：
美国
起止时间：
2016-09-15 至 2022-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1554880&HistoricalAwards=false
关键词：
CAREER Physics Chromatin Micromechanics Active

项目摘要

The DNA molecule in our cells is wrapped in a structure known as chromatin. Understanding how chromatin changes in time presents a fundamental question and is currently a frontier in both polymer physics as well as cell biology. To a physicist, chromatin is an exquisite example of a confined polymer that is subject to the basic laws of physics. To a biologist, chromatin controls gene expression, and physically packages DNA in a way that facilitates its replication and segregation. This project will lead to a mechanistic picture of active chromatin dynamics in live cells by integrating quantitative experimental approaches and theory from different areas of physics. As a part of this research program, the PI will develop a science outreach component targeting high school girls from underrepresented groups. In addition, this research program will provide training opportunities for undergraduate and graduate students, who will be trained in advanced optical microscopy techniques, small angle X-ray scattering, image processing, data analysis and polymer physics and statistical mechanics approaches pertinent to active systems far from equilibrium.The sequence of the human genome has been known for two decades, but its dynamic organization in three dimensions remains elusive. Methods like fluorescence in situ hybridization (FISH) or chromosome conformation capture (HiC) provided insights into how the chromatin is organized inside the cell nucleus. Methods like chromatin immunoprecipitation combined with sequencing (ChIP-Seq) helped us to map specific molecular players to the specific genomic loci within the context of specifics functions, usually transcriptional regulation. While FISH and HiC methods give us a 3D picture of the genome organization, it is a static picture, i.e. a snapshot of the human genome in a given time; they do not inform on the dynamic reorganization of the genome inside the nucleus. Similarly, Chip-Seq provides us with a snapshot of detailed 1D localization information of proteins of interest. The missing link in our current understanding is the connection between the 1D genomic information and the 3D topology of the cell nucleus in real time. The overall goal of this research program is to generate this missing link, i.e. to develop a real-time imaging of spatiotemporal dynamics of the human genome and understand the underlying physical laws. This research focuses on elucidating physics underlying nonequilibrium soft matter. Specifically, it presents development of an experimental and intellectual framework for understanding the dynamic behavior of chromatin in live cells. Chromatin presents an active polymer living in a confinement of the cell nucleus that is very different from the soft matter traditionally studied. It undergoes dynamic rearrangements, dissipates energy and exhibits self-organization far from thermodynamic equilibrium. Understanding of the mechanism/s beyond the active dynamics and elucidating the physical laws that such dynamics follows, will teach us new physics and its role in nuclear physiology.This project is being jointly supported by the Physics of Living Systems program in the Division of Physics and the Cellular Cluster in the Division of Molecular and Cellular Biosciences.

我们细胞中的DNA分子包裹在一种称为染色质的结构中。了解染色质如何随时间变化提出了一个基本问题，目前是聚合物物理学和细胞生物学的前沿。对于物理学家来说，染色质是一个受物理基本定律约束的受限聚合物的精致例子。对生物学家来说，染色质控制着基因的表达，并以一种便于复制和分离的方式对DNA进行物理包装。该项目将通过整合来自不同物理领域的定量实验方法和理论，导致活细胞中活性染色质动态的机械图。作为这项研究计划的一部分，PI将开发一个科学推广部分，目标是来自代表性不足群体的高中女生。此外，该研究计划将为本科生和研究生提供培训机会，他们将接受先进光学显微镜技术，小角度X射线散射，图像处理，数据分析以及与远离平衡的活性系统相关的聚合物物理和统计力学方法的培训。但它在三个方面的动态组织仍然难以捉摸。荧光原位杂交（FISH）或染色体构象捕获（HiC）等方法提供了对细胞核内染色质如何组织的见解。像染色质免疫沉淀结合测序（ChIP-Seq）这样的方法帮助我们在特定功能（通常是转录调控）的背景下将特定的分子参与者映射到特定的基因组位点。虽然FISH和HiC方法为我们提供了基因组组织的3D图像，但它是静态图像，即给定时间内人类基因组的快照;它们不能提供细胞核内基因组动态重组的信息。同样，Chip-Seq为我们提供了感兴趣蛋白质的详细1D定位信息的快照。我们目前的理解中缺少的一环是真实的细胞核的1D基因组信息和3D拓扑结构之间的联系。这项研究计划的总体目标是产生这一缺失的环节，即开发人类基因组时空动态的实时成像，并了解潜在的物理定律。这项研究的重点是阐明非平衡软物质的物理基础。具体来说，它提出了一个实验和知识框架的发展，了解染色质在活细胞中的动态行为。染色质是一种活跃的聚合物，生活在细胞核的限制中，这与传统上研究的软物质非常不同。它经历动态重排，耗散能量，并表现出远离热力学平衡的自组织。了解主动动力学之外的机制，阐明这种动力学所遵循的物理规律，将教会我们新的物理学及其在核生理学中的作用。本项目由物理学系生命系统物理学项目和分子与细胞生物科学系细胞群共同支持。

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