EFRI CEE: Epigenomic Regulation Over Multiple Length Scales: Understanding Chromatin Modifications Through Label Free Imaging and Multi-Scale Modeling

该项目将开发新的计算和成像技术，对染色质组织的理解达到新的水平。染色质是每个细胞核中DNA和蛋白质的浓缩复合物，其结构和功能是基因表达的核心决定因素，因此控制着生物体生长，发育和健康的各个方面。计算工作将用于通知实验成像，成像将相应地通知计算，以开发多个长度尺度的染色质结构的验证模型。这些模型将使科学家能够解决有关DNA在原子尺度上的局部变化如何与纳米尺度上的染色质变化相关的关键问题，并最终改变基因表达。开发的新技术将公开提供，这将促进从物理学和工程学到生物学的跨学科研究，并支持国家科学基金会的理解生命规则的目标。该项目将涉及多个跨学科的研究生和博士后学者团队，他们将接受科学和工程方面的成功职业培训。此外，还计划开设为期6周的暑期课程，以激励和培训高中生成为STEM劳动力。该项目将首先通过利用“热休克反应”来研究单染色质纤维问题，该反应通过激活热休克基因使细胞能够在高温下生存。这一基本过程可用于检测与基因表达变化相关的染色质结构变化。通过最先进的成像技术，依靠光谱内在对比光子定位光学纳米显微镜（SICLON），这项工作旨在解决染色质结构在体内低至5 nm的长度尺度。为了提取该区域染色质的动态，将通过组合机器学习、进化优化策略和时域有限差分方法来生成图像的计算机表示。该工作流程将迭代求解染色质构型并推断任何表观遗传反应的分子事件。该项目将建立在最近开发的多尺度染色质模型的基础上，非常适合基于分子的实验观察解释。作为第二项工作，该项目将通过调查甲基转移酶活性对异染色质结构域的影响来扩大识别异染色质结构域结构效应的系统。同样，这方面的工作将依赖于无标记成像技术的进一步发展，以实现10纳米以下的分辨率，其总体目标是定量和预测性地了解细胞中染色质的3D组织。该奖项与由生物科学理事会分子和细胞生物科学部遗传机制小组和研究与创新新兴前沿资助该奖项反映了NSF的法定使命，并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，被认为值得支持。

This project will develop novel computational and imaging technologies for a new level of understanding about chromatin organization. Chromatin is the condensed complex of DNA and proteins in every cell nucleus whose structure and function is a core determinant of gene expression, and as such controls every aspect of the growth, development and health of organisms. The computational work will be used to inform experimental imaging and the imaging will correspondingly inform the computation to develop validated models of chromatin structure at multiple length scales. These models will enable scientists to address key questions about how local changes in DNA at the atomic scale relate to changes in chromatin at the nanometer scale, and ultimately alter gene expression. The new technologies developed will be made publicly available, which will facilitate research across disciplines spanning physics and engineering to biology, and support the National Science Foundation's goal of Understanding the Rules of Life. The project will involve multiple cross-disciplinary teams of graduate students and postdoctoral scholars who will be trained for successful careers in science and engineering. A 6-week summer course is also planned to inspire and train high school students for the STEM workforce.The project will start by examining the single chromatin fiber problem through exploitation of the "heat shock response" that enables cells to survive high temperatures through activation of heat shock genes. This fundamental process can be used to detect changes in chromatin structure associated with changes in gene expression. Through state-of-the-art imaging, relying on spectroscopic intrinsic-contrast photon-localization optical nanoscopy (SICLON), this work seeks to resolve chromatin structure in vivo to as low as 5 nm length scale. To extract the dynamics of chromatin in this region, computer representations of the images will be generated through combined machine learning, evolutionary optimization strategies and finite difference time domain methods. The workflow will iteratively solve chromatin configurations and infer molecular events for any epigenetic response. The project will build upon a recently developed multiscale chromatin model ideally suited for molecular-based interpretation of experimental observations. As a secondary effort, the project will scale up systems for identifying structural effects of heterochromatin domains by investigating the impact of methyltransferase activity on these domains. Again, this aspect of the work will rely on further development of label-free imaging technologies to achieve sub-10 nm resolution, with the overall goal of quantitative and predictive understanding the 3D organization of chromatin in the cell.This award is co-funded by the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate and by the Emerging Frontiers in Research and Innovation Program in the Division of Emerging Frontiers and Multidisciplinary Activities in the Engineering Directorate.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.