EFRI CEE: Sculpting the genome by design: epigenetic and chromatin looping inputs to measure and manipulate chromatin organization and dynamics

设计基因组以实现新功能的能力有可能对社会产生广泛的积极影响。 DNA由看似简单的四种碱基（A、T、C和G）组成，通过与蛋白质结合形成染色质，这有助于将DNA浓缩到细胞核中并调节DNA的输出。以前的工作已经确定了几个因素的重要性，包括染色质压实，染色质相关蛋白的身份和修饰，作为DNA输出的贡献者。然而，我们仍然缺乏对机制的理解，这些机制将使我们能够有效地设计DNA和染色质结构以实现新的功能。该项目将承担发现和合成的挑战，以满足这一需要，通过聘请科学家团队桥接工程和生物学。对于参与该项目的研究生，耶鲁大学物理与工程生物学综合研究生课程将作为培养新一代跨学科科学强有力实践者的框架。该项目还将从代表性不足的群体中招募学习生物学，工程学和物理学的本科生加入这个跨学科团队，参加定义明确但独立的项目。让这些学生在高中和初中阶段的外联项目中担任指导和领导角色，将增强他们作为科学家、工程师和学者的成长和信心，同时也带来了生物的基本概念，该项目的科学目标是定义染色质组织的设计原则，并利用基因组作为测量和分析染色质组织的设备。记录动态染色质状态。从历史上看，对染色质组织的定量和全面理解的主要障碍是缺乏通用的、易处理的系统来探测和解释染色质动力学。该项目利用联合收割机将单个活细胞中特定染色质基因座的动态行为的高分辨率观察与系统级图像和数据分析管道相结合，该管道将来自细胞群体的单粒子跟踪数据分类为离散扩散状态。将采用强大的遗传工具，结合模块化工程策略，改变影响染色质结构的关键因素，包括SMC蛋白复合物，粘附素和凝聚素，以改变局部表观遗传景观。模拟将被用来测试新兴的模型的起源拓扑相关的域，如循环挤出，这些模型将进一步增强占两个动态和排除体积的染色质聚合物在三维空间，以及驱动循环形成的过程。这些见解将被利用来开发一种全新的方法，通过基于重组酶的状态机设计，将瞬时染色质构象记录为基因组本身的“记忆”，将生物计算扩展到细胞生物状态的动态采样。该奖项由生物科学理事会分子和细胞生物科学部的遗传机制集群共同资助，由数学和物理科学理事会物理部的生命系统物理学计划，以及工程理事会新兴前沿和多学科活动部的新兴前沿研究和创新计划。该奖项反映了NSF的法定使命，并通过使用基金会的学术价值和更广泛的影响审查标准。

The ability to design genomes towards new functions has the potential to exert a broad, positive influence on society. Built from deceptively simple four bases (A, T, C and G), DNA is packaged by association with proteins into chromatin, which helps to condense the DNA into the nucleus and to regulate the DNA output. Previous work has established the importance of several factors, including chromatin compaction, the identity and modifications of the chromatin-associated proteins, as contributors to DNA output. However, we still lack understanding of the mechanisms that will allow us to effectively design DNA and chromatin architectures towards new functions. This project will take on the challenges of discovery and synthesis to meet this need by engaging teams of scientists bridging engineering and biology. For the graduate students who participate in this project, Yale's Integrated Graduate Program in Physical and Engineering Biology will serve as a framework for training a new generation of powerful practitioners of interdisciplinary science. This project will also recruit undergraduates studying biology, engineering and physics from under-represented groups to this interdisciplinary team to participate in well-defined, yet independent, projects. Engaging these students in mentoring and leadership roles for outreach programs at the high school and middle school levels will enhance their growth and confidence as scientists, engineers and scholars, while also bringing the fundamental concepts of bio-inspired design to the broader community.The scientific goals of this project are to define the design principles that underlie chromatin organization and to leverage the genome as a device to measure and record dynamic chromatin states. Historically, a major barrier to the quantitative and comprehensive understanding of chromatin organization is the lack of versatile, tractable systems in which to probe and interpret chromatin dynamics. This project leverages methods to combine high-resolution observations of the dynamic behavior of specific chromatin loci in individual living cells with a systems-level image and data analysis pipeline that sorts single-particle-tracking data from a population of cells into discrete diffusive states. Powerful genetic tools will be employed, in combination with modular engineering strategies, to alter key factors that influence chromatin structure, including the SMC protein complexes, cohesin and condensin, to create changes in the local epigenetic landscape. Simulations will be employed to test emerging models for the origin of topologically-associating domains, such as loop extrusion; these models will be further enhanced by accounting for both the dynamics and excluded volume of the chromatin polymer in three dimensions as well as the processes that drive loop formation. These insights will be leveraged to develop an entirely novel method to record transient chromatin conformations as "memories" in the genome itself through recombinase-based state machine designs, extending biological computing to the dynamic sampling of a cell biological state.This award is co-funded by the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate, by the Physics of Living Systems Program in the Division of Physics in the Mathematical and Physical 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.