Collaborative Research: MODULUS: Uncovering and re-engineering chromatin modification circuits that dictate epigenetic cell memory

构成我们身体的不同细胞类型，如皮肤细胞或血细胞，即使它们具有相同的DNA，也有能力在个体的一生中保持不同的身份。细胞身份的记忆如何在个体的一生中得到保护？该项目揭示了关键的分子相互作用电路，使相同的DNA序列能够产生不同的和并发的长期细胞身份。这些知识对于理解与细胞身份丧失相关的疾病（如癌症）、培养干细胞重编程的新方法，以及最终为细胞治疗编程人类细胞是有价值的。这个项目包括创建和分析改变DNA压缩的分子电路的数学模型。这些数学模型丰富了当前定量分子生物学、系统生物学和合成生物学的教学课程。研究生接受基于分子生物学、数学建模和随机过程数学理论的高度跨学科的培训。该项目的教育方面通过外联和课程开发活动影响K-12和本科学生、科学领域代表性不足的群体成员和数学领域的女性。该项目的目的是揭示染色质修饰回路介导表观遗传细胞记忆（ECM）的基本原理。ECM是细胞在随后的细胞分裂中保持不同细胞类型特异性基因表达模式而不改变基因序列的能力。该项目的关键假设是，染色质修饰回路中的协同正反馈回路与表观遗传擦除和读写过程之间的时间尺度分离相结合，控制ECM。为了验证这一假设，该项目采用了一种“从构建到理解”的方法，该方法由对新的多时间尺度随机过程的（准）平稳概率分布的严格数学分析驱动。这些过程自然地从染色质修饰电路的动力学中产生，并采取非遍历过程的小扰动的形式，捕获时间尺度分离。该项目有三个目标。Aim 1和Aim 2关注单个基因的染色质修饰回路，确定控制时间尺度分离的生化参数，并建立实验模型系统对其进行调节。Aim 2关注DNA甲基化在多大程度上使ECM倾向于抑制染色质状态，并提出了一种积极的自动调节机制来增强活性染色质状态的ECM。目的3研究如何通过将多个基因的染色质修饰回路连接在一起，创建任意基因表达模式的长期记忆。作为原理证明，Aim 3在表观遗传开关试验台上进行了实验，这是一个在参与细胞命运决定的基因调控网络中高度代表的基序，其中两个基因相互抑制。该项目由分子与细胞生物科学部的系统与合成生物学和遗传机制集群、数学系的数学生物学项目以及化学、生物工程、环境和运输系统部的细胞与生物化学工程项目共同资助。该奖项反映了美国国家科学基金会的法定使命，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。

The different cell types that make up our body, such as skin cells or blood cells, have the ability to maintain distinct identities for the lifetime of an individual even if they all have the same DNA. How is memory of cell’s identity safeguarded for an individual’s lifetime? This project uncovers key molecular interaction circuits that enable the same DNA sequence to give rise to distinct and concurrent long-term cellular identities. This knowledge is valuable to understand diseases linked to loss of cell identity, such as cancer, to educate new approaches to stem cell reprogramming, and, ultimately, to program human cells for cell therapy. This project involves creating and analyzing mathematical models of molecular circuits that alter DNA compaction. These mathematical models enrich current educational curricula in quantitative molecular biology, systems biology, and synthetic biology. Graduate students receive a highly interdisciplinary training grounded on molecular biology, mathematical modeling, and mathematical theory of stochastic processes. Education aspects of the project impact K-12 and undergraduate students, members of underrepresented groups in science and women in mathematics through outreach and curriculum development activities. The objective of this project is to uncover fundamental principles by which chromatin modification circuits mediate epigenetic cell memory (ECM). ECM is the ability of cells to maintain distinct cell-type-specific gene expression patterns through subsequent cell divisions without a change in genetic sequence. The key hypothesis of this project is that synergistic positive feedback loops within chromatin modification circuits govern ECM in combination with time scale separation between epigenetic erasure and read-write processes. To validate this hypothesis, this project follows a “build-to-understand” approach driven by rigorous mathematical analysis of the (quasi)-stationary probability distribution of new multi-time scale stochastic processes. These processes naturally arise from the dynamics of chromatin modification circuits and take the form of small perturbations of non-ergodic processes, that capture time scale separation. The project has three aims. Aim 1 and Aim 2 focus on a single gene’s chromatin modification circuit, identifies biochemical parameters that control time scale separation, and establish an experimental model system to tune them. Aim 2 is focused on the extent to which DNA methylation biases ECM towards a repressed chromatin state and proposes a positive autoregulation mechanism to enhance ECM of an active chromatin state. Aim 3 investigates how, by wiring multiple genes’ chromatin modification circuits together, a long-term memory of arbitrary gene expression patterns could be created. As a proof of principle, Aim 3 performs experiments on an epigenetic toggle switch test-bed, a motif highly represented in gene regulatory networks involved in cell fate determination, in which two gene mutually repress each other. This project is co-funded by the Systems and Synthetic Biology and Genetic Mechanisms clusters in the Division of Molecular and Cellular Biosciences, the Mathematical Biology program in the Division of Mathematics and the Cellular and Biochemical Engineering program in the Division of Chemical, Bioengineering, Environmental and Transport Systems.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.