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

构成我们身体的不同类型的细胞，如皮肤细胞或血细胞，有能力在一个人的一生中保持不同的身份，即使它们都有相同的DNA。细胞的身份记忆是如何在一个人的一生中得到保护的？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同时存在的长期细胞身份。这些知识对于理解与细胞特性丧失有关的疾病，如癌症，教育干细胞重新编程的新方法，以及最终为细胞治疗编程人类细胞，都是有价值的。这个项目包括创建和分析改变DNA紧凑性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育课程。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了K-12和本科生、科学方面代表性不足群体的成员以及数学方面的妇女。这个项目的目的是揭示染色质修饰电路介导表观遗传细胞记忆(ECM)的基本原理。ECM是细胞在不改变遗传序列的情况下，通过随后的细胞分裂保持独特的细胞类型特定基因表达模式的能力。该项目的关键假设是，染色质修饰电路中的协同正反馈回路结合表观遗传擦除和读写过程之间的时间尺度分离来管理ECM。为了验证这一假设，该项目遵循了一种由对新的多时间尺度随机过程的(准)平稳概率分布进行严格的数学分析而驱动的“构建到理解”的方法。这些过程自然地产生于染色质修饰电路的动力学，并采取非遍历过程的微小扰动的形式，从而捕捉到时间尺度的分离。该项目有三个目标。目标1和目标2着眼于单个基因的染色质修饰电路，识别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整。目的2着重于DNA甲基化在多大程度上使细胞外基质偏向抑制染色质状态，并提出一种正向自动调节机制来增强活跃染色质状态的细胞外基质。目的3研究如何通过将多个基因的染色质修饰电路连接在一起，创建对任意基因表达模式的长期记忆。作为原理的证明，Aim 3在表观遗传触发开关试验台上进行了实验，这是一个在涉及细胞命运决定的基因调控网络中高度代表的基序，在这个基序中，两个基因相互抑制。该项目由分子和细胞生物科学部的系统与合成生物学和遗传机制集群、数学部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和生化工程项目共同资助。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.