EFRI CEE: Chromatin and epigenetic engineering with synthetic genome regulators

在每个人类细胞中，基因组通过将DNA包裹在线轴状蛋白质圆柱体周围以适应细胞核内而紧密包装成称为染色质的复合物。 染色质的DNA和蛋白质成分都可以在细胞核中被修饰，产生“化学书签”。“细胞可以使用这些书签，以及DNA中碱基序列中的信息，作为在正确的时间和正确的位置打开和关闭基因的指令。 化学书签是如何工作的尚不清楚，但一些研究表明，放错位置的书签可能会导致不同疾病的发生。 该项目的目标是了解化学书签的功能。 该策略将使用合成生物学来重新编程DNA中所需区域的书签，以改变它们的开关行为。这将有助于揭示DNA书签如何控制不同细胞的命运和功能。 这项工作将通过整合来自工程，计算机科学，化学和生物学的学生和科学家来揭示存储在染色质中的信息用于制造不同细胞类型并管理其功能的原理，从而产生教育影响。这些结果可能会产生更广泛的社会影响，因为它们有助于开发纠正疾病相关书签错误的方法，或者使用合成开关来保护生物免受基于DNA的基因组的侵害-例如工程病毒，细菌和其他病原体-可能构成生物威胁。这个变革性和跨学科项目的中心目标是创造纳米级的所谓“表观遗传开关”可以在目标基因组位点塑造染色质纳米环境。 这类2nm尺度的开关可以被编程为在指定的位点重新连接表观遗传状态，并引起信息丰富和有意义的表型结果。这些表观遗传开关由合成的DNA结合聚酰胺分子组成，其可以被编程为靶向嵌入在不同染色质状态中的基因组位点。此外，使用模块化设计，这些合成基因组读取器可以与不同的小分子配体缀合，这些小分子配体模拟表观遗传信号或接合不同的细胞机器以重新连接覆盖的染色质或表观遗传状态。待开发的基础技术对以下方面具有广泛的影响：（i）阐明管理基因组结构、稳定性和对基因组信息的受管制访问的“生命规则”，（ii）揭示表观基因组或染色质组织的新原理，（iii）生命系统的表观遗传工程，以及（iv）创新的基因组靶向治疗。该奖项由工程理事会新兴前沿和多学科活动司的新兴前沿研究和创新计划，生物科学理事会分子和细胞生物科学司的遗传机制计划，以及数学和物理科学理事会化学部的生命过程化学计划。该奖项反映了NSF的法定使命，并已被认为是值得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的支持。

In each human cell, the genome is tightly packaged into a complex called chromatin by wrapping the DNA around spool-like protein cylinders to fit inside the nucleus. Both the DNA and protein components of chromatin can be modified in the nucleus to produce "chemical bookmarks." Cells can use these bookmarks, together with the information in the sequence of bases in the DNA, as instructions for switching genes on and off at the right time and in the right place. How chemical bookmarks work is still unclear, but some studies have shown that misplaced bookmarks can contribute to the onset of different diseases. The goal of this project is to understand how chemical bookmarks function. The strategy will be to use synthetic biology to reprogram the bookmarks at desired regions of the DNA to change their switching behavior. This will help reveal how DNA bookmarking controls the fate and function of different cells. The work will have educational impact by integrating students and scientists from engineering, computer sciences, chemistry and biology to uncover the principles by which information stored in chromatin is used to make different cell types and govern their function. The outcomes could have broader societal impact by contributing to development of methods for correcting disease-associated bookmarking errors, or by using synthetic switches to protect against organisms with DNA-based genomes - such as engineered viruses, bacteria and other pathogens - that may pose biological threats.The central goal of this transformative and transdisciplinary project is to create nanoscale so-called "epigenetic switches" that can sculpt the chromatin nano-environment at targeted genomic loci. This class of 2nm-scale switches can be programmed to rewire epigenetic states at specified loci and evoke informative and meaningful phenotypic outcomes. These epigenetic switches are composed of synthetic DNA binding polyamide molecules that can be programmed to target genomic sites embedded in diverse chromatin states. Moreover, using modular design, these synthetic genome readers can be conjugated to different small molecule ligands that mimic epigenetic signals or engage distinct cellular machines to rewire overlaid chromatin or epigenetic states. The foundational technology to be developed has wide-ranging broader impacts on: (i) elucidating "Rules of Life" that govern genome architecture, stability, and the regulated access to genomic information, (ii) revealing new principles of epigenome or chromatin organization, (iii) epigenetic engineering of living systems, and (iv) innovative genome-targeted therapeutics. This award was jointly funded by the Emerging Frontiers in Research and Innovation Program in the Division of Emerging Frontiers and Multidisciplinary Activities in the Engineering Directorate, by the Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate, and by the Chemistry of Life Processes Program in the Division of Chemistry in the Mathematical and Physical Sciences 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.