EFRI CEE: DNA origami tools to engineer chromatin structure and function in live cells

从酵母到人类的许多生物体都通过将其基因组反复包裹在组蛋白周围形成称为染色质的纳米级线轴来组织基因组。细胞利用染色质的组织来决定基因是活跃表达还是关闭。结合靶向特定基因、可视化其位置和结构、激活基因和检测活细胞中基因表达的能力，将是如何在活生物体中研究和控制基因的重大技术进步，并将在许多领域得到应用，包括医学、农业、能源和环境。DNA纳米技术是一种新兴技术，它利用DNA的折叠特性来设计纳米级的生物相容性结构，具有将这些功能联合收割机结合起来的潜力。一个5-PI团队将应用生物工程，细胞生物学，遗传学，单分子光谱学，超分辨率显微镜和多尺度分子建模来开发这种基于DNA的纳米器件，这些纳米器件也可以在活细胞中运行，并且可以“切换”以允许这些功能被随意触发。这项研究将被纳入大学课程，并将使研究生的跨学科，合作和国际培训成为可能。PI还将通过创建基于开放获取标准的视频和模块供K-12教师使用，扩大代表性不足的学生在STEM中的参与。遗传和表观遗传方法的最新进展使染色质工程技术能够1）靶向基因2）可视化染色质结构3）激活靶基因4）检测基因特异性转录。然而，目前的工具（包括超分辨率成像，染色质构象捕获和CRISPR/Cas9基因组工程）通常一次只能完成其中一个功能，在特定转录位点提供单通道静态视图。该项目将利用DNA纳米技术，以跨越目前的技术，探测和工程基因组和表观基因组功能。一个由五名PI组成的团队将开发多功能DNA折纸（DO）纳米器件，该器件将联合收割机靶向、功能修饰和RNA检测结合到一个平台上，在活细胞核中运行，并且是“可切换的”，允许实时检测和由内源性或外部信号触发的功能。这些成果将作为未来自动化设备的基础，这些设备可以靶向和调节基因组和表观基因组功能，包括基因表达，并作为科学，工程和医学应用的各种新工具集。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，工程理事会新兴前沿和多学科活动司的研究和创新新兴前沿计划，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的基金会的使命是履行其法定使命，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。

Numerous organisms from yeast to humans organize their genome by wrapping it repeatedly around histone proteins into nanoscale spools known as chromatin. Cells use the organization of chromatin to dictate whether a gene is actively expressed or turned off. Combining the ability to target a specific gene, visualize its location and structure, activate the gene, and detect gene expression in live cells would be a major technological advance in how genes are studied and controlled in living organisms, and lead to applications in many fields, including medicine, agriculture, energy and the environment. DNA nanotechnology, which uses well-understood folding properties of DNA to engineer nanoscale, biocompatible structures, is an emerging technology with the potential to combine these functions. A 5-PI team will apply bioengineering, cell biology, genetics, single molecule spectroscopy, super resolution microscopy and multi-scale molecular modeling to develop such DNA-based nanodevices that can also operate in live cells and be "switchable" to allow these functions to be triggered at will. The research will be integrated into university curricula, and will enable cross-disciplinary, collaborative and international training of graduate students. The PIs will also broaden participation of underrepresented students in STEM by creating open access standards-based videos and modules for use by K-12 teachers.Recent advances in genetic and epigenetic methods have enabled chromatin engineering technologies that 1) target genes to 2) visualize chromatin structure, 3) activate target genes, and 4) detect gene-specific transcription. However, current tools (including super-resolution imaging, chromatin conformation capture and genome engineering with CRISPR/Cas9) are usually only able to accomplish one of these functions at a time, giving single-channel, static views of the players and processes at a specific transcription site. This project will leverage DNA nanotechnology to leapfrog current technologies for probing and engineering genome and epigenome functions. A team of five PIs will develop multi-functional DNA origami (DO) nanodevices that combine targeting, functional modifications and RNA detection onto a single platform, operate in live cell nuclei, and are "switchable", allowing for real-time detection and for functions to be triggered by endogenous or external signals. The outcomes will serve as a foundation for future automated devices that target and regulate genome and epigenome functions, including gene expression, and serve as diverse new toolsets for science, engineering, and medical applications.This award is co-funded by the Genetic Mechanisms cluster in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate, the Emerging Frontiers in Research and Innovation program in the Division of Emerging Frontiers and Multidisciplinary Activities in the Engineering Directorate, and the Chemistry of Life Processes program in the Division of Chemistry in the Mathematics 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.