UKRI/BBSRC-NSF/BIO Building synthetic regulatory units to understand the complexity of mammalian gene expression

未来的合成细胞将用于多种最终用途，包括农业，生物技术和生物材料生产。如果研究人员能够随意打开和关闭特定的基因，并精确地调节这些基因的表达水平，这些合成细胞将表现得最好。这一目标的核心是深入了解DNA中的调控元件如何控制基因表达的时间和水平。该项目的长期目标是更好地定义不同DNA调控元件的功能，确定这些元件如何共同控制基因，并利用这些知识设计哺乳动物细胞，精确和可控地表达所需的一组基因。该项目将通过一个创新项目--酵母艺术项目来补充，该项目将被开发为一个主要的外展工具，以帮助公众更好地理解基因工程的目标和潜力。最近的工作大大增加了我们对增强子的理解--增强子是协调基因调控的三个基本基因组元件之一。与启动子和绝缘子一起，它们形成可检测的动态3D结构，驱动基因表达的精确时空程序。α-珠蛋白基因座提供了哺乳动物调节结构域的良好建立和易处理的模型，而其他基因座不容易定义和操纵。在从头DNA设计和合成方法的最新进展以及新的基因组工程和分析策略的推动下，已经产生了整个小鼠α-珠蛋白调节结构域的多个版本，并用于鉴定称为“促进剂”的新型基因组元件。这些增强子样元件没有固有的激活潜力，但在调节典型增强子的活性中起着至关重要的作用。受此经验启发，该项目旨在通过初步创建和分析11个新的假设驱动的小鼠遗传模型来解决基因表达领域的关键问题，这些模型基于天然内源性α-珠蛋白调控景观。将根据从这些初始构建体获得的结果设计进一步的等位基因。了解主要顺式调控元件之间的信息交流和传递的基本规则将改变我们对生命密码的理解，最终目标是合成最小的全功能哺乳动物等位基因和基因组。这项美英合作项目得到美国国家科学基金会（NSF）和英国生物技术和生物科学研究理事会（BBSRC）的支持，其中NSF资助美国调查员，BBSRC资助英国的合作伙伴。该奖项反映了NSF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 synthetic cells of the future will be produced for a multitude of end uses, including agriculture, biotechnology and production of biomaterials. These synthetic cells would perform best if researchers could turn specific genes on and off at will, and precisely tune the level at which these genes are expressed. Central to this goal is a deep understanding of how regulatory elements in the DNA control the timing and level that genes are expressed. The long-term goals of this project are to better define the functions of different DNA regulatory elements, to determine how these elements work together to control genes, and to use this knowledge to engineer mammalian cells that precisely and controllably express a desired set of genes. This project will be complemented by an innovative program, the yeast art program, that will be developed as a major outreach tool to help the public better understand the goals and potential of gene engineering.Recent work has greatly increased our understanding of enhancers - one of three fundamental genomic elements that orchestrate gene regulation. With promoters and insulators, they form detectable and dynamic 3-D structures that drive precise spatiotemporal programs of gene expression. The alpha-globin locus offers a well-established and tractable model of a mammalian regulatory domain, whereas other loci are not as easily defined and manipulated. Powered by recent advances in de novo DNA design and synthesis approaches, together with the new genomic engineering and analysis strategies, multiple versions of the entire mouse alpha-globin regulatory domain have been generated and used to identify novel genomic elements called ‘facilitators’. These enhancer-like elements have no inherent activation potential but play crucial roles in modulating the activity of canonical enhancers. Enlightened by this experience, this project aims to address key questions in the gene expression field by initially creating and analyzing 11 new hypothesis-driven mouse genetic models based on the natural endogenous alpha-globin regulatory landscape. Further alleles will be designed depending on the results obtained from these initial constructs. Understanding the rules underlying the communication and relay of information between the main classes of cis-regulatory elements will transform our understanding of the code for life, with the ultimate goal of synthesizing minimal fully-functional mammalian alleles and genomes.This collaborative US/UK project is supported by the US National Science Foundation (NSF) and the UK Biotechnology and Biological Sciences Research Council (BBSRC), where NSF funds the US investigator and BBSRC funds the partners in the UK.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.