GREAT: Genome Refactoring and Engineering Approach to study non-coding genes driving Translation

尽管基因组编辑和功能基因组学技术的进步增强了我们对遗传位点的定位能力，但迄今为止，对基因组特征的系统功能研究仅限于现有的天然基因组。因此，巨大的背景基因组变异引入了噪音和云发现。随后，我们对大部分未被探索的，但不可分割的理解，如非编码RNA（ncRNA），将被合成基因组学的激进方法彻底改变。合成酵母（Sc2.0）基因组为探索这些遗传元件的细微作用提供了宝贵的技术和资源。利用这一新的资源和技术，本提案中描述的工作旨在通过工程生物学方法阐明tRNA和rRNA生物学的重要方面。我们的动机是探索ncRNA生物学的三个基本方面：ncRNA组织，调节和进化。我们对这项提议的愿景是解开基因组的基本原理，消除生物学的复杂性和冗余，并最终将进化与工程结合起来，以优化翻译过程。我们的方法将从根本上重组基因组，提供了一个独特的机会，进行三个相互联系的工作包，系统地研究组织，调节和演变的tRNA和rRNA。实现总体目标的每一步都是重要的和实质性的，最重要的是，它们是相互补充的。这一提议将扩展我们实验室建立的最先进的合成基因组学方法，以克服与直接分析当前有关ncRNA生物学和分子进化的棘手生物学问题相关的限制。从长远来看，由于酵母是一种安全且易于处理的模式生物，该项目将为基因组基础提供新的线索，但也可能对医学和生物技术产生深远的影响。

Despite advances in genome-editing and functional genomics tecDespite advances in genome-editing and functional genomicstechnologies enhancing our ability to characterise genetic loci, systematic functional studies of genomic features have thus far beenlimited to existing natural genomes. As such, vast background genomic variation introduces noise and clouds discovery.Subsequently, our understanding of the largely underexplored, yet integral, such as non-coding RNAs (ncRNAs), would berevolutionised by the radical approach of synthetic genomics.The synthetic yeast (Sc2.0) genome provides an invaluable technology and resource for probing the nuanced roles of these geneticelements. Harnessing this new resource and technology, the work described in this proposal aims to elucidate important aspects oftRNA and rRNA biology through an engineering biology approach. Our motivation is to explore three fundamental aspects of ncRNAbiology: ncRNA organisation, regulation, and evolution. Our vision for this proposal is to unravel genomic fundamentals, removebiological complexity and redundancies, and ultimately couple evolution with engineering to optimise translation processes. Ourapproach will radically reorganise the genome, providing a unique opportunity to carry out three inter-linked work packages tosystematically study the organisation, regulation, and evolution of tRNAs and rRNAs. The steps towards the overarching goal are eachsignificant and substantial, and most importantly, complementary to each other.This proposal will thereby expand state-of-the-art synthetic genomics approaches established in our lab, to overcome the limitationsassociated with directly assaying currently intractable biological questions regarding ncRNA biology and molecular evolution. In thelong-term, since yeast is a safe and tractable model organism, this project will shed new light on genome fundamentals, but alsopotentially have profound impacts on medicine and biotechnologies.