Deciphering Plasticity of Essentiality

许多研究的重点是确定一组必要的基因，目的是破译对生物体生存和繁殖力至关重要的核心过程。通常，各种类型的诱变剂（例如转座子，化学品，X射线），RNA干扰和最近的CRISPR/Cas9用于破坏基因的功能或耗尽基因产物，并评估其对生存/适应性的影响。特别是反向遗传筛选（如RNAi），通过绕过对突变身份的全基因组搜索，加速了对必需基因的探索，这是诱变筛选的一个常见瓶颈。虽然，必需基因集已成功地确定了一些不同的模式生物，主要是在实验室条件下和实验室菌株，很明显，必要性是有条件的状态。例如，在特定条件下（例如营养有限）似乎是必需的基因在不同的环境中（标准实验室）可能不是必需的。重要的是，不同的菌株在基因组中具有不同的遗传变异，这可能会影响对生存和生育力至关重要的基因水平。我们的NSERC发现计划的长期目标是研究秀丽隐杆线虫基因组的自然背景如何塑造本质。约15%的C.在实验室条件下广泛使用的N2菌株中，线虫基因被鉴定为发育所必需的（“N2必需基因组”）。为了进一步了解essentialome，我们将：（1）使用CRISPR/Cas9方法将现有的致死等位基因引入各种天然C.从秀丽隐杆线虫自然多样性资源（CeNDR）（https：//www.elegansvariation.org/）编译的秀丽隐杆线虫遗传背景（2）研究这些天然基因组对已知致死等位基因的发育和适应性的影响（3）采用高通量全基因组方法来鉴定能够调节致死性的天然基因组变异（4）研究这些天然基因组对遗传相互作用网络的影响我的NSERC发现计划将提高我们对遗传相互作用和基本过程的性质的认识，给出基因组天然变异的影响。从国家的领域基因组学和生物信息学方法开始，同时开发现代未来的方法，该计划具有前所未有的潜力，可以建立一种分析/比较方法来解开有关essentialomes可塑性的突出问题，同时还提供了对相互作用体可塑性的见解。重要的是，NSERC对该计划的支持将有助于培养下一代高素质人才（HQP）的多学科环境，这些人才在分子遗传学，基因组学，生物信息学和系统生物学方面具有技能，这是加拿大的突出需求。

Identifying the essential set of genes had been the focus of many studies with the aim to decipher core processes critical for survival and fertility of an organism. Typically, various types of mutagenes (e.g. transposons, chemicals, X-rays), RNA interference and more recently CRISPR/Cas9 are used to either disrupt the function of the gene or deplete the gene product, and assess the effect of this on survival/fitness. Reverse genetic screens (e.g. RNAi), in particular, had accelerated the quest for essential genes by circumventing the genome-wide search for the mutation identity, a common bottleneck of the mutagenesis screens. Although, essential gene sets had been successfully determined in a number of different model organisms, mostly under the laboratory conditions and in laboratory strains, it is clear that the essentiality is conditional state. For example, a gene that appears to be essential under a specific condition (e.g. limited nutrition) may not be essential in a different environment (standard laboratory). Importantly, different strains have different genetic variants in the genome that may influence the level at which genes are critical for survival and fertility. The long-term goal of our NSERC Discovery program is to study how the natural context of Caenorhabditis elegans' genomes shapes the essentiality. About 15% of C. elegans genes are identified as essential for development in a widely used N2 strain under laboratory conditions ("N2 essentialome"). To further understand the essentialome, we will: (1)Introduce the existing lethal alleles using CRISPR/Cas9 approaches to a variety of natural C. elegans genetic backgrounds compiled from the Caenorhabditis elegans Natural Diversity Resource (CeNDR) (https://www.elegansvariation.org/) (2)Study the effect of these natural genomes on development and fitness of known lethal alleles (3)Employ high throughput genome-wide approaches to identify natural genome variations capable of modulating the lethality (4)Study the effect of these natural genomes on genetic interaction networks My NSERC discovery program will advance our knowledge on genetic interactions and the nature of essential processes given the effect of natural variations of genomes. Starting with the state-of-the field genomics and bioinformatics methods while developing modern future approaches, this program has an unprecedented potential to establish an analytical/comparative approach to untangling the outstanding questions on plasticity of essentialomes, but also providing an insight on plasticity of interactomes. Importantly, the NSERC support for this program will help foster the multidisciplinary environment for next generation of Highly Qualified Personnel (HQP) skilled in molecular genetics, genomics, bioinformatics and systems biology, an outstanding need in Canada.