Deciphering Plasticity of Essentiality

识别一组基本基因一直是许多研究的重点，目的是破译对生物体生存和繁殖至关重要的核心过程。通常，各种类型的诱变剂（例如转座子、化学物质、x射线）、RNA干扰和最近的CRISPR/Cas9被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（例如RNAi），通过绕过突变特性的全基因组搜索，加速了对必需基因的寻找，这是突变筛选的一个常见瓶颈。虽然在许多不同的模式生物中，主要是在实验室条件下和实验室菌株中，已经成功地确定了必要的基因集，但很明显，必要性是有条件的状态。例如，在特定条件下（如营养有限）似乎是必需的基因，在不同的环境下（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，这可能影响对生存和生育至关重要的基因的水平。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环境如何塑造本质。

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.