Identifying the Genetic Factors in Natural Genome Backgrounds That May Modulate Phenotypic Outcomes in C. elegans
Creators: name: Chida, Afiya Razia
Publisher: name: Cumming School of Medicine
Year: 2023
Subjects: subject: Natural Variation
subject: Single Nucleotide Variants
subject: Structural Variants
subject: Genetic Interaction Networks
subject: Phenotypic Variability
subject: Gene essentiality
subject: Complex Genomic Rearrangements
subject: Plasticity of Essentiality
subject: Genetic Modifiers
subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Genetics
subject: FOS: Biological sciences

description: Loss-of-function mutations in essential genes can lead to a severe phenotype characterized by reproductive stress or hindrance in development and survival. Whilst in some individuals these lethal mutations cause severe phenotypes, in others, phenotypic variability is observed. One of the factors causing this phenotypic heterogeneity is the genetic background that affects the primary mutation. This background is characterized by genetic modifiers - genes that interact and influence the role of causative gene by ameliorating or exacerbating a trait or disease. This thesis aims to explore the genetic modifiers of two essential genes– mat-1 (metaphase-to-anaphase defect) and cgh-1 (conserved germline helicase) in Caenorhabditis elegans, using natural isolate backgrounds. Both, cgh-1 and mat-1, contain hypomorphic temperature-sensitive alleles that allow propagation at a permissive temperature (15°C) while causing embryonic arrest at a restrictive temperature (25°C) in the reference N2 background. Previous studies revealed that phenotypic outcomes in case of CGH-1 and MAT-1 deficiencies are variable in two different genetic backgrounds (CB4856 and N2), suggesting the presence of genetic modifiers. We observed phenotypic variability of temperature sensitive variants in these genes across six natural isolates of C. elegans that are obtained from diverse geographical locations such as CB4856 (Honolulu, Hawaii), JUI400 (Seville, Spain), AB1 (Adelaide, Australia), GXW1 (Wuhan, China) and KR314 (Vancouver, Canada), along with N2 (Bristol, England). Here, using advanced bioinformatics approaches, I identified and validated the spectrum of variants present in these six C. elegans genomes, including Single Nucleotide Variants (SNVs) and complex Structural Variants (SVs) such as deletions, duplications, inversions, as well as complex genomic rearrangements that may act as potential genetic modifiers. This study is the first to explore the SV category in natural isolates of C. elegans. We prioritized the candidate modifiers (both in SNV and SV categories) from an extensive list of variants by analyzing the genetic interaction networks. With the help of wet-lab personnel using molecular biology techniques, these modifiers will be tested for their either supressing or enhancing effect on the primary mutation. Understanding the effect of genetic background on phenotypic outcomes is important, but could be a difficult task, especially in organisms like human. In this thesis, using model organism C. elegans, I contributed to the field by uncovering a spectrum of genetic variants (SNVs and SVs) in wild isolate genomes, and utilizing different approaches to find candidate genetic modifiers across the mutation spectra of natural isolates. Importantly, methods developed in this project could be helpful in translational research for devising better SV and modifier prediction strategies in humans.