Identifying the genetic factors in natural genome backgrounds that modulate essential phenotypic outcomes using C. elegans
Authors: Afiya Razia Chida 1,2; Victoria Rodrigues Alves Barbosa 1,2; Xiao Li 1,2; Tatiana Maroilley 1,2; Francesca Jean 1,2; Tahsin Hassan Rahit 1,2; Andrew Galbraith 1,2; Filip Cotra 1,2; Larisa Oncea 1,2; Maja Tarailo-Graovac 1,2
Affiliations: 1) Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; 2) Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
Keywords: Genetic interactions
Essential genes are vital for cellular development, metabolism, and reproduction; mutations with detrimental effects in these genes can cause severe defects. Essentiality varies based on different conditions, including genetic background. Our aim is to search for genetic factors that modulate gene essentiality in six diverse Caenorhabditis elegans natural isolate backgrounds - CB4856 (Hawaii, USA), JU1400 (Seville, Spain), AB1 (Adelaide, Australia), GXW1 (Wuhan, China) and KR314 (Vancouver, Canada), and N2 (Bristol, UK). The plasticity of essentiality might be influenced by genetic modifiers - variants that affect the causative gene by ameliorating or exacerbating a trait or disease. Our research focusses on identifying modifiers of two essential genes – mat-1 (Metaphase-to-Anaphase Transition defect), which is involved in cell division, and cgh-1 (Conserved Germline Helicase), which is important in oocyte development and gametogenesis. Previous studies with loss of CGH-1 and MAT-1 by RNA interference have suggested the presence of genetic modifiers in natural isolates (CB4856 and N2). To further investigate that, we individually knocked in conditional lethal temperature sensitive alleles of cgh-1(tn691) and mat-1(ye121) using CRISPR/Cas9 in all six isolates. At the permissive temperature (15°C), we observed about 100% hatch-rate in all isolates. However, at the restrictive temperatures (23°C & 25°C) both cgh-1(tn691) and mat-1(ye121) show evidence of phenotypic variability in different natural isolate backgrounds, ranging from 100% embryonic lethal to viable, indicating the presence of modifiers. Thus, to determine the genetic factors modulating the essentiality, the strains were subjected to whole genome sequencing followed by advanced bioinformatics analysis. We have detected and annotated a spectrum of variants, including single nucleotide variants and more complex structural variants, such as translocations and inversions. To identify potential genetic modifiers among them, we use genetic interaction network analysis, as well as in house developed machine learning approaches. To test the candidate modifiers, we are using CRIPSR/Cas9. Studying genetic modifiers using C. elegans natural backgrounds may improve the genomic approaches in the discovery of genetic modifiers in human diseases. This is crucial for proper diagnosis, prognosis, and more precise patient management.