BRC-BIO: Exploring the phenotypic consequences of copy number variation of the ribosomal RNA genes

A variety of genetic differences exist among individuals, but some forms of genetic variation have been more difficult to study than others. This project investigates one such form of variation: differences in how many copies an individual has of certain genes. The genes encoding ribosomal RNAs are present in hundreds of copies per genome, and two humans may have differences of hundreds of copies between them. Variation in these genes has recently been linked to cancer, aging, and cell function. This project will explore the minimal copy number requirements of these genes for development to healthy adulthood and advance our understanding of the interaction between copy number differences and health-relevant characteristics. Ultimate outcomes of this work may add new nuance to our understanding of the relationship between genotype and phenotype. The project will create new opportunities for undergraduate student training in genetics and molecular biology at SUNY Brockport. Research goals will also be incorporated into an undergraduate research course format to broaden accessibility of original research experiences for students. The phenotypic consequences of genetic interaction with ribosomal RNA gene (rDNA) copy number will be assessed using the model organism Caenorhabditis elegans, an animal that exhibits substantial variation in rDNA copy number between wild isolates. The lower bounds of copy number sufficiency for development and fertility will be explored through CRISPR-Cas9-based genetic engineering of the rDNA copy locus, and the impact of this variation on tumor formation and lifespan will be characterized. This project will furthermore explore rDNA copy number variation in the context of dysregulated cell function, using conditions of altered ribosome regulation or compromised small RNA gene regulation. A discovery-based undergraduate research course will provide students with training in single guide RNA cloning and application of a CRISPR-activation approach to overexpress target genes in rDNA copy number variant backgrounds. Students will train in hypothesis-based investigation, molecular techniques, and organismal phenotyping to assess the consequences of rDNA copy number variation in altered cellular environments. Lastly, this project will explore the small RNA landscape in the presence of rDNA copy number variation, providing further student exposure to genomic techniques and analysis. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.