View Program - 2022 Population, Evolutionary, and Quantitative Genetics Conference

Large blocks of repetitive, non-coding satellite DNA are a major component of eukaryotic genomes, but their exact functions or contributions remains unknown. While satellite DNA is typically seen as ‘junk’ DNA that accumulates in genomes, some also have roles in chromosome segregation and nuclear organization. However, few specific functions or fitness effects have been assigned to satellite loci. In order to study whether and how satellite DNA contributes to fitness, we used CRISPR to modify the Responder (Rsp) satellite in Drosophila melanogaster to investigate its specific fitness contributions. Rsp is the target of the Segregation Distorter (SD) meiotic driver: chromosomes with large Rsp loci (many copies of the Rsp element) are susceptible to destruction by SD, and heterozygous SD males only produce sperm bearing Rsp-lacking SD chromosomes. While complete Rsp deletions are viable and fertile, large, drive-susceptible Rsp loci are common in wild populations. In a previous study, a large deletion including Rsp significantly reduced fitness, suggesting Rsp may serve an unknown but important function. However, this large deletion removes many sequences, making it difficult to attribute fitness effects to Rsp specifically. Here we used CRISPR to make precise modifications of the Rsp locus, and used PacBio HiFi sequencing to investigate the modified loci. We show that Rsp deletions significantly reduce sensitivity to SD in previously sensitive backgrounds, indicating that we successfully altered the phenotype associated with the Rsp satellite. We are conducting relative fitness assays to determine the effect of the Rsp deletion on fitness relative to ancestral controls, and are generating Rsp deletions in different lines to determine whether the fitness effects are dependent on genetic background. In addition to the experimental work, we are using genomic data from a diverse set of world-wide natural populations of D. melanogaster to determine how the frequency of SD affects Rsp copy number in the wild. Using simulations and modelling, we will also detect any deviations of observed Rsp copy number from simulated neutral expectations, which may imply that natural selection acts on Rsp copy number. These experiments will help explain why drive-sensitive alleles of Rsp persist in natural populations- leaving them vulnerable to the selfish SD system- and could more broadly help explain why satellite DNA makes up such a large proportion of eukaryotic genomes.

Fitness contributions of the Responder satellite in Drosophila melanogaster