Age-specific genomic and transcriptomic variation reveals limited evidence for cis- regulatory interactions modulating aging in Saccharomyces cerevisiae

Abstract The budding yeast Saccharomyces cerevisiae is a well-established model for studying the genetic basis of complex traits, and it is a powerful system for investigating mechanisms of aging. Here, we examine the genomic and transcriptomic factors contributing to increased replicative age in recombinant yeast populations harboring standing genetic variation. Using Fluorescence-Activated Cell Sorting (FACS), we isolated young and aged cohort pairs across twelve biological replicates and sequenced their progeny to assess patterns of differentiation at the nucleotide and transcription levels. Most differentiated alleles were located in coding regions, including significant variants within 132 unique genes. Transcriptomic analysis revealed 60 differentially expressed genes in aged populations, including 18 genes with increased expression in aged cohorts, and 42 genes with decreased expression. Although only two genes (RFA3 and WSC4) were implicated in both genomic and transcriptomic analyses, functional overlap associated with protein homeostasis, DNA repair, and cell cycle regulation was evident across datasets. Notably, we found no strong evidence that differentially expressed genes were more likely to occur in close proximity to significant gene variants. This suggests that late-life survival is not predominantly governed by local cis-regulatory interactions (e.g. variants within or near coding regions). These findings underscore the power of integrating genomic and transcriptomic data to elucidate the genetics of complex traits such as aging, demonstrating how multi-omics approaches can reveal functional relationships that may be overlooked by single-layer analyses. Significance Statement While many individual genes contributing to aging and lifespan have been identified, our understanding of the polygenic interactions and regulatory processes that contribute to phenotypic variation in these traits is much more limited. Using a recombinant population of yeast, we identify novel links between genetic variation and the phenotype of replicative age. Additionally, we find little evidence for local cis-regulatory interactions, suggesting that downstream regulation or trans-regulatory processes may serve more dominant roles in modulating aging. These results reveal new insights into the role of polygenicity in the evolution and regulation of age-associated phenotypes. Competing Interest Statement The authors have declared no competing interest. Data Availability Statement Raw sequencing data have been deposited in the NCBI Sequence Read Archive under accession PRJNA1368902, and will be released upon publication. Code and processed data used for all analyses will be available in a GitHub repository (https://github.com/Katie-McHugh/regulation_of_aging/tree/Dryad). Additional datasets, including raw images and intermediate data files, will be archived with Dryad (DOI: 10.5061/dryad.34tmpg4x4) and made publicly available upon acceptance of the manuscript.