Post-transcriptional mechanisms modulate the consequences of adaptive copy number variation (RPF)

Copy-number variants (CNVs) are large-scale amplifications or deletions of DNA that can drive rapid adaptive evolution and result in large-scale changes in gene expression. Whereas alterations in the copy number of one or more genes within a CNV can confer a selective advantage, other genes within a CNV can decrease fitness when their dosage is changed. Dosage compensation - in which the gene expression output from multiple gene copies is less than expected - is one means by which an organism can mitigate the fitness costs of deleterious gene amplification. Previous research has shown evidence for dosage compensation at both the transcriptional level and at the level of protein expression; however, the extent of compensation differs substantially between genes, strains, and studies. Here, we investigated sources of dosage compensation at multiple levels of gene expression regulation by defining the transcriptome, translatome and proteome of experimentally evolved yeast (Saccharomyces cerevisiae) strains containing adaptive CNVs. We quantified the gene expression output at each step and found evidence of widespread dosage compensation at the protein abundance (~47%) level. By contrast we find only limited evidence for dosage compensation at the transcriptional (~8%) and translational (~3%) level. We also find substantial divergence in the expression of unamplified genes in evolved strains that could be due to either the presence of a CNV or adaptation to the environment. Detailed analysis of 82 amplified and 411 unamplified genes with significantly discrepant relationships between RNA and protein abundances identified enrichment for upstream open reading frames (uORFs). These uORFs are enriched for binding site motifs for SSD1, an RNA binding protein that has previously been associated with tolerance of aneuploidy. Our findings suggest that, in the presence of CNVs, SSD1 may act to alter the expression of specific genes by potentiating uORF mediated translational regulation. We grew four strains (DGY1726, DGY1735, DGY1741, DGY743) of CNV containing yeast, Saccharomyces cerevisiae, and their ancestor (DGY1657) in glutamine-limited media in chemostat conditions [as per PMID: 30562346] in replicate DGY1726 (gln_ctrl02_c2); DGY1735 (gln_03_c1); DGY1741 (gln_05_c2); DGY1743 (gln_06_c2); DGY1657 (Anc). All strains are derived from FY4 / S288C. Genome sequencing of all strains: (ONT) PRJNA591579 (Illumina) PRJNA451489.