Multilevel gene expression changes in lineages containing adaptive copy number variants.

Area of Science:

• Evolutionary biology
• Genetics
• Molecular biology

Background:

• Copy-number variants (CNVs) are key drivers of adaptive evolution.
• CNVs can confer fitness advantages but may also impose costs.
• Recurrent CNV evolution at the GAP1 locus was observed in yeast under glutamine limitation.

Purpose of the Study:

• To investigate the role of gene expression in adaptation mediated by CNVs.
• To understand how CNVs affect gene expression at multiple regulatory levels (transcriptome, translatome, proteome).
• To identify regulatory mechanisms influenced by adaptive CNVs.

Main Methods:

• Evolution experiments with Saccharomyces cerevisiae in glutamine-limited chemostats.
• Measurement of transcriptome, translatome, and proteome in evolved yeast strains with unique CNVs.
• Analysis of gene expression efficiency at RNA, translation, and protein levels.

Main Results:

• CNV amplification positively correlated with RNA abundance, but this effect diminished at the proteome level (post-transcriptional dosage compensation).
• Widespread divergence in gene expression efficiency was observed across regulatory steps.
• Genes with altered translational efficiency were enriched for regulatory elements like upstream open reading frames and RNA binding sites.

Conclusions:

• Adaptive CNVs induce significant changes in gene expression at multiple regulatory levels.
• Post-transcriptional mechanisms play a role in buffering the effects of CNV amplification.
• Evolutionary adaptation involving CNVs involves complex alterations in gene expression regulation.