Chromosomal or segmental aneuploidy—the gain or loss of whole or partial chromosomes—is typically deleterious for organisms, a hallmark of cancers, and only occasionally adaptive. To understand the cellular and organismal consequences of aneuploidy, it is important to determine how altered gene doses impact gene expression. Previous studies show that, for some Drosophila cell lines but not others, the dose effect of segmental aneuploidy can be moderately compensated at the mRNA level – aneuploid gene expression is shifted towards wild-type levels. Here, by analyzing genome-wide translation efficiency estimated with ribosome footprint data from the aneuploid Drosophila S2 cell line, we report that the dose effect of aneuploidy can be further compensated at the translational level. Intriguingly, we find no comparable translational compensation in the aneuploid Kc167 cell line. Comparing the properties of aneuploid genes from the two cell lines suggests that selective constraint on gene expression, but neither sequence features nor functions, may partly explain why the two cell lines differ in translational compensation. Our results, together with previous observations that compensation at the mRNA level also varies among Drosophila cell lines and yeast strains, suggest that dosage compensation of aneuploidy is not general but contingent on genotypic and/or developmental context.
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