Expression reduction in mammalian X chromosome evolution refutes Ohno’s hypothesis of dosage compensation

Abstract

Susumu Ohno proposed in 1967 that, during the origin of mammalian sex chromosomes from a pair of autosomes, per-allele expression levels of X-linked genes were doubled to compensate for the degeneration of their Y homologs. This conjecture forms the foundation of the current evolutionary model of sex chromosome dosage compensation, but has been tested in mammals only indirectly via a comparison of expression levels between X-linked and autosomal genes in the same genome. The test results have been controversial, because examinations of different gene sets led to different conclusions that either support or refute Ohno's hypothesis. Here we resolve this uncertainty by directly comparing mammalian X-linked genes with their one-to-one orthologs in species that diverged before the origin of the mammalian sex chromosomes. Analyses of RNA sequencing data and proteomic data provide unambiguous evidence for expression halving (i.e., no change in per-allele expression level) of X-linked genes during evolution, with the exception of only ∼5% of genes that encode members of large protein complexes. We conclude that Ohno's hypothesis is rejected for the vast majority of genes, reopening the search for the evolutionary force driving the origin of chromosome-wide X inactivation in female mammals.