The evolution of X chromosome inactivation in mammals: the demise of Ohno's hypothesis?

Abstract

Ohno's hypothesis states that dosage compensation in mammals evolved in two steps: a twofold hyperactivation of the X chromosome in both sexes to compensate for gene losses on the Y chromosome, and silencing of one X (X-chromosome inactivation, XCI) in females to restore optimal dosage. Recent tests of this hypothesis have returned contradictory results. In this review, we explain this ongoing controversy and argue that a novel view on dosage compensation evolution in mammals is starting to emerge. Ohno's hypothesis may be true for a few, dosage-sensitive genes only. If so few genes are compensated, then why has XCI evolved as a chromosome-wide mechanism? This and several other questions raised by the new data in mammals are discussed, and future research directions are proposed.

Fig. 1

Sex chromosome and dosage compensation evolution in mammals. a Sex chromosome evolution in mammals. Sry, the male-determining gene, initiated the evolution of the sex chromosomes from a pair of autosomes. The proto-X and proto-Y stopped recombining at a region including Sry and probably other genes, thus forming X- and Y-specific regions. These regions grew larger during evolution through additional recombination suppression events (probably inversions on the Y chromosomes) and gradually diverged. Pseudo-autosomal regions (PARs) are remnant of the autosomal ancestry of the sex chromosomes. In its non-recombining male-specific region, the Y has lost most of its genes because of degenerative processes collectively known as Hill-Robertson effects [57, 73]. b The evolution of dosage compensation in mammals, as hypothesized by Ohno [6], formalized later by Charlesworth [74, 75], and explicitly modeled by [48]. The gene loss on the Y implies dosage imbalance between the sex chromosomes and the autosomes in males. In the first step of Ohno’s hypothesis, expression of the X chromosome is doubled in both sexes; proper dosage is restored in males, but is now twice the dosage of autosomes in females. In the second step, the inactivation of one of the two Xs in females evolves in order to get the dosage of the X back to autosomal level. The predicted values of both the expression ratios X:AA and X:XX (see Box 1 and text for more details) are shown at the bottom of panel b. Expression on the autosomes may have changed during evolution, hence the less precise prediction for the X:AA ratio than for X:XX one (Box 1), as emphasized by the tilde symbol

Fig. 2

Dosage compensation of a minority of human X-linked genes. a X:AA and X:XX ratios for humans are shown (find more details about these ratios in the text and in Box 1). Results are shown for (1) all human genes or including only genes with a minimum expression level of FPKM > 1 (All genes), (2) 1:1 orthologs between human and chicken, for which ancestral expression could be computed using expression data in chicken (Box 1), considering all of them or only those with a minimum expression level of FPKM > 1 (1:1 orthologs with chicken), and (3) genes involved in large protein complexes (with 7 or more proteins) that are likely dosage-sensitive (Dosage-sensitive genes). Boxplots of the X:AA or X:XX medians for different tissues are shown. Extreme outliers can be seen for “Expressed genes” (“All genes” category), they correspond to Brain (highest ratio) and lung (lowest ratio). Data for preparing the “All genes” part and the X:AA of “Dosage-sensitive genes” part are from [32] and are based on 12 tissues. All the other boxplots were obtained from ten tissues in [34]. The blue dashed lines indicate the expected ratios with global dosage compensation (1), and without any dosage compensation (0.5), see text and Fig. 1b for more details. b Sketch summing up the differences in dosage compensation status and mechanisms among the genes on the X chromosome. Most of the genes on the Xi are inactivated, except for the PARs and some XCI-escapees, and XCI is thus a global process. The hyperexpression, on the contrary, appears to be a local process affecting only the dosage-sensitive genes. Dosage compensation through hyperexpression and XCI as envisioned by Ohno thus only affects dosage-sensitive genes [32]. Some dosage-sensitive genes are compensated through another mechanism, namely down-regulation of their autosomal partners, as shown for some genes involved in protein–protein interaction networks [33]

Fig. 3

Steps in the evolution of XCI. Major events the evolution of XCI in placentals and marsupials are shown in the tree of amniotes. XCI, probably pXCI (shown in green), evolved early in the evolution of XY chromosomes, as shown here. However, independent XCI evolution in placental and marsupial lineages cannot be ruled out (see text). Also shown is how the mechanism of XCI was later refined independently in placentals with the evolution of the lncRNA Xist (from the protein-coding gene Lnx3) and Rex1 and became rXCI (shown in brown), and in marsupials with the evolution of the lncRNA with Xist-like properties Rsx (which has not evolved from Lnx3). In some placentals, pXCI is found as well (in early embryo and extra-embryonic tissues); it is not known whether pXCI has re-evolved or has been conserved, hence the question marks. Two major players in the evolution of XCI, Lnx3 (parent of Xist) and Rnf12, were probably close to Sox3 (parent of Sry) in the proto-X, and the same small region has apparently been involved in both the evolution of sex determination and XCI (see text). Birds and monotremes sex chromosome systems evolved independently from that in therians, and serve as outgroups here