Ohno’s Hypothesis of X Chromosome Dosage Compensation Refuted

Contributed by: Jianzhi Zhang

 

The X and Y chromosomes of humans originated from a pair of autosomes in the common ancestor of placental and marsupial mammals.  In his classic book entitled “Sex Chromosomes and Sex-Linked Genes”, Susumu Ohno (1967) (1) wrote, “During the course of evolution, an ancestor to placental mammals must have escaped a peril resulting from the hemizygous existence of all the X-linked genes in the male by doubling the rate of product output of each X-linked gene,” (p. 99).  This presumed doubling of expression on X would cause X tetraploidy in females, which is believed to be the driving force behind the evolution of the random inactivation of one X chromosome in females.  As a result, the expressions of X-linked genes become equalized between males and females.  

The prevailing evolutionary model of sex chromosome dosage compensation.  Each arrowhead represents the expression of one allele, with the height of the arrowhead indicating the expression level of the allele. Two recent studies found no upregulation of X-linked genes, thus rejecting Ohno’s hypothesis.

So, are expressions of X-linked genes doubled to compensate the loss of their Y homologs, as Ohno hypothesized 45 years ago?  In the last few years, a number of groups tested Ohno’s hypothesis indirectly by comparing the expressions of X-linked and autosomal genes in humans or mice (2-11).  These authors reached different conclusions either supporting or refuting Ohno’s hypothesis, depending on the transcriptome data used and the genes compared.  This controversy is now resolved by a direct comparison of the expression levels of human X-linked genes with those of their one-to-one orthologs in chicken. 

Julien et al. (12) and Lin et al. (13) analyzed the same RNA-Seq data published last year.  They found that the expression ratio between a human X-linked gene and its one-to-one ortholog in the “proto-X” chromosome in chicken has a median of ~0.5.  That is, the per-allele expression level of X-linked genes is on average unchanged!  This finding conclusively refutes Ohno’s hypothesis.

Does this finding imply that a two-fold change in gene expression has such a small fitness effect that dosage compensation is hardly needed?  The answer appears different for different genes.  First, following a recent analysis (14), Lin et al. found that proto-X genes that encode members of large protein complexes did experience an on average two-fold up-regulation during sex chromosome evolution, likely because of the high dose sensitivity of large protein complex members.  But these genes constitute only ~5% of all X-linked genes and therefore do not show up in the chromosome-wide analysis.  Second, there are X-linked genes that have now migrated to autosomes, which may have been a strategy to avoid a dose change.  Third, a genome-wide study showed that haploinsufficiency is rare in yeast.  It is possible that the same is true in mammals.  Fourth, even for one-to-one orthologous genes in autosomes, a two-fold expression difference between human and chicken is not uncommon, suggesting that perhaps expression levels need not be so finely regulated and conserved.  Together, the analyses suggest that, for most genes on the proto-X, a 50% expression reduction is quite tolerable and need not be compensated.

Because Ohno’s hypothesis is the basis of the current model of male:female X chromosome dosage compensation, its invalidation opens the research for a new evolutionary explanation of X inactivation in female mammals. 

References

1. Ohno S (1967) Sex Chromosomes and Sex-Linked Genes. New York: Springer-Verlag.

2. Gupta V, Parisi M, Sturgill D, Nuttall R, Doctolero M, et al. (2006) Global analysis of X-chromosome dosage compensation. J Biol 5: 3.

3. Nguyen DK, Disteche CM (2006) Dosage compensation of the active X chromosome in mammals. Nat Genet 38: 47-53.

4. Lin H, Gupta V, Vermilyea MD, Falciani F, Lee JT, O'Neill LP, and Turner, BM (2007) Dosage compensation in the mouse balances up-regulation and silencing of X-linked genes. PLoS Biol 5: e326.

5. Xiong Y, Chen X, Chen Z, Wang X, Shi S, Wang X, Zhang J, and He X (2010) RNA sequencing shows no dosage compensation of the active X-chromosome. Nat Genet 42: 1043-1047.

6. Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier L, Schlesinger F, Davis C, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, and Disteche CM (2011) Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet 43: 1179-1185.

7. Kharchenko PV, Xi R, Park PJ (2011) Evidence for dosage compensation between the X chromosome and autosomes in mammals. Nat Genet 43: 1167-1169.

8. Lin H, Halsall JA, Antczak P, O'Neill LP, Falciani F, and Turner BM (2011) Relative overexpression of X-linked genes in mouse embryonic stem cells is consistent with Ohno's hypothesis. Nat Genet 43: 1169-1170.

9. Yildirim E, Sadreyev RI, Pinter SF, Lee JT (2012) X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription. Nat Struct Mol Biol 19: 56-61.

10. He X, Chen X, Xiong Y, Chen Z, Wang X, Shi S, Wang X, and Zhang J (2011) He et al. reply. Nat Genet 43: 1171-1172.

11. Castagne R, Rotival M, Zeller T, Wild PS, Truong V, Tregouet DA, Munzel T, Ziegler A, Cambien F, Blankenberg S, and Tiret L (2011) The choice of the filtering method in microarrays affects the inference regarding dosage compensation of the active X-chromosome. PLoS One 6: e23956.

12. Julien P, Brawand D, Soumillon M, Necsulea A, Liechti A, Schutz F, Daish T, Grutzner F, and Kaessmann H (2012) Mechanisms and evolutionary patterns of mammalian and avian dosage compensation. PLoS Biol 10: e1001328.

13. Lin F, Xing K, Zhang J, He X (2012) Expression reduction in mammalian X chromosome evolution refutes Ohno's hypothesis of dosage compensation. Proc Natl Acad Sci U S A 109: 11752-11757.

14. Pessia E, Makino T, Bailly-Bechet M, McLysaght A, Marais GA (2012) Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome. Proc Natl Acad Sci U S A 109: 5346-5351.