XX female mammals undergo transcriptional silencing of most genes on one of their two X chromosomes to equalize X-linked gene dosage with XY males in a process referred to as X-chromosome inactivation (XCI). XCI is an example of epigenetic regulation1. Once enacted in individual cells of the early female embryo, XCI is stably transmitted such that most descendant cells maintain silencing of that X chromosome2. In eutherian mammals, XCI is thought to be triggered by the expression of the non-coding Xist RNA from the future inactive X chromosome (Xi)3,4,5; Xist RNA in turn is proposed to recruit protein complexes that bring about heterochromatinization of the Xi6,7. Here we test whether imprinted XCI, which results in preferential inactivation of the paternal X chromosome (Xp), occurs in mouse embryos inheriting an Xp lacking Xist. We find that silencing of Xp-linked genes can initiate in the absence of paternal Xist; Xist is, however, required to stabilize silencing along the Xp. Xp-linked gene silencing associated with mouse imprinted XCI, therefore, can initiate in the embryo independently of Xist RNA.
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Heard, E., Chaumeil, J., Masui, O. & Okamoto, I. Mammalian X-chromosome inactivation: an epigenetics paradigm. Cold Spring Harb. Symp. Quant. Biol. 69, 89–102 (2004)
Payer, B. & Lee, J. T. X chromosome dosage compensation: how mammals keep the balance. Annu. Rev. Genet. 42, 733–772 (2008)
Brown, C. J. et al. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349, 38–44 (1991)
Huynh, K. D. & Lee, J. T. Inheritance of a pre-inactivated paternal X chromosome in early mouse embryos. Nature 426, 857–862 (2003)
Okamoto, I., Otte, A. P., Allis, C. D., Reinberg, D. & Heard, E. Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 303, 644–649 (2004)
Plath, K. et al. Role of histone H3 lysine 27 methylation in X inactivation. Science 300, 131–135 (2003)
Silva, J. et al. Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes. Dev. Cell 4, 481–495 (2003)
Nesterova, T. B., Barton, S. C., Surani, M. A. & Brockdorff, N. Loss of Xist imprinting in diploid parthenogenetic preimplantation embryos. Dev. Biol. 235, 343–350 (2001)
Sheardown, S. A. et al. Stabilization of Xist RNA mediates initiation of X chromosome inactivation. Cell 91, 99–107 (1997)
Latham, K. E. & Rambhatla, L. Expression of X-linked genes in androgenetic, gynogenetic, and normal mouse preimplantation embryos. Dev. Genet. 17, 212–222 (1995)
Mak, W. et al. Reactivation of the paternal X chromosome in early mouse embryos. Science 303, 666–669 (2004)
Takagi, N. & Sasaki, M. Preferential inactivation of the paternally derived X chromosome in the extraembryonic membranes of the mouse. Nature 256, 640–642 (1975)
West, J. D., Frels, W. I., Chapman, V. M. & Papaioannou, V. E. Preferential expression of the maternally derived X chromosome in the mouse yolk sac. Cell 12, 873–882 (1977)
Chaumeil, J., Le Baccon, P., Wutz, A. & Heard, E. A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev. 20, 2223–2237 (2006)
Mak, W. et al. Mitotically stable association of polycomb group proteins eed and enx1 with the inactive X chromosome in trophoblast stem cells. Curr. Biol. 12, 1016–1020 (2002)
Kalantry, S. et al. The Polycomb group protein Eed protects the inactive X-chromosome from differentiation-induced reactivation. Nature Cell Biol. 8, 195–202 (2006)
Marahrens, Y., Panning, B., Dausman, J., Strauss, W. & Jaenisch, R. Xist-deficient mice are defective in dosage compensation but not spermatogenesis. Genes Dev. 11, 156–166 (1997)
Csankovszki, G., Panning, B., Bates, B., Pehrson, J. R. & Jaenisch, R. Conditional deletion of Xist disrupts histone macroH2A localization but not maintenance of X inactivation. Nature Genet. 22, 323–324 (1999)
Okamoto, I. et al. Evidence for de novo imprinted X-chromosome inactivation independent of meiotic inactivation in mice. Nature 438, 369–373 (2005)
Singer-Sam, J., Chapman, V., LeBon, J. M. & Riggs, A. D. Parental imprinting studied by allele-specific primer extension after PCR: paternal X chromosome-linked genes are transcribed prior to preferential paternal X chromosome inactivation. Proc. Natl Acad. Sci. USA 89, 10469–10473 (1992)
Cooper, D. W. Directed genetic change model for X chromosome inactivation in eutherian mammals. Nature 230, 292–294 (1971)
Hadjantonakis, A. K., Gertsenstein, M., Ikawa, M., Okabe, M. & Nagy, A. Non-invasive sexing of preimplantation stage mammalian embryos. Nature Genet. 19, 220–222 (1998)
Kalantry, S. & Magnuson, T. The Polycomb group protein EED is dispensable for the initiation of random X-chromosome inactivation. PLoS Genet. 2, e66 (2006)
Lahn, B. T. & Page, D. C. Four evolutionary strata on the human X chromosome. Science 286, 964–967 (1999)
Clemson, C. M., Hall, L. L., Byron, M., McNeil, J. & Lawrence, J. B. The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences. Proc. Natl Acad. Sci. USA 103, 7688–7693 (2006)
Jegalian, K. & Page, D. C. A proposed path by which genes common to mammalian X and Y chromosomes evolve to become X inactivated. Nature 394, 776–780 (1998)
Wallis, M. C., Waters, P. D. & Graves, J. A. Sex determination in mammals–before and after the evolution of SRY. Cell. Mol. Life Sci. 65, 3182–3195 (2008)
Duret, L., Chureau, C., Samain, S., Weissenbach, J. & Avner, P. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 312, 1653–1655 (2006)
Samollow, P. B., Ford, A. L. & VandeBerg, J. L. X-linked gene expression in the Virginia opossum: differences between the paternally derived Gpd and Pgk-A loci. Genetics 115, 185–195 (1987)
Kay, G. F. et al. Expression of Xist during mouse development suggests a role in the initiation of X chromosome inactivation. Cell 72, 171–182 (1993)
Acknowledgments We thank R. Jaenisch for Xist2lox mice and G. Martin for Zp3–Cre mice (Supplementary Methods). We also thank A. Fedoriw and K. Huynh, for advice on allele-specific RT–PCR, and are grateful to S. Malpani and L. Williams, for discussions; M. Calabrese, R. Chandler, D. Ciavatta, A. Fedoriw, C. Griffin, S. Malpani, J. Mugford, M. Pohlers, K. Shpargel and L. Williams, for critically reading the manuscript. We also acknowledge the Michael Hooker Microscopy Facility at the University of North Carolina at Chapel Hill for the use of their LeicaSP2 confocal microscope. This work was supported in part by an American Cancer Society Postdoctoral Fellowship to S.K. and by grants from the US National Institutes of Health to S.K. and T.M.
Author Contributions S.K. and T.M. had devised the study and designed the experimental strategy. S.K. conducted the experiments with assistance from S.P. in mouse genotyping, RNA FISH and RT–PCR experiments and from R.B.B. in RT–PCR experiments. S.K. and T.M. analysed the data. J.S. performed the statistical evaluation of the RNA FISH and RT–PCR data. S.K. wrote the paper and T.M. edited the paper. All authors discussed the results and commented on the manuscript.
About this article
Cite this article
Kalantry, S., Purushothaman, S., Bowen, R. et al. Evidence of Xist RNA-independent initiation of mouse imprinted X-chromosome inactivation. Nature 460, 647–651 (2009). https://doi.org/10.1038/nature08161
Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms
Briefings in Bioinformatics (2021)
WIREs RNA (2021)
Proceedings of the National Academy of Sciences (2020)
X chromosome‐linked long noncoding RNAlnc‐XLEC1regulatesc‐Myc‐dependent cell growth by collaborating with MBP‐1 in endometrial cancer
International Journal of Cancer (2019)
Frontiers in Genetics (2019)