X inactivation results in silencing of genes on one X chromosome in females. However, a number of genes escape from X inactivation. Persistence of escape genes in humans is largely unexplained, but is important for a normal phenotype. Indeed, women with a single X chromosome have Turner syndrome, due to haplo-insufficiency for escape genes. Thus, tissue-specific expression of sex-chromosomal genes is likely to be determined by a combination of gene copy number and dosage regulation in addition to hormonal influences. The role of escape genes in sex-specific differences and in sex chromosome aneuploidy is poorly understood. In this proposal we address the sex-specific expression and the role of escape genes in different tissues using genome-wide approaches. Based on our previous studies supported by this grant we will construct a new mouse model to evaluate escape from X inactivation in vivo. To determine expression from each X allele we will generate this model from two mouse species in which X inactivation is skewed, and use RNA-sequencing together with SNP identification to quantify allele-specific expression. The extent of X inactivation and escape for protein-coding genes and for non-coding RNA genes will be evaluated in different tissues and developmental stages. Escape genes are devoid of repressive histone modifications associated with X inactivation, such as tri-methylation of histone H3 lysine 27. Our preliminary evidence indicates that the histone demethylase KDM6A is associated with escape genes in early ES cell differentiation. Thus, we will manipulate the dose of this gene to determine how expression influences X-linked gene expression. The higher expression of escape genes in females suggests that these genes have roles in female-specific functions or processes. One example is Xist, an escape gene that produces a non-coding RNA essential for the onset of X inactivation during early development. An important factor in silencing by repressive chromatin modifications is the position of the inactive X in nuclei. We discovered two regions that bind CTCF only on the inactive X and produce non-coding RNAs that escape X inactivation. In fact, one of these genes is more highly expressed from the inactive than the active X. Both regions are associated with the nucleolus, a nuclear compartment that plays a role in maintenance of heterochromatin. We will examine the role of these regions by knockdown of the long non-coding RNAs in ES cells and in a mouse knockout. Our study will help understanding the role of escape genes in normal development, and in diseases associated with sex chromosome aneuploidy.

Public Health Relevance

X inactivation is an important process required to balance gene dosage between males and females. Equally important are those genes that escape X inactivation, which causes sex- specific differences in gene expression levels and play a role in sex chromosome disorders. Our proposal aims at a better understanding of the function of escape genes in relation to female- specific processes such as X inactivation.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Special Emphasis Panel (ZRG1-GGG-N (03))
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Carter, Anthony D
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University of Washington
Schools of Medicine
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Arnold, Arthur P; Disteche, Christine M (2018) Sexual Inequality in the Cancer Cell. Cancer Res 78:5504-5505
Cusanovich, Darren A; Hill, Andrew J; Aghamirzaie, Delasa et al. (2018) A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. Cell 174:1309-1324.e18
Dinarello, Charles Anthony (2018) An Interleukin-1 Signature in Breast Cancer Treated with Interleukin-1 Receptor Blockade: Implications for Treating Cytokine Release Syndrome of Checkpoint Inhibitors. Cancer Res 78:5200-5202
Ma, Wenxiu; Bonora, Giancarlo; Berletch, Joel B et al. (2018) X-Chromosome Inactivation and Escape from X Inactivation in Mouse. Methods Mol Biol 1861:205-219
Bonora, G; Deng, X; Fang, H et al. (2018) Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. Nat Commun 9:1445
Bonora, Giancarlo; Disteche, Christine M (2017) Structural aspects of the inactive X chromosome. Philos Trans R Soc Lond B Biol Sci 372:
Keown, Christopher L; Berletch, Joel B; Castanon, Rosa et al. (2017) Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain. Proc Natl Acad Sci U S A 114:E2882-E2890
Wei, Gengze; Deng, Xinxian; Agarwal, Saurabh et al. (2016) Patient Mutations of the Intellectual Disability Gene KDM5C Downregulate Netrin G2 and Suppress Neurite Growth in Neuro2a Cells. J Mol Neurosci 60:33-45
Disteche, Christine M (2016) Dosage compensation of the sex chromosomes and autosomes. Semin Cell Dev Biol 56:9-18
Berletch, Joel B; Ma, Wenxiu; Yang, Fan et al. (2015) Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model. Data Brief 5:761-9

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