Ronen D, Benvenisty N. Sex-dependent gene expression in human pluripotent stem cells. Cell Rep. 2014;8:923–32.
Article
PubMed
CAS
Google Scholar
Jansen R, Batista S, Brooks AI, Tischfield JA, Willemsen G, van Grootheest G, et al. Sex differences in the human peripheral blood transcriptome. BMC Genomics. 2014;15:33.
Article
PubMed
PubMed Central
Google Scholar
Arnold AP. Conceptual frameworks and mouse models for studying sex differences in physiology and disease: why compensation changes the game. Exp Neurol. 2014;259:2–9.
Article
PubMed
Google Scholar
Deng X, Berletch JB, Nguyen DK, Disteche CM. X chromosome regulation: diverse patterns in development, tissues and disease. Nat Rev Genet. 2014;15:367–78.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lyon MF. Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature. 1961;190:372–3.
Article
PubMed
CAS
Google Scholar
Lyon MF. Sex chromatin and gene action in the mammalian X-chromosome. Am J Hum Genet. 1962;14:135–48.
PubMed
CAS
PubMed Central
Google Scholar
Johnston CM, Lovell FL, Leongamornlert DA, Stranger BE, Dermitzakis ET, Ross MT. Large-scale population study of human cell lines indicates that dosage compensation is virtually complete. PLoS Genet. 2008;4, e9.
Article
PubMed
PubMed Central
Google Scholar
Carrel L, Willard HF. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature. 2005;434:400–4.
Article
PubMed
CAS
Google Scholar
Cotton AM, Bing G, Light N, Adoue V, Pastinen T, Brown CJ. Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome. Genome Biol. 2013;14:R122.
Article
PubMed
PubMed Central
Google Scholar
Berletch JB, Ma W, Yang F, Shendure J, Noble WS, Disteche CM, et al. Escape from X inactivation varies in mouse tissues. PLoS Genet. 2015;11, e1005079.
Article
PubMed
PubMed Central
Google Scholar
De Bonis ML, Cerase A, Matarazzo MR, Ferraro MR, Strazzullo M, Hansen RS, et al. Maintenance of X-and Y-inactivation of the pseudoautosomal (PAR2) gene SPRY2 is independent from DNA methylation and associated to multiple layers of epigenetic modifications. Hum Mol Genet. 2006;15:1123–32.
Article
PubMed
Google Scholar
Mele M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, et al. The human transcriptome across tissues and individuals. Science. 2015;348:660–5.
Article
PubMed
CAS
PubMed Central
Google Scholar
Armoskus C, Moreira D, Bollinger K, Jimenez O, Taniguchi S, TSAI H. Identification of sexually dimorphic genes in the neonatal mouse cortex and hippocampus. Brain Res. 2014;1562:22–38.
Article
Google Scholar
Zitzmann M, Bongers R, Werler S, Bogdanova N, Wistuba J, Kliesch S, et al. Gene expression patterns in relation to the clinical phenotype in Klinefelter syndrome. J Clin Endocrinol Metab. 2014;100:E518–23.
Article
PubMed
Google Scholar
Van der Meulen J, Sanghvi V, Mavrakis K, Durinck K, Fang F, Matthijssens F, et al. The H3K27me3 demethylase UTX is a gender-specific tumor suppressor in T-cell acute lymphoblastic leukemia. Blood. 2015;125:13–21.
Article
PubMed
Google Scholar
Snijders Blok L, Madsen E, Juusola J, Gilissen C, Baralle D, Reijnders MR, et al. Mutations in DDX3X are a common cause of unexplained intellectual disability with gender-specific effects on Wnt signaling. Am J Hum Genet. 2015;97:343–52.
Article
PubMed
CAS
Google Scholar
Dixon-McDougall T, Brown CJ. The making of a Barr body: the mosaic of factors that eXIST on the mammalian inactive X chromosome. Biochem Cell Biol. 2015. doi:10.1139/bcb-2015-0016.
PubMed
Google Scholar
Mohandas T, Sparkes RS, Shapiro LJ. Reactivation of an inactive human X chromosome: evidence for X inactivation by DNA methylation. Science. 1981;211:393–6.
Article
PubMed
CAS
Google Scholar
Tsai M, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010;329:689–93.
Article
PubMed
CAS
PubMed Central
Google Scholar
Cotton AM, Price EM, Jones MJ, Balaton BP, Kobor MS, Brown CJ. Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation. Hum Mol Genet. 2015;24:1528–39.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, et al. Global epigenomic reconfiguration during mammalian brain development. Science. 2013;341:1237905.
Article
PubMed
PubMed Central
Google Scholar
Carrel L, Willard HF. Heterogeneous gene expression from the inactive X chromosome: an X-linked gene that escapes X inactivation in some human cell lines but is inactivated in others. Proc Natl Acad Sci U S A. 1999;96:7364–9.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol. 2014;21:198–206.
Article
PubMed
CAS
PubMed Central
Google Scholar
Davidson RG, Nitowsky HM, Childs B. Demonstration of two populations of cells in the human female heterozygous for glucose-6-phosphate dehydrogenase variants. Genetics. 1963;50:481–5.
CAS
Google Scholar
Migeon BR, Moser HW, Moser AB, Axelman J, Sillence D, Norum RA. Adrenoleukodystrophy: evidence for X linkage, inactivation, and selection favoring the mutant allele in heterozygous cells. Proc Natl Acad Sci U S A. 1981;78:5066–70.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sudbrak R, Wiezorek G, Nuber UA, Mann W, Kirchner R, Erdogan F, et al. X chromosome-specific cDNA arrays: identification of genes that escape from X-inactivation and other applications. Hum Mol Genet. 2001;10:77–83.
Article
PubMed
CAS
Google Scholar
Craig IW, Mill J, Craig GM, Loat C, Schalkwyk LC. Application of microarrays to the analysis of the inactivation status of human X-linked genes expressed in lymphocytes. Eur J Hum Genet. 2004;12:639–46.
Article
PubMed
CAS
Google Scholar
Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, et al. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol. 2011;7:522.
Article
PubMed
PubMed Central
Google Scholar
Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, et al. The UCSC browser data retrieval tool. Nucleic Acids Res. 2004;32:493–6.
Article
Google Scholar
Brown GR, Hem V, Ovetsky KS, Wallin C, Ermolaeva O, Tolstoy I, et al. Gene: a gene-centered information resource at NCBI. Nucleic Acids Res. 2015;43:D36–42.
Article
PubMed
PubMed Central
Google Scholar
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, et al. The UCSC Genome Browser database: update 2006. Nucleic Acids Res. 2006;34:D590–8.
Article
PubMed
CAS
PubMed Central
Google Scholar
Almeida LG, Sakabe NJ, de Oliveira AR, Silva MC, Mundstein AS, Cohen T, et al. CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res. 2009;37:D816–9.
Article
PubMed
CAS
PubMed Central
Google Scholar
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014;515:355–64.
Article
PubMed
CAS
PubMed Central
Google Scholar
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2014. http://www.R-project.org/
Hothorn T, Bretz F, Westfall P. Simultaneous inference in general parametric models. Biom J. 2008;50:346–63.
Article
PubMed
Google Scholar
Venables WN, Ripley BD. Modern applied statistics with S. 4th ed. New York: Springer; 2002.
Book
Google Scholar
Sharpe D. Your chi-square test is statistically significant: now what? PARE. 2015;20.
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for the ENCODE project. Genome Res. 2012;22:1760–74.
Article
PubMed
CAS
PubMed Central
Google Scholar
Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 2006;7:S4.1–9.
Article
Google Scholar
Warburton PE, Giordano J, Cheung F, Gelfand Y, Benson G. Inverted repeat structure of the human genome: the X-chromosome contain a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Res. 2004;14:1861–9.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nino-Soto MI, Nuber UA, Basrur PK, Ropers HH, King WA. Differences in the pattern of X-linked gene expression between fetal bovine muscle and fibroblast cultures derived from the same muscle biopsies. Cytogenet. 2005;111:57–64.
Article
CAS
Google Scholar
Bennet-Baker PE, Wilkowski J, Burke DT. Age-associated activation of epigenetically repressed genes in the mouse. Genetics. 2003;165:2055–62.
Google Scholar
Clemson CM, Chow JC, Brown CJ, Lawrence JB. Stabilization and localization of Xist RNA are controlled by separate mechanisms and not sufficient for X inactivation. J Cell Biol. 1998;142:13–23.
Article
PubMed
CAS
PubMed Central
Google Scholar
Gartler SM, Dyer KA, Marshall Graves JA, Rocchi M. A two step model for mammalian X-chromosome inactivation. Prog Clin Biol Res. 1985;198:96–102.
Google Scholar
Graves JA, Young GJ. X-chromosome activity in heterokaryons and hybrids between mouse fibroblasts and teratocarcinoma stem cells. Exp Cell Res. 1982;141:87–97.
Article
PubMed
CAS
Google Scholar
Miller AP, Willard HF. Chromosomal basis of X chromosome inactivation: identification of a multigene domain in Xp11.21-p11.22 that escape X inactivation. Proc Natl Acad Sci U S A. 1998;95:8709–14.
Article
PubMed
CAS
PubMed Central
Google Scholar
Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi T, Borowsky M, et al. Spreading of X chromosome inactivation via a hierarchy of defined polycomb stations. Genome Res. 2012;22:1864–76.
Article
PubMed
CAS
PubMed Central
Google Scholar
Li N, Carrel L. Escape from X chromosome inactivation is an intrinsic property of the Jarid1c locus. Proc Natl Acad Sci U S A. 2008;105:17055–60.
Article
PubMed
CAS
PubMed Central
Google Scholar
Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2015;523:212–6.
Article
PubMed
CAS
Google Scholar
Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, et al. The DNA sequence of the human X chromosome. Nature. 2005;434:325–37.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wilson Sayres MA, Makova KD. Gene survival and death on the human Y chromosome. Mol Biol Evol. 2013;30:781–7.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lahn BT, Page DC. Four evolutionary strata on the human X chromosome. Science. 1999;286:964–7.
Article
PubMed
CAS
Google Scholar
Veitia RA, Veyrunes F, Bottani S, Birchler JA. X chromosome inactivation and active X upregulation in therian mammals: facts, questions, and hypotheses. J Mol Cell Biol. 2015;7:2–11.
Article
PubMed
Google Scholar