1. Hughes J.F., Page D.C. (2016) The history of the Y chromosome in man. Nat. Genet., 48, 588–589. [PubMed] [Google Scholar]
2. Veitia R.A., Veyrunes F., Bottani S., Birchler J.A. (2015) X chromosome inactivation and active X upregulation in therian mammals: facts, questions, and hypotheses. J. Mol. Cell. Biol., 7, 2–11. [PubMed] [Google Scholar]
3. Marin R., Cortez D., Lamanna F., Pradeepa M.M., Leushkin E., Julien P., Liechti A., Halbert J., Brüning T., Mössinger K. (2017) Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage. Genome Res., 27, 1974–1987. [PMC free article] [PubMed] [Google Scholar]
4. Nam K., Munch K., Hobolth A., Dutheil J.Y., Veeramah K.R., Woerner A.E., Hammer M.F., Mailund T., Schierup M.H. (2015) Extreme selective sweeps independently targeted the X chromosomes of the great apes. Proc. Natl. Acad. Sci. USA, 112, 6413–6418. [PMC free article] [PubMed] [Google Scholar]
5. Carelli F.N., Hayakawa T., Go Y., Imai H., Warnefors M., Kaessmann H. (2016) The life history of retrocopies illuminates the evolution of new mammalian genes. Genome Res., 26, 301–314. [PMC free article] [PubMed] [Google Scholar]
6. Sosa E., Flores L., Yan W., McCarrey J.R. (2015) Escape of X-linked miRNA genes from meiotic sex chromosome inactivation. Development, 142, 3791–3800. [PMC free article] [PubMed] [Google Scholar]
7. Royo H., Seitz H., ElInati E., Peters A.H.F.M., Stadler M.B., Turner J.M.A. (2015) Silencing of X-linked microRNAs by meiotic sex chromosome inactivation. PLoS Genet., 11, e1005461.. [PMC free article] [PubMed] [Google Scholar]
8. Balaton B.P., Brown C.J. (2016) Escape artists of the X chromosome. Trends Genet., 32, 348–359. [PubMed] [Google Scholar]
9. Wang S., Su J.-H., Beliveau B.J., Bintu B., Moffitt J.R., Wu C.-T., Zhuang X. (2016) Spatial organization of chromatin domains and compartments in single chromosomes. Science, 353, 598–602. [PMC free article] [PubMed] [Google Scholar]
10. Giorgetti L., Lajoie B.R., Carter A.C., Attia M., Zhan Y., Xu J., Chen C.J., Kaplan N., Chang H.Y., Heard E., Dekker J. (2016) Structural organization of the inactive X chromosome in the mouse. Nature, 535, 575–579. [PMC free article] [PubMed] [Google Scholar]
11. Deng X., Ma W., Ramani V., Hill A., Yang F., Ay F., Berletch J.B., Blau C.A., Shendure J., Duan Z., Noble W.S., Disteche C.M. (2015) Bipartite structure of the inactive mouse X chromosome. Genome Biol., 16, 152.. [PMC free article] [PubMed] [Google Scholar]
12. Darrow E.M., Huntley M.H., Dudchenko O., Stamenova E.K., Durand N.C., Sun Z., Huang S.-C., Sanborn A.L., Machol I., Shamim M.. et al. (2016) Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Proc. Natl. Acad. Sci. USA, 113, E4504–E4512. [PMC free article] [PubMed] [Google Scholar]
13. Barutcu A.R., Maass P.G., Lewandowski J.P., Weiner C.L., Rinn J.L. (2018) A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nat. Commun., 9, 1444.. [PMC free article] [PubMed] [Google Scholar]
14. Yang F., Deng X., Ma W., Berletch J.B., Rabaia N., Wei G., Moore J.M., Filippova G.N., Xu J., Liu Y.. et al. (2015) The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biol., 16, 52.. [PMC free article] [PubMed] [Google Scholar]
15. Yamada N., Hasegawa Y., Yue M., Hamada T., Nakagawa S., Ogawa Y. (2015) Xist exon 7 contributes to the stable localization of Xist RNA on the inactive X-chromosome. PLoS Genet., 11, e1005430.. [PMC free article] [PubMed] [Google Scholar]
16. Okamoto I., Patrat C., Thépot D., Peynot N., Fauque P., Daniel N., Diabangouaya P., Wolf J.-P., Renard J.-P., Duranthon V., Heard E. (2011) Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development. Nature, 472, 370–374. [PubMed] [Google Scholar]
17. Petropoulos S., Edsgärd D., Reinius B., Deng Q., Panula S.P., Codeluppi S., Plaza Reyes A., Linnarsson S., Sandberg R., Lanner F. (2016) Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell, 165, 1012–1026. [PMC free article] [PubMed] [Google Scholar]
18. Vallot C., Patrat C., Collier A.J., Huret C., Casanova M., Liyakat Ali T.M., Tosolini M., Frydman N., Heard E., Rugg-Gunn P.J., Rougeulle C. (2017) XACT noncoding RNA competes with XIST in the control of X chromosome activity during human early development. Cell Stem Cell, 20, 102–111. [PMC free article] [PubMed] [Google Scholar]
19. Moreira de Mello J.C., Fernandes G.R., Vibranovski M.D., Pereira L.V. (2017) Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing. Sci. Rep., 7, 10794.. [PMC free article] [PubMed] [Google Scholar]
20. Geens M., Chuva De Sousa Lopes S.M. (2017) X chromosome inactivation in human pluripotent stem cells as a model for human development: back to the drawing board? Hum. Reprod. Update, 23, 520–532. [PubMed] [Google Scholar]
21. Sahakyan A., Kim R., Chronis C., Sabri S., Bonora G., Theunissen T.W., Kuoy E., Langerman J., Clark A.T., Jaenisch R., Plath K. (2017) Human naive pluripotent stem cells model X chromosome dampening and X inactivation. Cell Stem Cell, 20, 87–101. [PMC free article] [PubMed] [Google Scholar]
22. Guo G., von Meyenn F., Rostovskaya M., Clarke J., Dietmann S., Baker D., Sahakyan A., Myers S., Bertone P., Reik W., Plath K., Smith A. (2017) Epigenetic resetting of human pluripotency. Development, 144, 2748–2763. [PMC free article] [PubMed] [Google Scholar]
23. Migeon B.R., Beer M.A., Bjornsson H.T. (2017) Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X. PLoS One, 12, e0170403.. [PMC free article] [PubMed] [Google Scholar]
24. Mutzel V., Okamoto I., Dunkel I., Saitou M., Giorgetti L., Heard E., Schulz E.G. (2017) Two coupled feedback loops explain random mono-allelic Xist upregulation at the onset of X-chromosome inactivation. BioXRIV. 10.1101/204909.
25. Chu C., Zhang Q.C., da Rocha S.T., Flynn R.A., Bharadwaj M., Calabrese J.M., Magnuson T., Heard E., Chang H.Y. (2015) Systematic discovery of Xist RNA binding proteins. Cell, 161, 404–416. [PMC free article] [PubMed] [Google Scholar]
26. Minajigi A., Froberg J.E., Wei C., Sunwoo H., Kesner B., Colognori D., Lessing D., Payer B., Boukhali M., Haas W., Lee J.T. (2015) Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science, 349, aab2276–aab2276. [PMC free article] [PubMed] [Google Scholar]
27. McHugh C.A., Chen C.-K., Chow A., Surka C.F., Tran C., McDonel P., Pandya-Jones A., Blanco M., Burghard C., Moradian A.. et al. (2015) The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature, 521, 232–236. [PMC free article] [PubMed] [Google Scholar]
28. Moindrot B., Brockdorff N. (2016) RNA binding proteins implicated in Xist-mediated chromosome silencing. Semin. Cell Dev. Biol., 56, 58–70. [PubMed] [Google Scholar]
29. da Rocha S.T., Heard E. (2017) Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation. Nat. Struct. Mol. Biol., 24, 197–204. [PubMed] [Google Scholar]
30. Pintacuda G., Wei G., Roustan C., Kirmizitas B.A., Solcan N., Cerase A., Castello A., Mohammed S., Moindrot B., Nesterova T.B.. et al. (2017) hnRNPK recruits PCGF3/5-PRC1 to the Xist RNA B-repeat to establish polycomb-mediated chromosomal silencing. Mol. Cell, 68, 955–969. [PMC free article] [PubMed] [Google Scholar]
31. Almeida M., Pintacuda G., Masui O., Koseki Y., Gdula M., Cerase A., Brown D., Mould A., Innocent C., Nakayama M.. et al. (2017) PCGF3/5–PRC1 initiates polycomb recruitment in X chromosome inactivation. Science, 356, 1081–1084. [PMC free article] [PubMed] [Google Scholar]
32. Kolpa H.J., Fackelmayer F.O., Lawrence J.B. (2016) SAF-A requirement in anchoring XIST RNA to chromatin varies in transformed and primary cells. Dev. Cell, 39, 9–10. [PMC free article] [PubMed] [Google Scholar]
33. Ridings-Figueroa R., Stewart E.R., Nesterova T.B., co*ker H., Pintacuda G., Godwin J., Wilson R., Haslam A., Lilley F., Ruigrok R.. et al. (2017) The nuclear matrix protein CIZ1 facilitates localization of Xist RNA to the inactive X-chromosome territory. Genes. Dev., 31, 876–888. [PMC free article] [PubMed] [Google Scholar]
34. Sunwoo H., Colognori D., Froberg J.E., Jeon Y., Lee J.T. (2017) Repeat E anchors Xist RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1). Proc. Natl. Acad. Sci. USA, 114, 10654–10659. [PMC free article] [PubMed] [Google Scholar]
35. Wang J., Syrett C.M., Kramer M.C., Basu A., Atchison M.L., Anguera M.C. (2016) Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X. Proc. Natl. Acad. Sci. USA, 113, E2029–E2038. [PMC free article] [PubMed] [Google Scholar]
36. Syrett C.M., Sindhava V., Hodawadekar S., Myles A., Liang G., Zhang Y., Nandi S., Cancro M., Atchison M., Anguera M.C. (2017) Loss of Xist RNA from the inactive X during B cell development is restored in a dynamic YY1-dependent two-step process in activated B cells. PLoS Genet., 13, e1007050.. [PMC free article] [PubMed] [Google Scholar]
37. Jeon Y., Lee J.T. (2011) YY1 tethers Xist RNA to the inactive X nucleation center. Cell, 146, 119–133. [PMC free article] [PubMed] [Google Scholar]
38. Patil D.P., Chen C.-K., Pickering B.F., Chow A., Jackson C., Guttman M., Jaffrey S.R. (2016) m(6)A RNA methylation promotes XIST-mediated transcriptional repression. Nature, 537, 369–373. [PMC free article] [PubMed] [Google Scholar]
39. Kelsey A.D., Yang C., Leung D., Minks J., Dixon-McDougall T., Baldry S.E.L., Bogutz A.B., Lefebvre L., Brown C.J. (2015) Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST. Genome Biol., 16, 208. [PMC free article] [PubMed] [Google Scholar]
40. Loda A., Brandsma J.H., Vassilev I., Servant N., Loos F., Amirnasr A., Splinter E., Barillot E., Poot R.A., Heard E.. et al. (2017) Genetic and epigenetic features direct differential efficiency of Xist-mediated silencing at X-chromosomal and autosomal locations. Nat. Commun., 8, 690. [PMC free article] [PubMed] [Google Scholar]
41. Tukiainen T., Villani A.-C., Yen A., Rivas M.A., Marshall J.L., Satija R., Aguirre M., Gauthier L., Fleharty M., Kirby A.. et al. (2017) Landscape of X chromosome inactivation across human tissues. Nature, 550, 244–248. [PMC free article] [PubMed] [Google Scholar]
42. Balaton B.P., Cotton A.M., Brown C.J. (2015) Derivation of consensus inactivation status for X-linked genes from genome-wide studies. Biol. Sex Dif., 6, 35. [PMC free article] [PubMed] [Google Scholar]
43. Marks H., Kerstens H.H.D., Barakat T.S., Splinter E., Dirks R.A.M., van Mierlo G., Joshi O., Wang S.-Y., Babak T., Albers C.A.. et al. (2015) Dynamics of gene silencing during X inactivation using allele-specific RNA-seq. Genome Biol., 16, 149.. [PMC free article] [PubMed] [Google Scholar]
44. Naqvi S., Bellott D.W., Lin K.S., Page D.C. (2018) Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution. Genome Res., 10.1101/gr.230433.117. [PMC free article] [PubMed] [Google Scholar]
45. Lyon M.F. (1998) X-Chromosome inactivation: a repeat hypothesis. Cytogenet. Genome Res., 80, 133–137. [PubMed] [Google Scholar]
46. Yang C., McLeod A.J., Cotton A.M., de Leeuw C.N., Laprise S., Banks K.G., Simpson E.M., Brown C.J. (2012) Targeting of >1.5 Mb of human DNA into the mouse X chromosome reveals presence of cis-acting regulators of epigenetic silencing. Genetics, 192, 1281–1293. [PMC free article] [PubMed] [Google Scholar]
47. Cotton A.M., Chen C.-Y., Lam L.L., Wasserman W.W., Kobor M.S., Brown C.J. (2014) Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains. Hum. Mol. Genet., 23, 1211–1223. [PMC free article] [PubMed] [Google Scholar]
48. Horvath L.M., Li N., Carrel L. (2013) Deletion of an X-inactivation boundary disrupts adjacent gene silencing. PLoS Genet., 9, e1003952.. [PMC free article] [PubMed] [Google Scholar]
49. Carrel L., Brown C.J. (2017) When the Lyon(ized chromosome) roars: ongoing expression from an inactive X chromosome. Philos. Trans. R. Soc. Lond. B Biol. Sci., 372, 20160355.. [PMC free article] [PubMed] [Google Scholar]
50. Peeters S.B., Korecki A.J., Simpson E.M., Brown C.J. (2018) Human cis-acting elements regulating escape from X-chromosome inactivation function in mouse. Hum. Mol. Genet., 27, 1252–1262. [PMC free article] [PubMed] [Google Scholar]
51. Ding Z., Ni Y., Timmer S.W., Lee B.-K., Battenhouse A., Louzada S., Yang F., Dunham I., Crawford G.E., Lieb J.D.. et al. (2014) Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PLoS Genet., 10, e1004798. [PMC free article] [PubMed] [Google Scholar]
52. Fieremans N., Van Esch H., Holvoet M., Van Goethem G., Devriendt K., Rosello M., Mayo S., Martinez F., Jhangiani S., Muzny D.M.. et al. (2016) Identification of intellectual disability genes in female patients with a skewed X-inactivation pattern. Hum. Mutat., 37, 804–811. [PMC free article] [PubMed] [Google Scholar]
53. Arnold A.P., Reue K., Eghbali M., Vilain E., Chen X., Ghahramani N., Itoh Y., Li J., Link J.C., Ngun T.. et al. (2016) The importance of having two X chromosomes. Philos. Trans. R. Soc. Lond. B Biol. Sci., 371, 20150113.. [PMC free article] [PubMed] [Google Scholar]
54. Printzlau F., Wolstencroft J., Skuse D.H. (2017) Cognitive, behavioral, and neural consequences of sex chromosome aneuploidy. J. Neurosci. Res., 95, 311–319. [PubMed] [Google Scholar]
55. Sharma R., Harris V.M., Cavett J., Kurien B.T., Liu K., Koelsch K.A., Fayaaz A., Chaudhari K.S., Radfar L., Lewis D.. et al. (2017) Rare X chromosome abnormalities in systemic lupus erythematosus and Sjögren's syndrome. Arthritis Rheumatol., 69, 2187–2192. [PMC free article] [PubMed] [Google Scholar]
56. Dunford A., Weinstock D.M., Savova V., Schumacher S.E., Cleary J.P., Yoda A., Sullivan T.J., Hess J.M., Gimelbrant A.A., Beroukhim R.. et al. (2017) Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias. Nat. Genet., 49, 10–16. [PMC free article] [PubMed] [Google Scholar]
57. Cheng F., Liu C., Lin C.-C., Zhao J., Jia P., Li W.-H., Zhao Z. (2015) A gene gravity model for the evolution of cancer genomes: a study of 3, 000 cancer genomes across 9 cancer types. PLoS Comp. Biol., 11, e1004497. [PMC free article] [PubMed] [Google Scholar]
58. Chaligné R., Popova T., Mendoza-Parra M.-A., Saleem M.-A.M., Gentien D., Ban K., Piolot T., Leroy O., Mariani O., Gronemeyer H.. et al. (2015) The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer. Genome Res., 25, 488–503. [PMC free article] [PubMed] [Google Scholar]
59. Skare Ø., Gjessing H.K., Gjerdevik M., Haaland Ø.A., Romanowska J., Lie R.T., Jugessur A. (2017) A new approach to chromosome-wide analysis of X-linked markers identifies new associations in Asian and European case-parent triads of orofacial clefts. PLoS One, 12, e0183772.. [PMC free article] [PubMed] [Google Scholar]
60. Carrette L.L.G., Wang C.-Y., Wei C., Press W., Ma W., Kelleher R.J., Lee J.T. (2017) A mixed modality approach towards Xi reactivation for Rett syndrome and other X-linked disorders. Proc. Natl. Acad. Sci. USA, 115, E668–E675. [PMC free article] [PubMed] [Google Scholar]
61. Jiang J., Jing Y., Cost G.J., Chiang J.-C., Kolpa H.J., Cotton A.M., Carone D.M., Carone B.R., Shivak D.A., Guschin D.Y.. et al. (2013) Translating dosage compensation to trisomy 21. Nature, 500, 296–300. [PMC free article] [PubMed] [Google Scholar]
62. Kilens S., Meistermann D., Moreno D., Chariau C., Gaignerie A., Reignier A., Lelièvre Y., Casanova M., Vallot C., Nedellec S.. et al. (2018) Parallel derivation of isogenic human primed and naive induced pluripotent stem cells. Nat. Commun., 9, 360.. [PMC free article] [PubMed] [Google Scholar]
