REFERENCES
2. Ercan S, Lieb JD. C. elegans dosage compensation: a window into mechanisms of domain-scale gene regulation. Chromosom Res 2009;17:215-27.
3. Hallacli E, Akhtar A. X chromosomal regulation in flies: when less is more. Chromosom Res 2009;17:603-19.
4. Maduro C, de Hoon B, Gribnau J. Fitting the puzzle pieces: the bigger picture of XCI. Trends Biochem Sci 2016;41:138-47.
5. Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N. Requirement for Xist in X chromosome inactivation. Nature 1996;379:131-7.
6. Pintacuda G, Cerase A. X inactivation lessons from differentiating mouse embryonic stem cells. Stem Cell Rev Reports 2015;11:699-705.
7. Shen Y, Matsuno Y, Fouse SD, Rao N, Root S, Xu R, Pellegrini M, Riggs AD, Fan G. X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. Proc Natl Acad Sci U S A 2008;105:4709-14.
8. Chaumeil J, Okamoto I, Guggiari M, Heard E. Integrated kinetics of X chromosome inactivation in differentiating embryonic stem cells. Cytogenet Genome Res 2002;99:75-84.
9. Stavropoulos N, Lu N, Lee JT. A functional role for Tsix transcription in blocking Xist RNA accumulation but not in X-chromosome choice. Proc Natl Acad Sci U S A 2001;98:10232-7.
10. Del Rosario BC, Del Rosario AM, Anselmo A, Wang PI, Sadreyev RI, Lee JT. Genetic intersection of Tsix and Hedgehog signaling during the initiation of X-chromosome inactivation. Dev Cell 2017;43:359-71.e6.
11. Lee JT, Davidow LS, Warshawsky D. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 1999;21:400-4.
12. Shibata S, Lee JT. Characterization and quantitation of differential Tsix transcripts: implications for Tsix function. Hum Mol Genet 2003;12:125-36.
13. Payer B, Lee JT. Coupling of X-chromosome reactivation with the pluripotent stem cell state. RNA Biol 2014;11:798-807.
14. Barakat TS, Gunhanlar N, Pardo CG, Achame EM, Ghazvini M, Boers R, Kenter A, Rentmeester E, Grootegoed JA, Gribnau J. RNF12 activates Xist and is essential for X chromosome inactivation. PLoS Genet 2011;7:e1002001.
15. Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C. Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. Hum Mol Genet 2011;20:705-18.
16. Tian D, Sun S, Lee JT. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 2010;143:390-403.
17. Augui S, Nora EP, Heard E. Regulation of X-chromosome inactivation by the X-inactivation centre. Nat Rev Genet 2011;12:429-42.
18. Brown CJ, Hendrich BD, Rupert JL, Lafrenière RG, Xing Y, Lawrence J, Willard HF. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992;71:527-42.
19. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008;322:750-6.
21. Plath K, Talbot D, Hamer KM, Otte AP, Yang TP, Jaenisch R, Panning B. Developmentally regulated alterations in Polycomb repressive complex 1 proteins on the inactive X chromosome. J Cell Biol 2004;167:1025-35.
22. Schoeftner S, Sengupta AK, Kubicek S, Mechtler K, Spahn L, Koseki H, Jenuwein T, Wutz A. Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. EMBO J 2006;25:3110-22.
23. Costanzi C, Pehrson JR. Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals. Nature 1998;393:599-601.
24. Heard E, Rougeulle C, Arnaud D, Avner P, Allis CD, Spector DL. Methylation of histone H3 at Lys-9 Is an early mark on the X chromosome during X inactivation. Cell 2001;107:727-38.
25. Rougeulle C, Chaumeil J, Sarma K, Allis CD, Reinberg D, Avner P, Heard E. Differential histone H3 Lys-9 and Lys-27 methylation profiles on the X chromosome. Mol Cell Biol 2004;24:5475-84.
26. Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y. Role of histone H3 lysine 27 methylation in X inactivation. Science 2003;300:131-5.
27. Sarma K, Cifuentes-Rojas C, Ergun A, Del Rosario A, Jeon Y, White F, Sadreyev R, Lee JT. ATRX directs binding of PRC2 to Xist RNA and Polycomb targets. Cell 2014;159:869-83.
28. Almeida M, Pintacuda G, Masui O, Koseki Y, Gdula M, Cerase A, Brown D, Mould A, Innocent C, Nakayama M, Schermelleh L, Nesterova TB, Koseki H, Brockdorff N. PCGF3/5-PRC1 initiates Polycomb recruitment in X chromosome inactivation. Science 2017;356:1081-4.
29. Brockdorff N. Polycomb complexes in X chromosome inactivation. Philos Trans R Soc B Biol Sci 2017;372:20170021.
30. Sharp AJA, Stathaki E, Migliavacca E, Brahmachary M, Montgomery SB, Dupre Y, Antonarakis SE. DNA methylation profiles of human active and inactive X chromosomes. Genome Res 2011;21:1592-600.
31. 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.
32. Bhatnagar S, Zhu X, Ou J, Lin L, Chamberlain L, Zhu LJ, Wajapeyee N, Green MR. Genetic and pharmacological reactivation of the mammalian inactive X chromosome. Proc Natl Acad Sci U S A 2014;111:12591-8.
33. Lessing D, Dial TO, Wei C, Payer B, Carrette LL, Kesner B, Szanto A, Jadhav A, Maloney DJ, Simeonov A, Theriault J, Hasaka T, Bedalov A, Bartolomei MS, Lee JT. A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X reactivation. Proc Natl Acad Sci U S A 2016;113:14366-71.
34. Sripathy S, Leko V, Adrianse RL, Loe T, Foss EJ, Dalrymple E, Lao U, Gatbonton-Schwager T, Carter KT, Payer B, Paddison PJ, Grady WM, Lee JT, Bartolomei MS, Bedalov A. Screen for reactivation of MeCP2 on the inactive X chromosome identifies the BMP/TGF-β superfamily as a regulator of XIST expression. Proc Natl Acad Sci U S A 2017;114:1619-24.
35. Huynh KO, Lee JT. Inheritance of a pre-inactivated paternal X chromosome in early mouse embryos. Nature 2003;426:857-62.
36. Okamoto I. Epigenetic dynamics of imprinted X inactivation during early mouse development. Science 2004;303:644-9.
37. van den Berg IM, Galjaard RJ, Laven JS, van Doorninck JH. XCI in preimplantation mouse and human embryos: first there is remodelling. Hum Genet 2011;130:203-15.
38. Sirchia SM, Tabano S, Monti L, Recalcati MP, Gariboldi M, Grati FR, Porta G, Finelli P, Radice P, Miozzo M. Misbehaviour of XIST RNA in breast cancer cells. PLoS One 2009;4:e5559.
39. Chaligné R, Popova T, Mendoza-Parra MA, Saleem MA, Gentien D, Ban K, Piolot T, Leroy O, Mariani O, Gronemeyer H, Vincent-Salomon A, Stern MH, Heard E. The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer. Genome Res 2015;25:488-503.
40. Chan KM, Zhang H, Malureanu L, van Deursen J, Zhang Z. Diverse factors are involved in maintaining X chromosome inactivation. Proc Natl Acad Sci U S A 2011;108:16699-704.
41. Minkovsky A, Sahakyan A, Bonora G, Damoiseaux R, Dimitrova E, Rubbi L, Pellegrini M, Radu CG, Plath K. A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2′-dC upon inhibition of ribonucleotide reductase. Epigenetics Chromatin 2015;8:42.
42. Moindrot B, Cerase A, Coker H, Masui O, Grijzenhout A, Pintacuda G, Schermelleh L, Nesterova TB, Brockdorff N. A pooled shRNA screen identifies Rbm15, Spen, and Wtap as factors required for Xist RNA-mediated silencing. Cell Rep 2015;12:562-72.
43. Monfort A, Di Minin G, Postlmayr A, Freimann R, Arieti F, Thore S, Wutz A. Identification of Spen as a crucial factor for Xist function through forward genetic screening in haploid embryonic stem cells. Cell Rep 2015;12:554-61.
44. Ferrè F, Colantoni A, Helmer-Citterich M. Revealing protein-lncRNA interaction. Brief Bioinform 2016;17:106-16.
45. Barra J, Leucci E. Probing long non-coding RNA-protein interactions. Front Mol Biosci 2017;4:45.
46. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 2011;44:667-78.
47. Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY. Systematic discovery of Xist RNA binding proteins. Cell 2015;161:404-16.
48. Minajigi A, Froberg JE, Wei C, Sunwoo H, Kesner B, Colognori D, Lessing D, Payer B, Boukhali M, Haas W, Lee JT. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science 2015;349:aab2276.
49. McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, Guttman M. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 2015;521:232-6.
50. Engreitz JM, Ollikainen N, Guttman M. Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol 2016;17:756-70.
51. Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, Bowman SK, Kesner BA, Maier VK, Kingston RE, Lee JT. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 2013;504:465-9.
52. Kiledjian M, Dreyfuss G. Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. EMBO J 1992;11:2655-64.
53. Ouyang Y, Salstrom J, Diaz-Perez S, Nahas S, Matsuno Y, Dawson D, Teitell MA, Horvath S, Riggs AD, Gatti RA, Marahrens Y. Inhibition of Atm and/or Atr disrupts gene silencing on the inactive X chromosome. Biochem Biophys Res Commun 2005;337:875-80.
54. Ariyoshi M, Schwabe JW. A conserved structural motif reveals the essential transcriptional repression function of spen proteins and their role in developmental signaling. Genes Dev 2003;17:1909-20.
55. Colley SM, Iyer KR, Leedman PJ. The RNA coregulator SRA, its binding proteins and nuclear receptor signaling activity. IUBMB Life 2008;60:159-64.
56. Patil DP, Chen CK, Pickering BF, Chow A, Jackson C, Guttman M, Jaffrey SR. M6A RNA methylation promotes XIST-mediated transcriptional repression. Nature 2016;537:369-73.
57. Horiuchi K, Kawamura T, Iwanari H, Ohashi R, Naito M, Kodama T, Hamakubo T. Identification of Wilms' tumor 1-associating protein complex and its role in alternative splicing and the cell cycle. J Biol Chem 2013;288:33292-302.
58. Hasegawa Y, Brockdorff N, Kawano S, Tsutui K, Tsutui K, Nakagawa S. The matrix protein hnRNP U is required for chromosomal localization of xist RNA. Dev Cell 2010;19:469-76.
59. Tang L, Nogales E, Ciferri C. Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription. Prog Biophys Mol Biol 2010;102:122-8.
60. Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Blüthgen N, Dekker J, Heard E. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012;485:381-5.
61. Simmler MC, Cunningham DB, Clerc P, Vermat T, Caudron B, Cruaud C, Pawlak A, Szpirer C, Weissenbach J, Claverie JM, Avner P. A 94 kb genomic sequence 3' to the murine Xist gene reveals an AT rich region containing a new testis specific gene Tsx. Hum Mol Genet 1996;5:1713-26.
62. Ogawa Y, Lee JT. Xite, X-inactivation intergenic transcription elements that regulate the probability of choice. Mol Cell 2003;11:731-43.
63. Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, Eggen A, Avner P, Duret L. Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine. Genome Res 2002;12:894-908.
64. Augui S, Filion GJ, Huart S, Nora E, Guggiari M, Maresca M, Stewart AF, Heard E. Sensing X chromosome pairs before X inactivation via a novel X-pairing region of the Xic. Science 2007;318:1632-6.
65. van Bemmel JG, Mira-Bontenbal H, Gribnau J. Cis- and trans-regulation in X inactivation. Chromosoma 2016;125:41-50.
66. Zhang L, Huang H, Zhou F, Schimmel J, Pardo CG, Zhang T, Barakat TS, Sheppard KA, Mickanin C, Porter JA, Vertegaal AC, van Dam H, Gribnau J, Lu CX, ten Dijke P. RNF12 controls embryonic stem cell fate and morphogenesis in zebrafish embryos by targeting Smad7 for degradation. Mol Cell 2012;46:650-61.
67. Figueroa DM, Darrow EM, Chadwick BP. Two novel DXZ4-associated long noncoding RNAs show developmental changes in expression coincident with heterochromatin formation at the human (Homo sapiens) macrosatellite repeat. Chromosom Res 2015;23:733-52.
68. Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. Bipartite structure of the inactive mouse X chromosome. Genome Biol 2015;16:152.
69. Horakova AH, Moseley SC, Mclaughlin CR, Tremblay DC, Chadwick BP. The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome. Hum Mol Genet 2012;21:4367-77.
70. Darrow EM, Huntley MH, Dudchenko O, Stamenova EK, Durand NC, Sun Z, Huang SC, Sanborn AL, Machol I, Shamim M, Seberg AP, Lander ES, Chadwick BP, Aiden EL. Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Proc Natl Acad Sci U S A 2016;113:E4504-12.
71. Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J. Structural organization of the inactive X chromosome in the mouse. Nature 2016;535:575-9.
72. Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res 2005;33:D284-8.
73. Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD. PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res 2017;45:D183-9.
74. Alvarez-Saavedra M, Sáez MA, Kang D, Zoghbi HY, Young JI. Cell-specific expression of wild-type MeCP2 in mouse models of Rett syndrome yields insight about pathogenesis. Hum Mol Genet 2007;16:2315-25.
75. Garg SK, Lioy DT, Cheval H, McGann JC, Bissonnette JM, Murtha MJ, Foust KD, Kaspar BK, Bird A, Mandel G. Systemic delivery of MeCP2 rescues behavioral and cellular deficits in female mouse models of Rett syndrome. J Neurosci 2013;33:13612-20.
