1. Rastan, S. & Robertson, E. J. X-chromosome deletions in embryo-derived (EK) cell lines associated with lack of X-chromosome inactivation. J. Embryol. Exp. Morphol. 90, 379–388 (1985).

2. Augui, S., Nora, E. P. & Heard, E. Regulation of X-chromosome inactivation by the X-inactivation centre. Nat. Rev. Genet. 12, 429–442 (2011).

3. Galupa, R. & Heard, E. X-chromosome inactivation: new insights into cis and trans regulation. Curr. Opin. Genet. Dev. 31, 57–66 (2015).

4. Pollex, T. & Heard, E. Recent advances in X-chromosome inactivation research. Curr. Opin. Cell Biol. 24, 825–832 (2012).

5. Borsani, G. et al. Characterization of a murine gene expressed from the inactive X chromosome. Nature 351, 325–329 (1991).

6. Brockdorff, N. et al. Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. Nature 351, 329–331 (1991).

7. Brockdorff, N. et al. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71, 515–526 (1992).

8. 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).

9. Brown, C. J. et al. 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 71, 527–542 (1992).

10. Okamoto, I. et al. Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development. Nature 472, 370–374 (2011).

11. 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).

12. Borensztein, M. et al. Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. Nat. Struct. Mol. Biol. 24, 226–233 (2017).

13. Takagi, N. & Abe, K. Detrimental effects of two active X chromosomes on early mouse development. Development 109, 189–201 (1990).

14. Lee, J. T. Regulation of X-chromosome counting by Tsix and Xite sequences. Science 309, 768–771 (2005).

15. Luikenhuis, S., Wutz, A. & Jaenisch, R. Antisense transcription through the Xist locus mediates Tsix function in embryonic stem cells. Mol. Cell. Biol. 21, 8512–8520 (2001).

16. Stavropoulos, N., Lu, N. & Lee, J. T. A functional role for Tsix transcription in blocking Xist RNA accumulation but not in X-chromosome choice. Proc. Natl Acad. Sci. USA 98, 10232–10237 (2001).

17. Navarro, P., Pichard, S., Ciaudo, C., Avner, P. & Rougeulle, C. Tsix transcription across the Xist gene alters chromatin conformation without affecting Xist transcription: implications for X-chromosome inactivation. Genes Dev. 19, 1474–1484 (2005).

18. Sado, T., Hoki, Y. & Sasaki, H. Tsix silences Xist through modification of chromatin structure. Dev. Cell. 9, 159–165 (2005).

19. Navarro, P., Page, D. R., Avner, P. & Rougeulle, C. Tsix-mediated epigenetic switch of a CTCF-flanked region of the Xist promoter determines the Xist transcription program. Genes Dev. 20, 2787–2792 (2006).

20. Ohhata, T., Hoki, Y., Sasaki, H. & Sado, T. Crucial role of antisense transcription across the Xist promoter in Tsix-mediated Xist chromatin modification. Development 135, 227–235 (2008).

21. Debrand, E., Chureau, C., Arnaud, D., Avner, P. & Heard, E. Functional analysis of the DXPas34 locus, a 3’ regulator of Xist expression. Mol. Cell. Biol. 19, 8513–8525 (1999).

22. Lee, J. T., Davidow, L. S. & Warshawsky, D. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat. Genet. 21, 400–404 (1999).

23. Lee, J. T. & Lu, N. Targeted mutagenesis of Tsix leads to nonrandom X inactivation. Cell 99, 47–57 (1999).

24. Navarro, P. et al. Molecular coupling of Xist regulation and pluripotency. Science 321, 1693–1695 (2008).

25. Navarro, P. et al. Molecular coupling of Tsix regulation and pluripotency. Nature 468, 457–460 (2010).

26. Jonkers, I. et al. RNF12 is an X-Encoded dose-dependent activator of X chromosome inactivation. Cell 139, 999–1011 (2009).

27. Barakat, T. S. et al. RNF12 activates Xist and is essential for X chromosome inactivation. PLoS Genet. 7, e1002001 (2011).

28. Gontan, C. et al. RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation. Nature 485, 386–390 (2012).

29. Barakat, T. S. et al. The trans-activator RNF12 and cis-acting elements effectuate X chromosome inactivation independent of X-pairing. Mol. Cell 53, 965–978 (2014).

30. Schulz, E. G. & Heard, E. Role and control of X chromosome dosage in mammalian development. Curr. Opin. Genet. Dev. 23, 109–115 (2013).

31. Xu, N., Tsai, C.-L. & Lee, J. T. Transient homologous chromosome pairing marks the onset of X inactivation. Science 311, 1149–1152 (2006).

32. Bacher, C. P. et al. Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat. Cell Biol. 8, 293–299 (2006).

33. Xu, N., Donohoe, M. E., Silva, S. S. & Lee, J. T. Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nat. Genet. 39, 1390–1396 (2007).

34. Masui, O. et al. Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation. Cell 145, 447–458 (2011).

35. Augui, S. et al. Sensing X chromosome pairs before X inactivation via a novel X-pairing region of the Xic. Science 318, 1632–1636 (2007).

36. Sun, S., Fukue, Y., Nolen, L., Sadreyev, R. & Lee, J. T. Characterization of Xpr (Xpct) reveals instability but no effects on X-chromosome pairing or Xist expression. Transcription 1, 46–56 (2010).

37. Donohoe, M. E., Silva, S. S., Pinter, S. F., Xu, N. & Lee, J. T. The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting. Nature 460, 128–132 (2009).

38. Comings, D. E. The rationale for an ordered arrangement of chromatin in the interphase nucleus. Am. J. Hum. Genet. 20, 440–460 (1968).

39. 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).

40. Chen, C.-K. et al. Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing. Science 354, 468–472 (2016).

41. Kosak, S. T. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296, 158–162 (2002).

42. Skok, J. A. et al. Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes. Nat. Immunol. 8, 378–387 (2007).

43. Brown, K. E. et al. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91, 845–854 (1997).

44. Skok, J. A. et al. Nonequivalent nuclear location of immunoglobulin alleles in B lymphocytes. Nat. Immunol. 2, 848–854 (2001).

45. Hewitt, S. L. et al. RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci. Nat. Immunol. 10, 655–664 (2009).

46. Duncan, I. W. Transvection effects in Drosophila. Annu. Rev. Genet. 36, 521–556 (2002).

47. Fukaya, T. & Levine, M. Transvection. Curr. Biol. 27, R1047–R1049 (2017).

48. Lim, B., Heist, T., Levine, M. & Fukaya, T. Visualization of transvection in living Drosophila embryos. Mol. Cell 70, 287–296.e6 (2018).

49. Kumaran, R. I. & Spector, D. L. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J. Cell. Biol. 180, 51–65 (2008).

50. Finlan, L. E. et al. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet. 4, e1000039 (2008).

51. Reddy, K. L., Zullo, J. M., Bertolino, E. & Singh, H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452, 243–247 (2008).

52. Dialynas, G., Speese, S., Budnik, V., Geyer, P. K. & Wallrath, L. L. The role of Drosophila Lamin C in muscle function and gene expression. Development 137, 3067–3077 (2010).

53. Pollex, T., Piolot, T. & Heard, E. Live-cell imaging combined with immunofluorescence, RNA, or DNA FISH to study the nuclear dynamics and expression of the X-inactivation center. Methods Mol. Biol. 1042, 13–31 (2013).

54. Krueger, C. et al. Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status. PLoS ONE 7, e38983 (2012).

55. Chow, J. C. et al. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 141, 956–969 (2010).

56. Paulose, J. K., Rucker, E. B. & Cassone, V. M. Toward the beginning of time: circadian rhythms in metabolism precede rhythms in clock gene expression in mouse embryonic stem cells. PLoS ONE 7, e49555 (2012).

57. Yagita, K. et al. Development of the circadian oscillator during differentiation of mouse embryonic stem cells in vitro. Proc. Natl Acad. Sci. USA 107, 3846–3851 (2010).

58. Clowney, E. J. et al. Nuclear aggregation of olfactory receptor genes governs their monogenic expression. Cell 151, 724–737 (2012).

59. Armelin-Correa, L. M., Gutiyama, L. M., Brandt, D. Y. C. & Malnic, B. Nuclear compartmentalization of odorant receptor genes. Proc. Natl Acad. Sci. USA 111, 2782–2787 (2014).

60. Luo, L. et al. The nuclear periphery of embryonic stem cells is a transcriptionally permissive and repressive compartment. J. Cell. Sci. 122, 3729–3737 (2009).

61. Boyle, S. et al. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum. Mol. Genet. 10, 211–219 (2001).

62. Joyce, E. F., Erceg, J. & Wu, C.-T. Pairing and anti-pairing: a balancing act in the diploid genome. Curr. Opin. Genet. Dev. 37, 119–128 (2016).

63. Osborne, C. S. et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nat. Genet. 36, 1065–1071 (2004).

64. Brown, J. M. et al. Coregulated human globin genes are frequently in spatial proximity when active. J. Cell. Biol. 172, 177–187 (2006).

65. Brown, J. M. et al. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J. Cell. Biol. 182, 1083–1097 (2008).

66. Chu, H.-P. et al. PAR-TERRA directs homologous sex chromosome pairing. Nat. Struct. Mol. Biol. 24, 620–631 (2017).

67. Kung, J. T. et al. Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF. Mol. Cell 57, 361–375 (2015).

68. Aguilar-Arnal, L. et al. Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nat. Struct. Mol. Biol. 20, 1206–1213 (2013).

69. Norris, D. P. et al. Evidence that random and imprinted Xist expression is controlled by preemptive methylation. Cell 77, 41–51 (1994).

70. Schulz, E. G. et al. The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network. Cell. Stem. Cell. 14, 203–216 (2014).

71. Giorgetti, L., Piolot, T. & Heard, E. High-resolution 3D DNA FISH using plasmid probes and computational correction of optical aberrations to study chromatin structure at the sub-megabase scale. Methods Mol. Biol. 1262, 37–53 (2015).

72. Chaumeil, J., Augui, S., Chow, J. C. & Heard, E. Combined immunofluorescence, RNA fluorescent in situ hybridization, and DNA fluorescent in situ hybridization to study chromatin changes, transcriptional activity, nuclear organization, and X-chromosome inactivation. Methods Mol. Biol. 463, 297–308 (2008).

73. Giorgetti, L. et al. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell 157, 950–963 (2014).