Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Jul 1;25(13):2661–2671. doi: 10.1093/nar/25.13.2661

Identification and characterization of the human XIST gene promoter: implications for models of X chromosome inactivation.

B D Hendrich 1, R M Plenge 1, H F Willard 1
PMCID: PMC146792  PMID: 9185579

Abstract

The XIST gene in both humans and mice is expressed exclusively from the inactive X chromosome and is required for X chromosome inactivation to occur early in development. In order to understand transcriptional regulation of the XIST gene, we have identified and characterized the human XIST promoter and two repeated DNA elements that modulate promoter activity. As determined by reporter gene constructs, the XIST minimal promoter is constitutively active at high levels in human male and female cell lines and in transgenic mice. We demonstrate that this promoter activity is dependent in vitro upon binding of the common transcription factors SP1, YY1 and TBP. We further identify two cis -acting repeated DNA sequences that influence reporter gene activity. First, DNA fragments containing a set of highly conserved repeats located within the 5'-end of XIST stimulate reporter activity 3-fold in transiently transfected cell lines. Second, a 450 bp alternating purine-pyrimidine repeat located 25 kb upstream of the XIST promoter partially suppresses promoter activity by approximately 70% in transient transfection assays. These results indicate that the XIST promoter is constitutively active and that critical steps in the X inactivation process must involve silencing of XIST on the active X chromosome by factors that interact with and/or recognize sequences located outside the minimal promoter.

Full Text

The Full Text of this article is available as a PDF (366.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Ariel M., Robinson E., McCarrey J. R., Cedar H. Gamete-specific methylation correlates with imprinting of the murine Xist gene. Nat Genet. 1995 Mar;9(3):312–315. doi: 10.1038/ng0395-312. [DOI] [PubMed] [Google Scholar]
  3. Beard C., Li E., Jaenisch R. Loss of methylation activates Xist in somatic but not in embryonic cells. Genes Dev. 1995 Oct 1;9(19):2325–2334. doi: 10.1101/gad.9.19.2325. [DOI] [PubMed] [Google Scholar]
  4. Becker K. G., Jedlicka P., Templeton N. S., Liotta L., Ozato K. Characterization of hUCRBP (YY1, NF-E1, delta): a transcription factor that binds the regulatory regions of many viral and cellular genes. Gene. 1994 Dec 15;150(2):259–266. doi: 10.1016/0378-1119(94)90435-9. [DOI] [PubMed] [Google Scholar]
  5. Ben-Hattar J., Beard P., Jiricny J. Cytosine methylation in CTF and Sp1 recognition sites of an HSV tk promoter: effects on transcription in vivo and on factor binding in vitro. Nucleic Acids Res. 1989 Dec 25;17(24):10179–10190. doi: 10.1093/nar/17.24.10179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brockdorff N., Ashworth A., Kay G. F., Cooper P., Smith S., McCabe V. M., Norris D. P., Penny G. D., Patel D., Rastan S. Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome. Nature. 1991 May 23;351(6324):329–331. doi: 10.1038/351329a0. [DOI] [PubMed] [Google Scholar]
  7. Brockdorff N., Ashworth A., Kay G. F., McCabe V. M., Norris D. P., Cooper P. J., Swift S., Rastan S. 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. 1992 Oct 30;71(3):515–526. doi: 10.1016/0092-8674(92)90519-i. [DOI] [PubMed] [Google Scholar]
  8. Brown C. J., Ballabio A., Rupert J. L., Lafreniere R. G., Grompe M., Tonlorenzi R., Willard H. F. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature. 1991 Jan 3;349(6304):38–44. doi: 10.1038/349038a0. [DOI] [PubMed] [Google Scholar]
  9. Brown C. J., Hendrich B. D., Rupert J. L., Lafrenière R. G., Xing Y., Lawrence J., Willard H. F. 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 Oct 30;71(3):527–542. doi: 10.1016/0092-8674(92)90520-m. [DOI] [PubMed] [Google Scholar]
  10. Brown C. J., Lafreniere R. G., Powers V. E., Sebastio G., Ballabio A., Pettigrew A. L., Ledbetter D. H., Levy E., Craig I. W., Willard H. F. Localization of the X inactivation centre on the human X chromosome in Xq13. Nature. 1991 Jan 3;349(6304):82–84. doi: 10.1038/349082a0. [DOI] [PubMed] [Google Scholar]
  11. Buzin C. H., Mann J. R., Singer-Sam J. Quantitative RT-PCR assays show Xist RNA levels are low in mouse female adult tissue, embryos and embryoid bodies. Development. 1994 Dec;120(12):3529–3536. doi: 10.1242/dev.120.12.3529. [DOI] [PubMed] [Google Scholar]
  12. Cattanach B. M. Control of chromosome inactivation. Annu Rev Genet. 1975;9:1–18. doi: 10.1146/annurev.ge.09.120175.000245. [DOI] [PubMed] [Google Scholar]
  13. Cattanach B. M. Controlling elements in the mouse X-chromosome. 3. Influence upon both parts of an X divided by rearrangement. Genet Res. 1970 Dec;16(3):293–301. doi: 10.1017/s001667230000255x. [DOI] [PubMed] [Google Scholar]
  14. Cattanach B. M., Papworth D. Controlling elements in the mouse. V. Linkage tests with X-linked genes. Genet Res. 1981 Aug;38(1):57–70. doi: 10.1017/s0016672300020401. [DOI] [PubMed] [Google Scholar]
  15. Cattanach B. M., Pollard C. E., Perez J. N. Controlling elements in the mouse X-chromosome. I. Interaction with the X-linked genes. Genet Res. 1969 Dec;14(3):223–235. doi: 10.1017/s0016672300002068. [DOI] [PubMed] [Google Scholar]
  16. Cattanach B. M., Williams C. E. Evidence of non-random X chromosome activity in the mouse. Genet Res. 1972 Jun;19(3):229–240. doi: 10.1017/s001667230001449x. [DOI] [PubMed] [Google Scholar]
  17. Clemson C. M., McNeil J. A., Willard H. F., Lawrence J. B. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol. 1996 Feb;132(3):259–275. doi: 10.1083/jcb.132.3.259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Cohen M. M., Lin C. C., Sybert V., Orecchio E. J. Two human X-autosome translocations identified by autoradiography and fluorescence. Am J Hum Genet. 1972 Sep;24(5):583–597. [PMC free article] [PubMed] [Google Scholar]
  19. Collier D. A., Griffin J. A., Wells R. D. Non-B right-handed DNA conformations of homopurine.homopyrimidine sequences in the murine immunoglobulin C alpha switch region. J Biol Chem. 1988 May 25;263(15):7397–7405. [PubMed] [Google Scholar]
  20. Conaway R. C., Conaway J. W. General initiation factors for RNA polymerase II. Annu Rev Biochem. 1993;62:161–190. doi: 10.1146/annurev.bi.62.070193.001113. [DOI] [PubMed] [Google Scholar]
  21. Courtier B., Heard E., Avner P. Xce haplotypes show modified methylation in a region of the active X chromosome lying 3' to Xist. Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3531–3535. doi: 10.1073/pnas.92.8.3531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Eicher E. M. X-autosome translocations in the mouse: total inactivation versus partial inactivation of the X chromosome. Adv Genet. 1970;15:175–259. [PubMed] [Google Scholar]
  23. Hahn S., Buratowski S., Sharp P. A., Guarente L. Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences. Proc Natl Acad Sci U S A. 1989 Aug;86(15):5718–5722. doi: 10.1073/pnas.86.15.5718. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Hahn S. The Yin and the Yang of mammalian transcription. Curr Biol. 1992 Mar;2(3):152–154. doi: 10.1016/0960-9822(92)90268-f. [DOI] [PubMed] [Google Scholar]
  25. Harrington M. A., Jones P. A., Imagawa M., Karin M. Cytosine methylation does not affect binding of transcription factor Sp1. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2066–2070. doi: 10.1073/pnas.85.7.2066. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Heard E., Avner P. Role play in X-inactivation. Hum Mol Genet. 1994;3(Spec No):1481–1485. doi: 10.1093/hmg/3.suppl_1.1481. [DOI] [PubMed] [Google Scholar]
  27. Heard E., Kress C., Mongelard F., Courtier B., Rougeulle C., Ashworth A., Vourc'h C., Babinet C., Avner P. Transgenic mice carrying an Xist-containing YAC. Hum Mol Genet. 1996 Apr;5(4):441–450. doi: 10.1093/hmg/5.4.441. [DOI] [PubMed] [Google Scholar]
  28. Hendrich B. D., Brown C. J., Willard H. F. Evolutionary conservation of possible functional domains of the human and murine XIST genes. Hum Mol Genet. 1993 Jun;2(6):663–672. doi: 10.1093/hmg/2.6.663. [DOI] [PubMed] [Google Scholar]
  29. Herzing L. B., Romer J. T., Horn J. M., Ashworth A. Xist has properties of the X-chromosome inactivation centre. Nature. 1997 Mar 20;386(6622):272–275. doi: 10.1038/386272a0. [DOI] [PubMed] [Google Scholar]
  30. Höller M., Westin G., Jiricny J., Schaffner W. Sp1 transcription factor binds DNA and activates transcription even when the binding site is CpG methylated. Genes Dev. 1988 Sep;2(9):1127–1135. doi: 10.1101/gad.2.9.1127. [DOI] [PubMed] [Google Scholar]
  31. Kay G. F., Penny G. D., Patel D., Ashworth A., Brockdorff N., Rastan S. Expression of Xist during mouse development suggests a role in the initiation of X chromosome inactivation. Cell. 1993 Jan 29;72(2):171–182. doi: 10.1016/0092-8674(93)90658-d. [DOI] [PubMed] [Google Scholar]
  32. Lee J. T., Jaenisch R. Long-range cis effects of ectopic X-inactivation centres on a mouse autosome. Nature. 1997 Mar 20;386(6622):275–279. doi: 10.1038/386275a0. [DOI] [PubMed] [Google Scholar]
  33. Lee J. T., Strauss W. M., Dausman J. A., Jaenisch R. A 450 kb transgene displays properties of the mammalian X-inactivation center. Cell. 1996 Jul 12;86(1):83–94. doi: 10.1016/s0092-8674(00)80079-3. [DOI] [PubMed] [Google Scholar]
  34. Leppig K. A., Brown C. J., Bressler S. L., Gustashaw K., Pagon R. A., Willard H. F., Disteche C. M. Mapping of the distal boundary of the X-inactivation center in a rearranged X chromosome from a female expressing XIST. Hum Mol Genet. 1993 Jul;2(7):883–887. doi: 10.1093/hmg/2.7.883. [DOI] [PubMed] [Google Scholar]
  35. Lyon M. F. X-chromosome inactivation. Pinpointing the centre. Nature. 1996 Jan 11;379(6561):116–117. doi: 10.1038/379116a0. [DOI] [PubMed] [Google Scholar]
  36. Matsuura S., Episkopou V., Hamvas R., Brown S. D. Xist expression from an Xist YAC transgene carried on the mouse Y chromosome. Hum Mol Genet. 1996 Apr;5(4):451–459. doi: 10.1093/hmg/5.4.451. [DOI] [PubMed] [Google Scholar]
  37. McCarrey J. R., Dilworth D. D. Expression of Xist in mouse germ cells correlates with X-chromosome inactivation. Nat Genet. 1992 Nov;2(3):200–203. doi: 10.1038/ng1192-200. [DOI] [PubMed] [Google Scholar]
  38. McMahon A. P., Bradley A. The Wnt-1 (int-1) proto-oncogene is required for development of a large region of the mouse brain. Cell. 1990 Sep 21;62(6):1073–1085. doi: 10.1016/0092-8674(90)90385-r. [DOI] [PubMed] [Google Scholar]
  39. Naylor L. H., Clark E. M. d(TG)n.d(CA)n sequences upstream of the rat prolactin gene form Z-DNA and inhibit gene transcription. Nucleic Acids Res. 1990 Mar 25;18(6):1595–1601. doi: 10.1093/nar/18.6.1595. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Norris D. P., Patel D., Kay G. F., Penny G. D., Brockdorff N., Sheardown S. A., Rastan S. Evidence that random and imprinted Xist expression is controlled by preemptive methylation. Cell. 1994 Apr 8;77(1):41–51. doi: 10.1016/0092-8674(94)90233-x. [DOI] [PubMed] [Google Scholar]
  41. Panning B., Jaenisch R. DNA hypomethylation can activate Xist expression and silence X-linked genes. Genes Dev. 1996 Aug 15;10(16):1991–2002. doi: 10.1101/gad.10.16.1991. [DOI] [PubMed] [Google Scholar]
  42. Penny G. D., Kay G. F., Sheardown S. A., Rastan S., Brockdorff N. Requirement for Xist in X chromosome inactivation. Nature. 1996 Jan 11;379(6561):131–137. doi: 10.1038/379131a0. [DOI] [PubMed] [Google Scholar]
  43. Pillet N., Bonny C., Schorderet D. F. Characterization of the promoter region of the mouse Xist gene. Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):12515–12519. doi: 10.1073/pnas.92.26.12515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. RUSSELL L. B. ANOTHER LOOK AT THE SINGLE-ACTIVE-X HYPOTHESIS. Trans N Y Acad Sci. 1964 Apr;26:726–736. doi: 10.1111/j.2164-0947.1964.tb01939.x. [DOI] [PubMed] [Google Scholar]
  45. Salido E. C., Yen P. H., Mohandas T. K., Shapiro L. J. Expression of the X-inactivation-associated gene XIST during spermatogenesis. Nat Genet. 1992 Nov;2(3):196–199. doi: 10.1038/ng1192-196. [DOI] [PubMed] [Google Scholar]
  46. Seto E., Shi Y., Shenk T. YY1 is an initiator sequence-binding protein that directs and activates transcription in vitro. Nature. 1991 Nov 21;354(6350):241–245. doi: 10.1038/354241a0. [DOI] [PubMed] [Google Scholar]
  47. Shi Y., Seto E., Chang L. S., Shenk T. Transcriptional repression by YY1, a human GLI-Krüppel-related protein, and relief of repression by adenovirus E1A protein. Cell. 1991 Oct 18;67(2):377–388. doi: 10.1016/0092-8674(91)90189-6. [DOI] [PubMed] [Google Scholar]
  48. Simmler M. C., Cattanach B. M., Rasberry C., Rougeulle C., Avner P. Mapping the murine Xce locus with (CA)n repeats. Mamm Genome. 1993 Sep;4(9):523–530. doi: 10.1007/BF00364788. [DOI] [PubMed] [Google Scholar]
  49. Therman E., Sarto G. E., Patau K. Center for Barr body condensation on the proximal part of the human Xq: a hypothesis. Chromosoma. 1974 Jan 29;44(4):361–366. doi: 10.1007/BF00284895. [DOI] [PubMed] [Google Scholar]
  50. Thomas M. J., Freeland T. M., Strobl J. S. Z-DNA formation in the rat growth hormone gene promoter region. Mol Cell Biol. 1990 Oct;10(10):5378–5387. doi: 10.1128/mcb.10.10.5378. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Uberbacher E. C., Mural R. J. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11261–11265. doi: 10.1073/pnas.88.24.11261. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Willard H. F., Brown C. J., Carrel L., Hendrich B., Miller A. P. Epigenetic and chromosomal control of gene expression: molecular and genetic analysis of X chromosome inactivation. Cold Spring Harb Symp Quant Biol. 1993;58:315–322. doi: 10.1101/sqb.1993.058.01.037. [DOI] [PubMed] [Google Scholar]
  53. Willard H. F. X chromosome inactivation, XIST, and pursuit of the X-inactivation center. Cell. 1996 Jul 12;86(1):5–7. doi: 10.1016/s0092-8674(00)80071-9. [DOI] [PubMed] [Google Scholar]
  54. Yu M., Edenberg H. J. Structure and function of a long alternating purine-pyrimidine sequence in the mouse alcohol dehydrogenase Adh-1 gene. Arch Biochem Biophys. 1995 Jan 10;316(1):407–412. doi: 10.1006/abbi.1995.1054. [DOI] [PubMed] [Google Scholar]
  55. Zuccotti M., Monk M. Methylation of the mouse Xist gene in sperm and eggs correlates with imprinted Xist expression and paternal X-inactivation. Nat Genet. 1995 Mar;9(3):316–320. doi: 10.1038/ng0395-316. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES