Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1991 Sep;10(9):2569–2576. doi: 10.1002/j.1460-2075.1991.tb07797.x

Glucocorticoids are required for establishment and maintenance of an alteration in chromatin structure: induction leads to a reversible disruption of nucleosomes over an enhancer.

A Reik 1, G Schütz 1, A F Stewart 1
PMCID: PMC452954  PMID: 1678348

Abstract

Induction of the rat tyrosine aminotransferase gene (TAT) with glucocorticoid hormones leads to formation of a nuclease hypersensitive site at the hormone-dependent enhancer located 2.5 kb upstream of the start site of transcription. This enhancer comprises binding sites for the glucocorticoid receptor and additional transcription factors which are only recognized after hormone administration, as demonstrated by genomic footprinting. We show here that the alteration in chromatin structure occurs very rapidly and is also rapidly reversible after withdrawal of the hormone. At all stages nuclease hypersensitivity at this enhancer parallels the transcriptional activity of the TAT gene indicating that transcriptional stimulation requires ongoing enhancer activity. The enhancer region is nucleosomal before induction and after removal of the hormone but the nucleosomal pattern is disturbed in the presence of the hormone. The rapidity of chromatin changes implies that neither disruption nor reassembly of the nucleosomes is dependent on DNA replication. Addition of the glucocorticoid antagonist RU486 to induced cells has effects similar to washing out the glucocorticoid hormone, showing that maintenance of the hypersensitive site requires the ongoing binding of agonist by glucocorticoid receptor. These results describe an inducible enhancer which is regulated by a dynamic balance between two types of protein-DNA complexes, one of which is nucleosomal.

Full text

PDF
2569

Images in this article

Selected References

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

  1. Almer A., Rudolph H., Hinnen A., Hörz W. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 1986 Oct;5(10):2689–2696. doi: 10.1002/j.1460-2075.1986.tb04552.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Almouzni G., Méchali M., Wolffe A. P. Competition between transcription complex assembly and chromatin assembly on replicating DNA. EMBO J. 1990 Feb;9(2):573–582. doi: 10.1002/j.1460-2075.1990.tb08145.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Becker P. B., Gloss B., Schmid W., Strähle U., Schütz G. In vivo protein-DNA interactions in a glucocorticoid response element require the presence of the hormone. Nature. 1986 Dec 18;324(6098):686–688. doi: 10.1038/324686a0. [DOI] [PubMed] [Google Scholar]
  4. Becker P., Renkawitz R., Schütz G. Tissue-specific DNaseI hypersensitive sites in the 5'-flanking sequences of the tryptophan oxygenase and the tyrosine aminotransferase genes. EMBO J. 1984 Sep;3(9):2015–2020. doi: 10.1002/j.1460-2075.1984.tb02084.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bogenhagen D. F., Wormington W. M., Brown D. D. Stable transcription complexes of Xenopus 5S RNA genes: a means to maintain the differentiated state. Cell. 1982 Feb;28(2):413–421. doi: 10.1016/0092-8674(82)90359-2. [DOI] [PubMed] [Google Scholar]
  6. Bresnick E. H., John S., Berard D. S., LeFebvre P., Hager G. L. Glucocorticoid receptor-dependent disruption of a specific nucleosome on the mouse mammary tumor virus promoter is prevented by sodium butyrate. Proc Natl Acad Sci U S A. 1990 May;87(10):3977–3981. doi: 10.1073/pnas.87.10.3977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brüggemeier U., Kalff M., Franke S., Scheidereit C., Beato M. Ubiquitous transcription factor OTF-1 mediates induction of the MMTV promoter through synergistic interaction with hormone receptors. Cell. 1991 Feb 8;64(3):565–572. doi: 10.1016/0092-8674(91)90240-y. [DOI] [PubMed] [Google Scholar]
  8. Brüggemeier U., Rogge L., Winnacker E. L., Beato M. Nuclear factor I acts as a transcription factor on the MMTV promoter but competes with steroid hormone receptors for DNA binding. EMBO J. 1990 Jul;9(7):2233–2239. doi: 10.1002/j.1460-2075.1990.tb07393.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Carr K. D., Richard-Foy H. Glucocorticoids locally disrupt an array of positioned nucleosomes on the rat tyrosine aminotransferase promoter in hepatoma cells. Proc Natl Acad Sci U S A. 1990 Dec;87(23):9300–9304. doi: 10.1073/pnas.87.23.9300. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Cato A. C., Skroch P., Weinmann J., Butkeraitis P., Ponta H. DNA sequences outside the receptor-binding sites differently modulate the responsiveness of the mouse mammary tumour virus promoter to various steroid hormones. EMBO J. 1988 May;7(5):1403–1410. doi: 10.1002/j.1460-2075.1988.tb02957.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cereghini S., Yaniv M. Assembly of transfected DNA into chromatin: structural changes in the origin-promoter-enhancer region upon replication. EMBO J. 1984 Jun;3(6):1243–1253. doi: 10.1002/j.1460-2075.1984.tb01959.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Chiu C. P., Blau H. M. Reprogramming cell differentiation in the absence of DNA synthesis. Cell. 1984 Jul;37(3):879–887. doi: 10.1016/0092-8674(84)90423-9. [DOI] [PubMed] [Google Scholar]
  13. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Clark-Adams C. D., Norris D., Osley M. A., Fassler J. S., Winston F. Changes in histone gene dosage alter transcription in yeast. Genes Dev. 1988 Feb;2(2):150–159. doi: 10.1101/gad.2.2.150. [DOI] [PubMed] [Google Scholar]
  15. Cordingley M. G., Riegel A. T., Hager G. L. Steroid-dependent interaction of transcription factors with the inducible promoter of mouse mammary tumor virus in vivo. Cell. 1987 Jan 30;48(2):261–270. doi: 10.1016/0092-8674(87)90429-6. [DOI] [PubMed] [Google Scholar]
  16. De Bernardin W., Koller T., Sogo J. M. Structure of in-vivo transcribing chromatin as studied in simian virus 40 minichromosomes. J Mol Biol. 1986 Oct 5;191(3):469–482. doi: 10.1016/0022-2836(86)90142-7. [DOI] [PubMed] [Google Scholar]
  17. Emerson B. M., Felsenfeld G. Specific factor conferring nuclease hypersensitivity at the 5' end of the chicken adult beta-globin gene. Proc Natl Acad Sci U S A. 1984 Jan;81(1):95–99. doi: 10.1073/pnas.81.1.95. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Enver T., Brewer A. C., Patient R. K. Role for DNA replication in beta-globin gene activation. Mol Cell Biol. 1988 Mar;8(3):1301–1308. doi: 10.1128/mcb.8.3.1301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Ericsson C., Grossbach U., Björkroth B., Daneholt B. Presence of histone H1 on an active Balbiani ring gene. Cell. 1990 Jan 12;60(1):73–83. doi: 10.1016/0092-8674(90)90717-s. [DOI] [PubMed] [Google Scholar]
  20. Fascher K. D., Schmitz J., Hörz W. Role of trans-activating proteins in the generation of active chromatin at the PHO5 promoter in S. cerevisiae. EMBO J. 1990 Aug;9(8):2523–2528. doi: 10.1002/j.1460-2075.1990.tb07432.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Gottesfeld J., Bloomer L. S. Assembly of transcriptionally active 5S RNA gene chromatin in vitro. Cell. 1982 Apr;28(4):781–791. doi: 10.1016/0092-8674(82)90057-5. [DOI] [PubMed] [Google Scholar]
  22. Grange T., Roux J., Rigaud G., Pictet R. Cell-type specific activity of two glucocorticoid responsive units of rat tyrosine aminotransferase gene is associated with multiple binding sites for C/EBP and a novel liver-specific nuclear factor. Nucleic Acids Res. 1991 Jan 11;19(1):131–139. doi: 10.1093/nar/19.1.131. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Gross D. S., Garrard W. T. Nuclease hypersensitive sites in chromatin. Annu Rev Biochem. 1988;57:159–197. doi: 10.1146/annurev.bi.57.070188.001111. [DOI] [PubMed] [Google Scholar]
  24. Groyer A., Schweizer-Groyer G., Cadepond F., Mariller M., Baulieu E. E. Antiglucocorticosteroid effects suggest why steroid hormone is required for receptors to bind DNA in vivo but not in vitro. Nature. 1987 Aug 13;328(6131):624–626. doi: 10.1038/328624a0. [DOI] [PubMed] [Google Scholar]
  25. Grunstein M. Nucleosomes: regulators of transcription. Trends Genet. 1990 Dec;6(12):395–400. doi: 10.1016/0168-9525(90)90299-l. [DOI] [PubMed] [Google Scholar]
  26. Gruss C., Gutierrez C., Burhans W. C., DePamphilis M. L., Koller T., Sogo J. M. Nucleosome assembly in mammalian cell extracts before and after DNA replication. EMBO J. 1990 Sep;9(9):2911–2922. doi: 10.1002/j.1460-2075.1990.tb07482.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Han M., Grunstein M. Nucleosome loss activates yeast downstream promoters in vivo. Cell. 1988 Dec 23;55(6):1137–1145. doi: 10.1016/0092-8674(88)90258-9. [DOI] [PubMed] [Google Scholar]
  28. Han M., Kim U. J., Kayne P., Grunstein M. Depletion of histone H4 and nucleosomes activates the PHO5 gene in Saccharomyces cerevisiae. EMBO J. 1988 Jul;7(7):2221–2228. doi: 10.1002/j.1460-2075.1988.tb03061.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Herrera R. E., Shaw P. E., Nordheim A. Occupation of the c-fos serum response element in vivo by a multi-protein complex is unaltered by growth factor induction. Nature. 1989 Jul 6;340(6228):68–70. doi: 10.1038/340068a0. [DOI] [PubMed] [Google Scholar]
  30. Jantzen H. M., Strähle U., Gloss B., Stewart F., Schmid W., Boshart M., Miksicek R., Schütz G. Cooperativity of glucocorticoid response elements located far upstream of the tyrosine aminotransferase gene. Cell. 1987 Apr 10;49(1):29–38. doi: 10.1016/0092-8674(87)90752-5. [DOI] [PubMed] [Google Scholar]
  31. Kim U. J., Han M., Kayne P., Grunstein M. Effects of histone H4 depletion on the cell cycle and transcription of Saccharomyces cerevisiae. EMBO J. 1988 Jul;7(7):2211–2219. doi: 10.1002/j.1460-2075.1988.tb03060.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Knezetic J. A., Luse D. S. The presence of nucleosomes on a DNA template prevents initiation by RNA polymerase II in vitro. Cell. 1986 Apr 11;45(1):95–104. doi: 10.1016/0092-8674(86)90541-6. [DOI] [PubMed] [Google Scholar]
  33. Ladiges W. C., Raff R. F., Brown S., Deeg H. J., Storb R. The canine major histocompatibility complex. Supertypic specificities defined by the primed lymphocyte test (PLT). Immunogenetics. 1984;19(4):359–365. doi: 10.1007/BF00345410. [DOI] [PubMed] [Google Scholar]
  34. Lee M. S., Garrard W. T. Transcription-induced nucleosome 'splitting': an underlying structure for DNase I sensitive chromatin. EMBO J. 1991 Mar;10(3):607–615. doi: 10.1002/j.1460-2075.1991.tb07988.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Lorch Y., LaPointe J. W., Kornberg R. D. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell. 1987 Apr 24;49(2):203–210. doi: 10.1016/0092-8674(87)90561-7. [DOI] [PubMed] [Google Scholar]
  36. Matsui T. Transcription of adenovirus 2 major late and peptide IX genes under conditions of in vitro nucleosome assembly. Mol Cell Biol. 1987 Apr;7(4):1401–1408. doi: 10.1128/mcb.7.4.1401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Miller A. M., Nasmyth K. A. Role of DNA replication in the repression of silent mating type loci in yeast. Nature. 1984 Nov 15;312(5991):247–251. doi: 10.1038/312247a0. [DOI] [PubMed] [Google Scholar]
  38. Mueller P. R., Wold B. In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science. 1989 Nov 10;246(4931):780–786. doi: 10.1126/science.2814500. [DOI] [PubMed] [Google Scholar]
  39. Nacheva G. A., Guschin D. Y., Preobrazhenskaya O. V., Karpov V. L., Ebralidse K. K., Mirzabekov A. D. Change in the pattern of histone binding to DNA upon transcriptional activation. Cell. 1989 Jul 14;58(1):27–36. doi: 10.1016/0092-8674(89)90399-1. [DOI] [PubMed] [Google Scholar]
  40. Oddos J., Grange T., Carr K. D., Matthews B., Roux J., Richard-Foy H., Pictet R. Nucleotide sequence of 10 kilobases of rat tyrosine aminotransferase gene 5' flanking region. Nucleic Acids Res. 1989 Nov 11;17(21):8877–8878. doi: 10.1093/nar/17.21.8877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Perlmann T., Eriksson P., Wrange O. Quantitative analysis of the glucocorticoid receptor-DNA interaction at the mouse mammary tumor virus glucocorticoid response element. J Biol Chem. 1990 Oct 5;265(28):17222–17229. [PubMed] [Google Scholar]
  42. Perlmann T., Wrange O. Specific glucocorticoid receptor binding to DNA reconstituted in a nucleosome. EMBO J. 1988 Oct;7(10):3073–3079. doi: 10.1002/j.1460-2075.1988.tb03172.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Pfaffle P., Gerlach V., Bunzel L., Jackson V. In vitro evidence that transcription-induced stress causes nucleosome dissolution and regeneration. J Biol Chem. 1990 Oct 5;265(28):16830–16840. [PubMed] [Google Scholar]
  44. Pfeifer G. P., Steigerwald S. D., Mueller P. R., Wold B., Riggs A. D. Genomic sequencing and methylation analysis by ligation mediated PCR. Science. 1989 Nov 10;246(4931):810–813. doi: 10.1126/science.2814502. [DOI] [PubMed] [Google Scholar]
  45. Piña B., Brüggemeier U., Beato M. Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter. Cell. 1990 Mar 9;60(5):719–731. doi: 10.1016/0092-8674(90)90087-u. [DOI] [PubMed] [Google Scholar]
  46. Richard-Foy H., Hager G. L. Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO J. 1987 Aug;6(8):2321–2328. doi: 10.1002/j.1460-2075.1987.tb02507.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Saluz H., Jost J. P. A simple high-resolution procedure to study DNA methylation and in vivo DNA-protein interactions on a single-copy gene level in higher eukaryotes. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2602–2606. doi: 10.1073/pnas.86.8.2602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Schmid E., Schmid W., Jantzen M., Mayer D., Jastorff B., Schütz G. Transcription activation of the tyrosine aminotransferase gene by glucocorticoids and cAMP in primary hepatocytes. Eur J Biochem. 1987 Jun 15;165(3):499–506. doi: 10.1111/j.1432-1033.1987.tb11467.x. [DOI] [PubMed] [Google Scholar]
  49. Schmid W., Strähle U., Schütz G., Schmitt J., Stunnenberg H. Glucocorticoid receptor binds cooperatively to adjacent recognition sites. EMBO J. 1989 Aug;8(8):2257–2263. doi: 10.1002/j.1460-2075.1989.tb08350.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Sergeant A., Bohmann D., Zentgraf H., Weiher H., Keller W. A transcription enhancer acts in vitro over distances of hundreds of base-pairs on both circular and linear templates but not on chromatin-reconstituted DNA. J Mol Biol. 1984 Dec 15;180(3):577–600. doi: 10.1016/0022-2836(84)90028-7. [DOI] [PubMed] [Google Scholar]
  51. Simpson R. T. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature. 1990 Jan 25;343(6256):387–389. doi: 10.1038/343387a0. [DOI] [PubMed] [Google Scholar]
  52. Sorger P. K., Pelham H. R. Yeast heat shock factor is an essential DNA-binding protein that exhibits temperature-dependent phosphorylation. Cell. 1988 Sep 9;54(6):855–864. doi: 10.1016/s0092-8674(88)91219-6. [DOI] [PubMed] [Google Scholar]
  53. Stewart A. F., Herrera R. E., Nordheim A. Rapid induction of c-fos transcription reveals quantitative linkage of RNA polymerase II and DNA topoisomerase I enzyme activities. Cell. 1990 Jan 12;60(1):141–149. doi: 10.1016/0092-8674(90)90724-s. [DOI] [PubMed] [Google Scholar]
  54. Stewart A. F., Reik A., Schütz G. A simpler and better method to cleave chromatin with DNase 1 for hypersensitive site analyses. Nucleic Acids Res. 1991 Jun 11;19(11):3157–3157. doi: 10.1093/nar/19.11.3157. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Stewart A. F., Schütz G. Camptothecin-induced in vivo topoisomerase I cleavages in the transcriptionally active tyrosine aminotransferase gene. Cell. 1987 Sep 25;50(7):1109–1117. doi: 10.1016/0092-8674(87)90177-2. [DOI] [PubMed] [Google Scholar]
  56. Strähle U., Schmid W., Schütz G. Synergistic action of the glucocorticoid receptor with transcription factors. EMBO J. 1988 Nov;7(11):3389–3395. doi: 10.1002/j.1460-2075.1988.tb03212.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Tanguay R. L., Pfeifer G. P., Riggs A. D. PCR-aided DNaseI footprinting of single copy gene sequences in permeabilized cells. Nucleic Acids Res. 1990 Oct 11;18(19):5902–5902. doi: 10.1093/nar/18.19.5902. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Thomas G. H., Elgin S. C. Protein/DNA architecture of the DNase I hypersensitive region of the Drosophila hsp26 promoter. EMBO J. 1988 Jul;7(7):2191–2201. doi: 10.1002/j.1460-2075.1988.tb03058.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Wasylyk B., Chambon P. Transcription by eukaryotic RNA polymerases A and B of chromatin assembled in vitro. Eur J Biochem. 1979 Aug 1;98(2):317–327. doi: 10.1111/j.1432-1033.1979.tb13191.x. [DOI] [PubMed] [Google Scholar]
  60. Weih F., Stewart A. F., Boshart M., Nitsch D., Schütz G. In vivo monitoring of a cAMP-stimulated DNA-binding activity. Genes Dev. 1990 Aug;4(8):1437–1449. doi: 10.1101/gad.4.8.1437. [DOI] [PubMed] [Google Scholar]
  61. Willmann T., Beato M. Steroid-free glucocorticoid receptor binds specifically to mouse mammary tumour virus DNA. Nature. 1986 Dec 18;324(6098):688–691. doi: 10.1038/324688a0. [DOI] [PubMed] [Google Scholar]
  62. Wolffe A. P., Brown D. D. DNA replication in vitro erases a Xenopus 5S RNA gene transcription complex. Cell. 1986 Oct 24;47(2):217–227. doi: 10.1016/0092-8674(86)90444-7. [DOI] [PubMed] [Google Scholar]
  63. Workman J. L., Roeder R. G. Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell. 1987 Nov 20;51(4):613–622. doi: 10.1016/0092-8674(87)90130-9. [DOI] [PubMed] [Google Scholar]
  64. Workman J. L., Taylor I. C., Kingston R. E. Activation domains of stably bound GAL4 derivatives alleviate repression of promoters by nucleosomes. Cell. 1991 Feb 8;64(3):533–544. doi: 10.1016/0092-8674(91)90237-s. [DOI] [PubMed] [Google Scholar]
  65. Wrange O., Eriksson P., Perlmann T. The purified activated glucocorticoid receptor is a homodimer. J Biol Chem. 1989 Mar 25;264(9):5253–5259. [PubMed] [Google Scholar]
  66. Wu C., Wong Y. C., Elgin S. C. The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell. 1979 Apr;16(4):807–814. doi: 10.1016/0092-8674(79)90096-5. [DOI] [PubMed] [Google Scholar]
  67. Zaret K. S., Yamamoto K. R. Reversible and persistent changes in chromatin structure accompany activation of a glucocorticoid-dependent enhancer element. Cell. 1984 Aug;38(1):29–38. doi: 10.1016/0092-8674(84)90523-3. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES