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Nuclear Receptors and ATP Dependent Chromatin Remodeling: A Complex Story

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Nuclear Receptors

Part of the book series: Proteins and Cell Regulation ((PROR,volume 8))

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Abstract

Nuclear receptors are a class of tightly regulated and highly inducible transcription factors and thus represent an excellent model for the study of transcription. The activity of these transcription factors is controlled by their interactions with co-regulatory proteins that act to remodel chromatin, modify histones, and initiate the transcriptional process. This review will focus on the use of nuclear receptors in understanding the role of ATP-dependent chromatin remodeling enzymes in transcription.

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References

  1. Bain, D. L., Heneghan, A. F., Connaghan-Jones, K. D., and Miura, M. T. (2007). Nuclear receptor structure: Implications for function. Annu Rev Physiol 69, 201–220.

    Article  PubMed  CAS  Google Scholar 

  2. Giguere, V. (1999). Orphan nuclear receptors: From gene to function. Endocr Rev 20, 689–725.

    Article  PubMed  CAS  Google Scholar 

  3. McKenna, N. J., Lanz, R. B., and O’Malley, B. W. (1999). Nuclear receptor coregulators: Cellular and molecular biology. Endocr Rev 20, 321–344.

    Article  PubMed  CAS  Google Scholar 

  4. Uhlmann, F. (2001). Chromosome condensation: Packaging the genome. Curr Biol 11, R384–R387.

    Article  PubMed  CAS  Google Scholar 

  5. Bernstein, E. and Hake, S. B. (2006). The nucleosome: A little variation goes a long way. Biochem Cell Biol 84, 505–517.

    Article  PubMed  CAS  Google Scholar 

  6. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. (1997). Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251–260.

    Article  PubMed  CAS  Google Scholar 

  7. Aoyagi, S., Trotter, K. W., and Archer, T. K. (2005). ATP-dependent chromatin remodeling complexes and their role in nuclear receptor-dependent transcription in vivo. Vitam Horm 70, 281–307.

    Article  PubMed  CAS  Google Scholar 

  8. Hayes, J. J. and Hansen, J. C. (2001). Nucleosomes and the chromatin fiber. Curr Opin Genet Dev 11, 124–129.

    Article  PubMed  CAS  Google Scholar 

  9. Felsenfeld, G. and Groudine, M. (2003). Controlling the double helix. Nature 421, 448–453.

    Article  PubMed  CAS  Google Scholar 

  10. Archer, T. K., Lefebvre, P., Wolford, R. G., and Hager, G. L. (1992). Transcription factor loading on the MMTV promoter: A bimodal mechanism for promoter activation. Science (New York, N.Y) 255, 1573–1576.

    CAS  Google Scholar 

  11. Workman, J. L. and Kingston, R. E. (1998). Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem 67, 545–579.

    Article  PubMed  CAS  Google Scholar 

  12. Miranda, T. B. and Jones, P. A. (2007). DNA methylation: The nuts and bolts of repression. J Cell Physiol 213, 384–390.

    Article  PubMed  CAS  Google Scholar 

  13. Kouzarides, T. (2007). Chromatin modifications and their function. Cell 128, 693–705.

    Article  PubMed  CAS  Google Scholar 

  14. Grunstein, M. (1997). Histone acetylation in chromatin structure and transcription. Nature 389, 349–352.

    Article  PubMed  CAS  Google Scholar 

  15. Shogren-Knaak, M., Ishii, H., Sun, J. M., Pazin, M. J., Davie, J. R., and Peterson, C. L. (2006). Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science (New York, N.Y) 311, 844–847.

    CAS  Google Scholar 

  16. Wang, G. G., Allis, C. D., and Chi, P. (2007). Chromatin remodeling and cancer, Part I: Covalent histone modifications. Trends Mol Med 13, 363–372.

    Article  PubMed  CAS  Google Scholar 

  17. Kingston, R. E. and Narlikar, G. J. (1999). ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev 13, 2339–2352.

    Article  PubMed  CAS  Google Scholar 

  18. Martens, J. A. and Winston, F. (2003). Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr Opin Genet Dev 13, 136–142.

    Article  PubMed  CAS  Google Scholar 

  19. Trotter, K. W. and Archer, T. K. (2008). The BRG1 transcriptional coregulator. Nucl Recept Signal 6, e004.

    PubMed  Google Scholar 

  20. Lonard, D. M. and O’Malley, B. W. (2007). Nuclear receptor coregulators: Judges, juries, and executioners of cellular regulation. Mol Cell 27, 691–700.

    Article  PubMed  CAS  Google Scholar 

  21. Collingwood, T. N., Urnov, F. D., and Wolffe, A. P. (1999). Nuclear receptors: Coactivators, corepressors and chromatin remodeling in the control of transcription. J Mol Endocrinol 23, 255–275.

    Article  PubMed  CAS  Google Scholar 

  22. Spencer, T. E., Jenster, G., Burcin, M. M., Allis, C. D., Zhou, J., Mizzen, C. A., McKenna, N. J., Onate, S. A., Tsai, S. Y., Tsai, M. J., and O’Malley, B. W. (1997). Steroid receptor coactivator-1 is a histone acetyltransferase. Nature 389, 194–198.

    Article  PubMed  CAS  Google Scholar 

  23. Voegel, J. J., Heine, M. J., Zechel, C., Chambon, P., and Gronemeyer, H. (1996). TIF2, a 160 kDa transcriptional mediator for the ligand-dependent activation function AF-2 of nuclear receptors. EMBO J 15, 3667–3675.

    PubMed  CAS  Google Scholar 

  24. Anzick, S. L., Kononen, J., Walker, R. L., Azorsa, D. O., Tanner, M. M., Guan, X. Y., Sauter, G., Kallioniemi, O. P., Trent, J. M., and Meltzer, P. S. (1997). AIB1, a steroid receptor coactivator amplified in breast and ovarian cancer. Science (New York, N.Y) 277, 965–968.

    CAS  Google Scholar 

  25. Onate, S. A., Tsai, S. Y., Tsai, M. J., and O’Malley, B. W. (1995). Sequence and characterization of a coactivator for the steroid hormone receptor superfamily. Science (New York, N.Y) 270, 1354–1357.

    CAS  Google Scholar 

  26. Hong, H., Kohli, K., Trivedi, A., Johnson, D. L., and Stallcup, M. R. (1996). GRIP1, a novel mouse protein that serves as a transcriptional coactivator in yeast for the hormone binding domains of steroid receptors. Proc Natl Acad Sci USA 93, 4948–4952.

    Article  PubMed  CAS  Google Scholar 

  27. Hanstein, B., Eckner, R., DiRenzo, J., Halachmi, S., Liu, H., Searcy, B., Kurokawa, R., and Brown, M. (1996). p300 is a component of an estrogen receptor coactivator complex. Proc Natl Acad Sci U S A 93, 11540–11545.

    Article  PubMed  CAS  Google Scholar 

  28. Chen, J. D. and Evans, R. M. (1995). A transcriptional co-repressor that interacts with nuclear hormone receptors. Nature 377, 454–457.

    Article  PubMed  CAS  Google Scholar 

  29. Horlein, A. J., Naar, A. M., Heinzel, T., Torchia, J., Gloss, B., Kurokawa, R., Ryan, A., Kamei, Y., Soderstrom, M., Glass, C. K. et al. (1995). Ligand-independent repression by the thyroid hormone receptor mediated by a nuclear receptor co-repressor. Nature 377, 397–404.

    Article  PubMed  CAS  Google Scholar 

  30. Jackson, T. A., Richer, J. K., Bain, D. L., Takimoto, G. S., Tung, L., and Horwitz, K. B. (1997). The partial agonist activity of antagonist-occupied steroid receptors is controlled by a novel hinge domain-binding coactivator L7/SPA and the corepressors N-CoR or SMRT. Mol Endocrinol (Baltimore, MD) 11, 693–705.

    Article  CAS  Google Scholar 

  31. Shang, Y. and Brown, M. (2002). Molecular determinants for the tissue specificity of SERMs. Science (New York, N.Y) 295, 2465–2468.

    CAS  Google Scholar 

  32. Dotzlaw, H., Moehren, U., Mink, S., Cato, A. C., Iniguez Lluhi, J. A., and Baniahmad, A. (2002). The amino terminus of the human AR is target for corepressor action and antihormone agonism. Mol Endocrinol (Baltimore, Md) 16, 661–673.

    Article  CAS  Google Scholar 

  33. Chen, J., Kinyamu, H. K., and Archer, T. K. (2006). Changes in attitude, changes in latitude: Nuclear receptors remodeling chromatin to regulate transcription. Mol Endocrinol (Baltimore, Md) 20, 1–13.

    Article  CAS  Google Scholar 

  34. Neigeborn, L. and Carlson, M. (1984). Genes affecting the regulation of SUC2 gene expression by glucose repression in Saccharomyces cerevisiae. Genetics 108, 845–858.

    PubMed  CAS  Google Scholar 

  35. Winston, F. and Carlson, M. (1992). Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet 8, 387–391.

    PubMed  CAS  Google Scholar 

  36. Stern, M., Jensen, R., and Herskowitz, I. (1984). Five SWI genes are required for expression of the HO gene in yeast. J Mol Biol 178, 853–868.

    Article  PubMed  CAS  Google Scholar 

  37. Muchardt, C. and Yaniv, M. (1993). A human homologue of Saccharomyces cerevisiae SNF2/SWI2 and Drosophila brm genes potentiates transcriptional activation by the glucocorticoid receptor. EMBO J 12, 4279–4290.

    PubMed  CAS  Google Scholar 

  38. Yoshinaga, S. K., Peterson, C. L., Herskowitz, I., and Yamamoto, K. R. (1992). Roles of SWI1, SWI2, and SWI3 proteins for transcriptional enhancement by steroid receptors. Science (New York, NY) 258, 1598–1604.

    CAS  Google Scholar 

  39. Ichinose, H., Garnier, J. M., Chambon, P., and Losson, R. (1997). Ligand-dependent interaction between the estrogen receptor and the human homologues of SWI2/SNF2. Gene 188, 95–100.

    Article  PubMed  CAS  Google Scholar 

  40. Tamkun, J. W., Deuring, R., Scott, M. P., Kissinger, M., Pattatucci, A. M., Kaufman, T. C., and Kennison, J. A. (1992). Brahma: A regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2/SWI2. Cell 68, 561–572.

    Article  PubMed  CAS  Google Scholar 

  41. Reyes, J. C., Barra, J., Muchardt, C., Camus, A., Babinet, C., and Yaniv, M. (1998). Altered control of cellular proliferation in the absence of mammalian brahma (SNF2alpha). EMBO J 17, 6979–6991.

    Article  PubMed  CAS  Google Scholar 

  42. Bultman, S., Gebuhr, T., Yee, D., La Mantia, C., Nicholson, J., Gilliam, A., Randazzo, F., Metzger, D., Chambon, P., Crabtree, G., and Magnuson, T. (2000). A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. Mol Cell 6, 1287–1295.

    Article  PubMed  CAS  Google Scholar 

  43. Kadam, S. and Emerson, B. M. (2003). Transcriptional specificity of human SWI/SNF BRG1 and BRM chromatin remodeling complexes. Mol Cell 11, 377–389.

    Article  PubMed  CAS  Google Scholar 

  44. Fryer, C. J. and Archer, T. K. (1998). Chromatin remodelling by the glucocorticoid receptor requires the BRG1 complex. Nature 393, 88–91.

    Article  PubMed  CAS  Google Scholar 

  45. Marshall, T. W., Link, K. A., Petre-Draviam, C. E., and Knudsen, K. E. (2003). Differential requirement of SWI/SNF for androgen receptor activity. J Biol Chem 278, 30605–30613.

    Article  PubMed  CAS  Google Scholar 

  46. Wang, W., Cote, J., Xue, Y., Zhou, S., Khavari, P. A., Biggar, S. R., Muchardt, C., Kalpana, G. V., Goff, S. P., Yaniv, M., Workman, J. L., and Crabtree, G. R. (1996). Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. EMBO J 15, 5370–5382.

    PubMed  CAS  Google Scholar 

  47. Nie, Z., Xue, Y., Yang, D., Zhou, S., Deroo, B. J., Archer, T. K., and Wang, W. (2000). A specificity and targeting subunit of a human SWI/SNF family-related chromatin-remodeling complex. Mol Cell Biol 20, 8879–8888.

    Article  PubMed  CAS  Google Scholar 

  48. Lemon, B., Inouye, C., King, D. S., and Tjian, R. (2001). Selectivity of chromatin-remodelling cofactors for ligand-activated transcription. Nature 414, 924–928.

    Article  PubMed  CAS  Google Scholar 

  49. Yan, Z., Cui, K., Murray, D. M., Ling, C., Xue, Y., Gerstein, A., Parsons, R., Zhao, K., and Wang, W. (2005). PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes. Genes Dev 19, 1662–1667.

    Article  PubMed  CAS  Google Scholar 

  50. Phelan, M. L., Sif, S., Narlikar, G. J., and Kingston, R. E. (1999). Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol Cell 3, 247–253.

    Article  PubMed  CAS  Google Scholar 

  51. Guidi, C. J., Sands, A. T., Zambrowicz, B. P., Turner, T. K., Demers, D. A., Webster, W., Smith, T. W., Imbalzano, A. N., and Jones, S. N. (2001). Disruption of Ini1 leads to peri-implantation lethality and tumorigenesis in mice. Mol Cell Biol 21, 3598–3603.

    Article  PubMed  CAS  Google Scholar 

  52. Wang, Z., Zhai, W., Richardson, J. A., Olson, E. N., Meneses, J. J., Firpo, M. T., Kang, C., Skarnes, W. C., and Tjian, R. (2004). Polybromo protein BAF180 functions in mammalian cardiac chamber maturation. Genes Dev 18, 3106–3116.

    Article  PubMed  CAS  Google Scholar 

  53. Gao, X., Tate, P., Hu, P., Tjian, R., Skarnes, W. C., and Wang, Z. (2008). ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a. Proc Natl Acad Sci U S A 105, 6656–6661.

    Article  PubMed  Google Scholar 

  54. Belandia, B., Orford, R. L., Hurst, H. C., and Parker, M. G. (2002). Targeting of SWI/SNF chromatin remodelling complexes to estrogen-responsive genes. EMBO J 21, 4094–4103.

    Article  PubMed  CAS  Google Scholar 

  55. Inoue, H., Furukawa, T., Giannakopoulos, S., Zhou, S., King, D. S., and Tanese, N. (2002). Largest subunits of the human SWI/SNF chromatin-remodeling complex promote transcriptional activation by steroifd hormone receptors. J Biol Chem 277, 41674–41685.

    Article  PubMed  CAS  Google Scholar 

  56. Link, K. A., Burd, C. J., Williams, E., Marshall, T., Rosson, G., Henry, E., Weissman, B., and Knudsen, K. E. (2005). BAF57 governs androgen receptor action and androgen-dependent proliferation through SWI/SNF. Mol Cell Biol 25, 2200–2215.

    Article  PubMed  CAS  Google Scholar 

  57. Debril, M. B., Gelman, L., Fayard, E., Annicotte, J. S., Rocchi, S., and Auwerx, J. (2004). Transcription factors and nuclear receptors interact with the SWI/SNF complex through the BAF60c subunit. J Biol Chem 279, 16677–16686.

    Article  PubMed  CAS  Google Scholar 

  58. Koszewski, N. J., Henry, K. W., Lubert, E. J., Gravatte, H., and Noonan, D. J. (2003). Use of a modified yeast one-hybrid screen to identify BAF60a interactions with the Vitamin D receptor heterodimer. J Steroid Biochem Mol Biol 87, 223–231.

    Article  PubMed  CAS  Google Scholar 

  59. Trotter, K. W. and Archer, T. K. (2007). Nuclear receptors and chromatin remodeling machinery. Mol Cell Endocrinol 265–266, 162–167.

    Article  PubMed  CAS  Google Scholar 

  60. Flajollet, S., Lefebvre, B., Cudejko, C., Staels, B., and Lefebvre, P. (2007). The core component of the mammalian SWI/SNF complex SMARCD3/BAF60c is a coactivator for the nuclear retinoic acid receptor. Mol Cell Endocrinol 270, 23–32.

    Article  PubMed  CAS  Google Scholar 

  61. Hsiao, P. W., Fryer, C. J., Trotter, K. W., Wang, W., and Archer, T. K. (2003). BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation. Mol Cell Biol 23, 6210–6220.

    Article  PubMed  CAS  Google Scholar 

  62. Trotter, K. W., Fan, H. Y., Ivey, M. L., Kingston, R. E., and Archer, T. K. (2008). The HSA domain of BRG1 mediates critical interactions required for glucocorticoid receptor-dependent transcriptional activation in vivo. Mol Cell Biol 28, 1413–1426.

    Article  PubMed  CAS  Google Scholar 

  63. Szerlong, H., Hinata, K., Viswanathan, R., Erdjument-Bromage, H., Tempst, P., and Cairns, B. R. (2008). The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat Struct Mol Biol 15, 469–476.

    Article  PubMed  CAS  Google Scholar 

  64. Hebbar, P. B. and Archer, T. K. (2003). Chromatin remodeling by nuclear receptors. Chromosoma 111, 495–504.

    Article  PubMed  Google Scholar 

  65. Zhang, B., Chambers, K. J., Faller, D. V., and Wang, S. (2007). Reprogramming of the SWI/SNF complex for co-activation or co-repression in prohibitin-mediated estrogen receptor regulation. Oncogene 26, 7153–7157.

    Article  PubMed  CAS  Google Scholar 

  66. John, S., Sabo, P. J., Johnson, T. A., Sung, M. H., Biddie, S. C., Lightman, S. L., Voss, T. C., Davis, S. R., Meltzer, P. S., Stamatoyannopoulos, J. A., and Hager, G. L. (2008). Interaction of the glucocorticoid receptor with the chromatin landscape. Mol Cell 29, 611–624.

    Article  PubMed  CAS  Google Scholar 

  67. Archer, T. K., Cordingley, M. G., Wolford, R. G., and Hager, G. L. (1991). Transcription factor access is mediated by accurately positioned nucleosomes on the mouse mammary tumor virus promoter. Mol Cell Biol 11, 688–698.

    PubMed  CAS  Google Scholar 

  68. Trotter, K. W. and Archer, T. K. (2004). Reconstitution of glucocorticoid receptor-dependent transcription in vivo. Mol Cell Biol 24, 3347–3358.

    Article  PubMed  CAS  Google Scholar 

  69. Fan, H. Y., Trotter, K. W., Archer, T. K., and Kingston, R. E. (2005). Swapping function of two chromatin remodeling complexes. Mol Cell 17, 805–815.

    Article  PubMed  CAS  Google Scholar 

  70. Nagaich, A. K., Walker, D. A., Wolford, R., and Hager, G. L. (2004). Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling. Mol Cell 14, 163–174.

    Article  PubMed  CAS  Google Scholar 

  71. Voss, T. C., John, S., and Hager, G. L. (2006). Single-cell analysis of glucocorticoid receptor action reveals that stochastic post-chromatin association mechanisms regulate ligand-specific transcription. Mol Endocrinol (Baltimore, MD) 20, 2641–2655.

    Article  CAS  Google Scholar 

  72. Tsukiyama, T., Daniel, C., Tamkun, J., and Wu, C. (1995). ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor. Cell 83, 1021–1026.

    Article  PubMed  CAS  Google Scholar 

  73. Lazzaro, M. A. and Picketts, D. J. (2001). Cloning and characterization of the murine Imitation Switch (ISWI) genes: Differential expression patterns suggest distinct developmental roles for Snf2h and Snf2l. J Neurochem 77, 1145–1156.

    Article  PubMed  CAS  Google Scholar 

  74. Lazzaro, M. A., Pepin, D., Pescador, N., Murphy, B. D., Vanderhyden, B. C., and Picketts, D. J. (2006). The imitation switch protein SNF2L regulates steroidogenic acute regulatory protein expression during terminal differentiation of ovarian granulosa cells. Mol Endocrinol (Baltimore, MD) 20, 2406–2417.

    Article  CAS  Google Scholar 

  75. Hakimi, M. A., Bochar, D. A., Schmiesing, J. A., Dong, Y., Barak, O. G., Speicher, D. W., Yokomori, K., and Shiekhattar, R. (2002). A chromatin remodelling complex that loads cohesin onto human chromosomes. Nature 418, 994–998.

    Article  PubMed  CAS  Google Scholar 

  76. LeRoy, G., Orphanides, G., Lane, W. S., and Reinberg, D. (1998). Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science (New York, N.Y) 282, 1900–1904.

    CAS  Google Scholar 

  77. Alenghat, T., Yu, J., and Lazar, M. A. (2006). The N-CoR complex enables chromatin remodeler SNF2H to enhance repression by thyroid hormone receptor. EMBO J 25, 3966–3974.

    Article  PubMed  CAS  Google Scholar 

  78. Pepin, D., Vanderhyden, B. C., Picketts, D. J., and Murphy, B. D. (2007). ISWI chromatin remodeling in ovarian somatic and germ cells: Revenge of the NURFs. Trends Endocrinol Metab 18, 215–224.

    Article  PubMed  CAS  Google Scholar 

  79. Dilworth, F. J., Fromental-Ramain, C., Remboutsika, E., Benecke, A., and Chambon, P. (1999). Ligand-dependent activation of transcription in vitro by retinoic acid receptor alpha/retinoid X receptor alpha heterodimers that mimics transactivation by retinoids in vivo. Proc Natl Acad Sci U S A 96, 1995–2000.

    Article  PubMed  CAS  Google Scholar 

  80. Di Croce, L., Koop, R., Venditti, P., Westphal, H. M., Nightingale, K. P., Corona, D. F., Becker, P. B., and Beato, M. (1999). Two-step synergism between the progesterone receptor and the DNA-binding domain of nuclear factor 1 on MMTV minichromosomes. Mol Cell 4, 45–54.

    Article  PubMed  CAS  Google Scholar 

  81. Badenhorst, P., Xiao, H., Cherbas, L., Kwon, S. Y., Voas, M., Rebay, I., Cherbas, P., and Wu, C. (2005). The Drosophila nucleosome remodeling factor NURF is required for Ecdysteroid signaling and metamorphosis. Genes Dev 19, 2540–2545.

    Article  PubMed  CAS  Google Scholar 

  82. Tong, J. K., Hassig, C. A., Schnitzler, G. R., Kingston, R. E., and Schreiber, S. L. (1998). Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature 395, 917–921.

    Article  PubMed  CAS  Google Scholar 

  83. Wade, P. A., Jones, P. L., Vermaak, D., and Wolffe, A. P. (1998). A multiple subunit Mi-2 histone deacetylase from Xenopus laevis cofractionates with an associated Snf2 superfamily ATPase. Curr Biol 8, 843–846.

    Article  PubMed  CAS  Google Scholar 

  84. Xue, Y., Wong, J., Moreno, G. T., Young, M. K., Cote, J., and Wang, W. (1998). NURD, a novel complex with both ATP-dependent chromatin-remodeling and histone deacetylase activities. Mol Cell 2, 851–861.

    Article  PubMed  CAS  Google Scholar 

  85. Zhang, Y., LeRoy, G., Seelig, H. P., Lane, W. S., and Reinberg, D. (1998). The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell 95, 279–289.

    Article  PubMed  CAS  Google Scholar 

  86. Kumar, R., Wang, R. A., and Bagheri-Yarmand, R. (2003). Emerging roles of MTA family members in human cancers. Semin Oncol 30, 30–37.

    Article  PubMed  CAS  Google Scholar 

  87. Mazumdar, A., Wang, R. A., Mishra, S. K., Adam, L., Bagheri-Yarmand, R., Mandal, M., Vadlamudi, R. K., and Kumar, R. (2001). Transcriptional repression of oestrogen receptor by metastasis-associated protein 1 corepressor. Nat Cell Biol 3, 30–37.

    Article  PubMed  CAS  Google Scholar 

  88. Fujita, N., Jaye, D. L., Kajita, M., Geigerman, C., Moreno, C. S., and Wade, P. A. (2003). MTA3, a Mi-2/NuRD complex subunit, regulates an invasive growth pathway in breast cancer. Cell 113, 207–219.

    Article  PubMed  CAS  Google Scholar 

  89. Dhasarathy, A., Kajita, M., and Wade, P. A. (2007). The transcription factor snail mediates epithelial to mesenchymal transitions by repression of estrogen receptor-alpha. Mol Endocrinol (Baltimore, MD) 21, 2907–2918.

    Article  CAS  Google Scholar 

  90. Creekmore, A. L., Walt, K. A., Schultz-Norton, J. R., Ziegler, Y. S., McLeod, I. X., Yates, J. R., and Nardulli, A. M. (2008). The role of retinoblastoma-associated proteins 46 and 48 in estrogen receptor alpha mediated gene expression. Mol Cell Endocrinol 291, 79–86.

    Article  PubMed  CAS  Google Scholar 

  91. Johnson, D. R., Lovett, J. M., Hirsch, M., Xia, F., and Chen, J. D. (2004). NuRD complex component Mi-2beta binds to and represses RORgamma-mediated transcriptional activation. Biochem Biophys Res Commun 318, 714–718.

    Article  PubMed  CAS  Google Scholar 

  92. Morey, L., Brenner, C., Fazi, F., Villa, R., Gutierrez, A., Buschbeck, M., Nervi, C., Minucci, S., Fuks, F., and Di Croce, L. (2008). MBD3, a component of the NuRD complex, facilitates chromatin alteration and deposition of epigenetic marks. Mol Cell Biol 28, 5912–5923.

    Article  PubMed  CAS  Google Scholar 

  93. Darbre, P. D. and King, R. J. (1988). Role of receptor occupancy in the transition from responsive to unresponsive states in cultured breast tumor cells. J Cell Biochem 36, 83–89.

    Article  PubMed  CAS  Google Scholar 

  94. Cheng, A. S., Culhane, A. C., Chan, M. W., Venkataramu, C. R., Ehrich, M., Nasir, A., Rodriguez, B. A., Liu, J., Yan, P. S., Quackenbush, J., Nephew, K. P., Yeatman, T. J., and Huang, T. H. (2008). Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Res 68, 1786–1796.

    Article  PubMed  CAS  Google Scholar 

  95. Shen, X., Mizuguchi, G., Hamiche, A., and Wu, C. (2000). A chromatin remodelling complex involved in transcription and DNA processing. Nature 406, 541–544.

    Article  PubMed  CAS  Google Scholar 

  96. Mizuguchi, G., Shen, X., Landry, J., Wu, W. H., Sen, S., and Wu, C. (2004). ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science (New York, NY) 303, 343–348.

    CAS  Google Scholar 

  97. Shen, X., Ranallo, R., Choi, E., and Wu, C. (2003). Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol Cell 12, 147–155.

    Article  PubMed  CAS  Google Scholar 

  98. Wu, W. H., Alami, S., Luk, E., Wu, C. H., Sen, S., Mizuguchi, G., Wei, D., and Wu, C. (2005). Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat Struct Mol Biol 12, 1064–1071.

    Article  PubMed  CAS  Google Scholar 

  99. Ebbert, R., Birkmann, A., and Schuller, H. J. (1999). The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. Mol Microbiol 32, 741–751.

    Article  PubMed  CAS  Google Scholar 

  100. Lee, K. C. and Lee Kraus, W. (2001). Nuclear receptors, coactivators and chromatin: New approaches, new insights. Trends Endocrinol Metab 12, 191–197.

    Article  PubMed  CAS  Google Scholar 

  101. Belikov, S., Gelius, B., and Wrange, O. (2001). Hormone-induced nucleosome positioning in the MMTV promoter is reversible. EMBO J 20, 2802–2811.

    Article  PubMed  CAS  Google Scholar 

  102. Orlando, V., Strutt, H., and Paro, R. (1997). Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods (San Diego, Calif) 11, 205–214.

    CAS  Google Scholar 

  103. Solomon, M. J., Larsen, P. L., and Varshavsky, A. (1988). Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene. Cell 53, 937–947.

    Article  PubMed  CAS  Google Scholar 

  104. Bernstein, B. E., Humphrey, E. L., Liu, C. L., and Schreiber, S. L. (2004). The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. Methods Enzymol 376, 349–360.

    Article  PubMed  CAS  Google Scholar 

  105. Fryer, C. J. and Archer, T. K. (2001). Analyzing the contributions of chromatin structure in nuclear hormone receptor activated transcription in vivo. Methods Mol Biol 176, 283–296.

    PubMed  CAS  Google Scholar 

  106. Kinyamu, H. K., Fryer, C. J., Horwitz, K. B., and Archer, T. K. (2000). The mouse mammary tumor virus promoter adopts distinct chromatin structures in human breast cancer cells with and without glucocorticoid receptor. J Biol Chem 275, 20061–20068.

    Article  PubMed  CAS  Google Scholar 

  107. Flick, J. T., Eissenberg, J. C., and Elgin, S. C. (1986). Micrococcal nuclease as a DNA structural probe: Its recognition sequences, their genomic distribution and correlation with DNA structure determinants. J Mol Biol 190, 619–633.

    Article  PubMed  CAS  Google Scholar 

  108. Stenoien, D. L., Patel, K., Mancini, M. G., Dutertre, M., Smith, C. L., O’Malley, B. W., and Mancini, M. A. (2001). FRAP reveals that mobility of oestrogen receptor-alpha is ligand- and proteasome-dependent. Nat Cell Biol 3, 15–23.

    Article  PubMed  CAS  Google Scholar 

  109. Schaaf, M. J. and Cidlowski, J. A. (2003). Molecular determinants of glucocorticoid receptor mobility in living cells: The importance of ligand affinity. Mol Cell Biol 23, 1922–1934.

    Article  PubMed  CAS  Google Scholar 

  110. Rayasam, G. V., Elbi, C., Walker, D. A., Wolford, R., Fletcher, T. M., Edwards, D. P., and Hager, G. L. (2005). Ligand-specific dynamics of the progesterone receptor in living cells and during chromatin remodeling in vitro. Mol Cell Biol 25, 2406–2418.

    Article  PubMed  CAS  Google Scholar 

  111. Metivier, R., Penot, G., Hubner, M. R., Reid, G., Brand, H., Kos, M., and Gannon, F. (2003). Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115, 751–763.

    Article  PubMed  CAS  Google Scholar 

  112. Reid, G., Hubner, M. R., Metivier, R., Brand, H., Denger, S., Manu, D., Beaudouin, J., Ellenberg, J., and Gannon, F. (2003). Cyclic, proteasome-mediated turnover of unliganded and liganded ERalpha on responsive promoters is an integral feature of estrogen signaling. Mol Cell 11, 695–707.

    Article  PubMed  CAS  Google Scholar 

  113. Johnson, T. A., Elbi, C., Parekh, B. S., Hager, G. L., and John, S. (2008). Chromatin remodeling complexes interact dynamically with a glucocorticoid receptor-regulated promoter. Mol Biol Cell 19, 3308–3322.

    Article  PubMed  CAS  Google Scholar 

  114. Kininis, M. and Kraus, W. L. (2008). A global view of transcriptional regulation by nuclear receptors: Gene expression, factor localization, and DNA sequence analysis. Nucl Recept Signal 6, e005.

    PubMed  Google Scholar 

  115. Granjeaud, S., Bertucci, F., and Jordan, B. R. (1999). Expression profiling: DNA arrays in many guises. Bioessays 21, 781–790.

    Article  PubMed  CAS  Google Scholar 

  116. Buck, M. J. and Lieb, J. D. (2004). ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83, 349–360.

    Article  PubMed  CAS  Google Scholar 

  117. Ren, B., Robert, F., Wyrick, J. J., Aparicio, O., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T. L., Wilson, C. J., Bell, S. P., and Young, R. A. (2000). Genome-wide location and function of DNA binding proteins. Science (New York, NY) 290, 2306–2309.

    CAS  Google Scholar 

  118. Robyr, D. and Grunstein, M. (2003). Genomewide histone acetylation microarrays. Methods (San Diego, Calif) 31, 83–89.

    CAS  Google Scholar 

  119. Lee, W., Tillo, D., Bray, N., Morse, R. H., Davis, R. W., Hughes, T. R., and Nislow, C. (2007). A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39, 1235–1244.

    Article  PubMed  CAS  Google Scholar 

  120. Ozsolak, F., Song, J. S., Liu, X. S., and Fisher, D. E. (2007). High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 25, 244–248.

    Article  PubMed  CAS  Google Scholar 

  121. Bernstein, B. E., Humphrey, E. L., Erlich, R. L., Schneider, R., Bouman, P., Liu, J. S., Kouzarides, T., and Schreiber, S. L. (2002). Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A 99, 8695–8700.

    Article  PubMed  CAS  Google Scholar 

  122. Carroll, J. S., Liu, X. S., Brodsky, A. S., Li, W., Meyer, C. A., Szary, A. J., Eeckhoute, J., Shao, W., Hestermann, E. V., Geistlinger, T. R., Fox, E. A., Silver, P. A., and Brown, M. (2005). Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122, 33–43.

    Article  PubMed  CAS  Google Scholar 

  123. Carroll, J. S., Meyer, C. A., Song, J., Li, W., Geistlinger, T. R., Eeckhoute, J., Brodsky, A. S., Keeton, E. K., Fertuck, K. C., Hall, G. F., Wang, Q., Bekiranov, S., Sementchenko, V., Fox, E. A., Silver, P. A., Gingeras, T. R., Liu, X. S., and Brown, M. (2006). Genome-wide analysis of estrogen receptor binding sites. Nat Genet 38, 1289–1297.

    Article  PubMed  CAS  Google Scholar 

  124. Lin, C. Y., Vega, V. B., Thomsen, J. S., Zhang, T., Kong, S. L., Xie, M., Chiu, K. P., Lipovich, L., Barnett, D. H., Stossi, F., Yeo, A., George, J., Kuznetsov, V. A., Lee, Y. K., Charn, T. H., Palanisamy, N., Miller, L. D., Cheung, E., Katzenellenbogen, B. S., Ruan, Y., Bourque, G., Wei, C. L., and Liu, E. T. (2007). Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet 3, e87.

    Article  PubMed  CAS  Google Scholar 

  125. Bentley, D. R. (2006). Whole-genome re-sequencing. Curr Opin Genet Dev 16, 545–552.

    Article  PubMed  CAS  Google Scholar 

  126. Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., Thiessen, N., Griffith, O. L., He, A., Marra, M., Snyder, M., and Jones, S. (2007). Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods 4, 651–657.

    Article  PubMed  CAS  Google Scholar 

  127. Mardis, E. R. (2007). ChIP-seq: Welcome to the new frontier. Nature Methods 4, 613–614.

    Article  PubMed  CAS  Google Scholar 

  128. Wade, P. A. and Archer, T. K. (2006). Epigenetics: Environmental instructions for the genome. Environ Health Perspect 114, A.

    Article  Google Scholar 

  129. O’Malley, B. W., Qin, J., and Lanz, R. B. (2008). Cracking the coregulator codes. Curr Opin Cell Biol 20, 310–315.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This research was supported by the Intramural Research Program of the National Institute of Environmental Health Sciences, NIH; project number Z01 ES071006-09.

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  1. Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA

    Craig J. Burd & Trevor K. Archer

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  1. Craig J. Burd
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Correspondence to Trevor K. Archer .

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  1. School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom

    Chris M. Bunce

  2. Dept. Pharmacology & Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, 14263, U.S.A.

    Moray J. Campbell

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Burd, C.J., Archer, T.K. (2010). Nuclear Receptors and ATP Dependent Chromatin Remodeling: A Complex Story. In: Bunce, C., Campbell, M. (eds) Nuclear Receptors. Proteins and Cell Regulation, vol 8. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3303-1_14

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