Abstract
The regulation of gene transcription in eukaryotic systems involves a large number of factors. These proteins have been argued to form large, relatively long lived, multi-protein complexes on promoter elements during the process of transcription initiation and elongation. Recent advances in imaging technology have permitted for the first time a dissection of transcription events in real time. Using arrays of gene reporter elements and transcripiton factors tagged with the green fluorescent protein, it is now possible to observe targeting of a regulatory protein to response elements in living cells. Application of photobleaching technology to these systems allows a direct analysis of the rate at which factors are moving in the nucleoplasmic space, and the timing of their interactions with various intranuclear structures, including DNA regulatory sites. These technical breakthroughs have led to the unexpected finding that most transcription factors interact very briefly with promoter elements, and cycle on and off genes at relatively high rates. These findings stand in dramatic contrast to the classic view of large, static initiation complexes, and reveal a level of dynamic action not previously suspected in the process of transcriptional regulation.
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Bannister, A.J., Schneider, R., and Kouzarides, T. (2002). Histone methylation: dynamic or static? Cell 109, 801–806.
Becker, M., Baumann, C.T., John, S., Walker, D., Vigneron, M., McNally, J.G., and Hager, G.L. (2002). Dynamic behavior of transcription factors on a natural promoter in living cells. EMBO Reports 3, 1188–1194.
Becker, P., Renkawitz, R., and Schutz, G. (1984). Tissue-specific DNaseI hypersensitive sites in the 5′-flanking sequences of the tryptophan oxygenase and the tyrosine aminotransferase genes. EMBO J. 3, 2015–2020.
Becker, P.B. and Horz, W. (2002). ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247–273.
Belmont, A.S., Li, G., Sudlow, G., and Robinett, C. (1999). Visualization of large-scale chromatin structure and dynamics using the lac operator/lac repressor reporter system. Methods Cell Biol. 58:203–22, 203–222.
Berger, S.L. (1999). Gene activation by histone and factor acetyltransferases. Curr. Opin. Cell Biol. 11, 336–341.
Carrero, G., Crawford, E., Th’ng, J., de Vries, G., and Hendzel, M.J. (2004). Quantification of protein-protein and protein-DNA interactions in vivo, using fluorescence recovery after photobleaching. Methods Enzymol. 375, 415–442.
Chen, D., Ma, H., Hong, H., Koh, S.S., Huang, S.M., Schurter, B.T., Aswad, D.W., and Stallcup, M.R. (1999). Regulation of transcription by a protein methyltransferase. Science 284, 2174–2177.
Cubitt, A.B., Heim, R., Adams, S.R., Boyd, A.E., Gross, L.A., and Tsien, R.Y. (1995). Understanding, improving and using green fluorescent proteins. Trends. Biochem. Sci. 20, 448–455.
Dundr, M., Hoffmann-Rohrer, U., Hu, Q., Grummt, I., Rothblum, L.I., Phair, R.D., and Misteli, T. (2002). A kinetic framework for a mammalian RNA polymerase in vivo. Science 298, 1623–1626.
Elbi, C., Walker, D.A., Romero, G., Sullivan, W.P., Toft, D.O., Hager, G.L., and DeFranco, D.B. (2004). Molecular chaperones function as steroid receptor nuclear mobility factors. Proc. Natl. Acad. Sci. USA 101, 2876–2881.
Fletcher, T.M., Ryu, B.-W., Baumann, C.T., Warren, B.S., Fragoso, G., John, S., and Hager, G.L. (2000). Structure and dynamic properties of the glucocorticoid receptor-induced chromatin transition at the MMTV promoter. Mol. Cell. Biol. 20, 6466–6475.
Fletcher, T.M., Xiao, N., Mautino, G., Baumann, C.T., Wolford, R.G., Warren, B.S., and Hager, G.L. (2002). ATP-dependent mobilization of the glucocorticoid receptor during chromatin remodeling. Mol. Cell. Biol. 22, 3255–3263.
Francis, N.J. and Kingston, R.E. (2001). Mechanisms of transcriptional memory. Nat. Rev. Mol. Cell Biol. 2, 409–421.
Fryer, C.J. and Archer, T.K. (1998). Chromatin remodeling by the glucocorticoid receptor requires the BRG1 complex. Nature 393, 88–91.
Hager, G.L. (2001). Understanding nuclear receptor function: From DNA to chromatin to the interphase nucleus. Prog. Nucleic Acid. Res. Mol. Biol. 66, 279–305.
Hager, G.L. (1999). Studying nuclear receptors with GFP fusions. Methods Enzymol. 302, 73–84.
Hager, G.L., Elbi, C.C., and Becker, M. (2002). Protein dynamics in the nuclear compartment. Curr. Opin. Genet. Dev. 12, 137–141.
Hager, G.L., Nagaich, A.K., Johnson, T.A., Walker, D.A., and John, S. (2004). Dynamics of nuclear receptor movement and transcription. Biochim. Biophys. Acta 1677, 46–51.
Hassig, C.A., Fleischer, T.C., Billin, A.N., Schreiber, S.L., and Ayer, D.E. (1997). Histone deacetylase activity is required for full transcriptional repression by mSin3A. Cell 89, 341–347.
Heim, R. and Tsien, R.Y. (1996). Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Curr. Biol. 6, 178–182.
Hoogstraten, D., Nigg, A.L., Heath, H., Mullenders, L.H., van, D. R., Hoeijmakers, J.H., Vermeulen, W., and Houtsmuller, A.B. (2002). Rapid switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo. Mol. Cell 10, 1163–1174.
Houtsmuller, A.B., Rademakers, S., Nigg, A.L., Hoogstraten, D., Hoeijmakers, J.H., and Vermeulen, W. (1999). Action of DNA repair endonuclease ERCC1/XPF in living cells. Science 284, 958–961.
Htun, H., Barsony, J., Renyi, I., Gould, D.J., and Hager, G.L. (1996). Visualization of glucocorticoid receptor translocation and intranuclear organization in living cells with a green fluorescent protein chimera. Proc. Natl. Acad. Sci. USA 93, 4845–4850.
Janicki, S.M., Tsukamoto, T., Salghetti, S.E., Tansey, W.P., Sachidanandam, R., Prasanth, K.V., Ried, T., Shav-Tal, Y., Bertrand, E., Singer, R.H., and Spector, D.L. (2004). From silencing to gene expression: real-time analysis in single cells. Cell 116, 683–698.
Kim, T.K., and Maniatis, T. (1997). The mechanism of transcriptional synergy of an in vitro assembled interferon-beta enhanceosome. Mol. Cell 1, 119–129.
Kimura, H., Sugaya, K., and Cook, P.R. (2002). The transcription cycle of RNA polymerase II in living cells. J. Cell Biol. 159, 777–782.
Kornberg, R.D., and Lorch, Y. (2002). Chromatin and transcription: where do we go from here. Curr. Opin. Genet. Dev. 12, 249–251.
Kramer, P., Fragoso, G., Pennie, W.D., Htun, H., Hager, G.L., and Sinden, R.R. (1999). Transcriptional state of the mouse mammary tumor virus promoter can effect topological domain size in vivo. J. Biol. Chem. 274, 28590–28597.
McNally, J.G., Mueller, W.G., Walker, D., Wolford, R.G., and Hager, G.L. (2000). The glucocorticoid receptor: Rapid exchange with regulatory sites in living cells. Science 287, 1262–1265.
Nagaich, A.K., and Hager, G.L. (2004). UV laser cross-linking: A real-time assay to study dynamic protein/DNA interactions during chromatin remodeling. Sci. STKe 256, PL13.
Nagaich, A.K., Rayasam, G.V., Martinez, E.D., Johnson, T.A., Elbi, C., John, S., and Hager, G.L. (2004a). Subnuclear trafficking and gene targeting by nuclear receptors. Ann. N. Y. Acad. Sci. Vol. 1024, 213–220.
Nagaich, A.K., Walker, D.A., Wolford, R.G., and Hager, G.L. (2004b). Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling. Mol. Cell 14, 163–174.
Phair, R.D., Gorski, S.A., and Misteli, T. (2004). Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy. Methods Enzymol. 375, 393–414.
Prasher, D.C. (1995). Using GFP to see the light. Trends Genet. 11, 320–323.
Rayasam, G.V., Elbi, C., Walker, D.A., Wolford, R.G., 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.
Rigaud, G., Roux, J., Pictet, R., and Grange, T. (1991). In vivo footprinting of rat TAT gene: dynamic interplay between the glucocorticoid receptor and a liver-specific factor. Cell 67, 977–986.
Selker, E.U. (1990). DNA methylation and chromatin structure: A view from below. Trends Biochem. Sci. 15, 103–107.
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.
Sprague, B.L. and McNally, J.G. (2005). FRAP analysis of binding: proper and fitting. Trends Cell Biol. 15, 84–91.
Stenoien, D.L., Nye, A.C., Mancini, M.G., Patel, K., Dutertre, M., O’Malley, B.W., Smith, C.L., Belmont, A.S., and Mancini, M.A. (2001a). Ligand-mediated assembly and real-time cellular dynamics of estrogen receptor alpha-coactivator complexes in living cells. Mol. Cell Biol. 21, 4404–4412.
Stenoien, D.L., Patel, K., Mancini, M.G., Dutertre, M., Smith, C.L., O’Malley, B.W., and Mancini, M.A. (2001b). FRAP reveals that mobility of oestrogen receptor-alpha is ligand-and proteasome-dependent. Nat. Cell Biol. 3, 15–23.
Strahl, B.D. and Allis, C.D. (2000). The language of covalent histone modifications. Nature 403, 41–45.
Suen, C.S., Berrodin, T.J., Mastroeni, R., Cheskis, B.J., Lyttle, C.R., and Frail, D.E. (1998). A transcriptional coactivator, steroid receptor coactivator-3, selectively augments steroid receptor transcriptional activity. J. Biol. Chem. 273, 27645–27653.
Thanos, D., and Maniatis, T. (1995). Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83, 1091–1100.
Truss, M., Chalepakis, G., and Beato, M. (1992). Interplay of steroid hormone receptors and transcription factors on the mouse mammary tumor virus promoter. J. Steroid Biochem. Molec. Biol. 43, 365–378.
Walker, D., Htun, H., and Hager, G.L. (1999). Using inducible vectors to study intracellular trafficking of GFP-tagged steroid/nuclear receptors in living cells. Methods (Companion to Methods in Enzymology) 19, 386–393.
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Hager, G.L., Nagaich, A.K. (2006). Transcription Factor Dynamics. In: Ma, J. (eds) Gene Expression and Regulation. Springer, New York, NY. https://doi.org/10.1007/978-0-387-40049-5_30
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DOI: https://doi.org/10.1007/978-0-387-40049-5_30
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