Skip to main content

Transcription Factor Dynamics

  • Chapter
Gene Expression and Regulation

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Bannister, A.J., Schneider, R., and Kouzarides, T. (2002). Histone methylation: dynamic or static? Cell 109, 801–806.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Becker, P.B. and Horz, W. (2002). ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247–273.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Berger, S.L. (1999). Gene activation by histone and factor acetyltransferases. Curr. Opin. Cell Biol. 11, 336–341.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Francis, N.J. and Kingston, R.E. (2001). Mechanisms of transcriptional memory. Nat. Rev. Mol. Cell Biol. 2, 409–421.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Hager, G.L. (1999). Studying nuclear receptors with GFP fusions. Methods Enzymol. 302, 73–84.

    Article  PubMed  CAS  Google Scholar 

  • Hager, G.L., Elbi, C.C., and Becker, M. (2002). Protein dynamics in the nuclear compartment. Curr. Opin. Genet. Dev. 12, 137–141.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Kornberg, R.D., and Lorch, Y. (2002). Chromatin and transcription: where do we go from here. Curr. Opin. Genet. Dev. 12, 249–251.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Prasher, D.C. (1995). Using GFP to see the light. Trends Genet. 11, 320–323.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Selker, E.U. (1990). DNA methylation and chromatin structure: A view from below. Trends Biochem. Sci. 15, 103–107.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Sprague, B.L. and McNally, J.G. (2005). FRAP analysis of binding: proper and fitting. Trends Cell Biol. 15, 84–91.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Strahl, B.D. and Allis, C.D. (2000). The language of covalent histone modifications. Nature 403, 41–45.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Thanos, D., and Maniatis, T. (1995). Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83, 1091–1100.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Higher Education Press

About this chapter

Cite this chapter

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

Download citation

Publish with us

Policies and ethics