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DNA Dynamics and Chromosome Structure

Structural Features of Transcription Factor IIIA Bound to a Nucleosome in Solution

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Pages 697-707 | Received 16 Jul 2003, Accepted 14 Oct 2003, Published online: 27 Mar 2023

REFERENCES

  • Almouzni, G., Mechali M., and Wolffe A. P.. 1990. Competition between transcription complex assembly and chromatin assembly on replicating DNA. EMBO J. 9:573–582.
  • Bauer, W. R., Hayes J. J., White J. H., and Wolffe A. P.. 1994. Nucleosome structural changes due to acetylation. J. Mol. Biol. 236:685–690.
  • Bouvet, P., Dimitrov S., and Wolffe A. P.. 1994. Specific regulation of Xenopus chromosomal 5S rRNA gene transcription in vivo by histone H1. Genes Dev. 8:1147–1159.
  • Brown, R. S., Sander C., and Wolffe A. P.. 1985. The primary structure of transcription factor TFIIIA has 12 consecutive repeats. FEBS Lett. 186:271–274.
  • Brunger, A., Adams P., Clore G., DeLano W., Gros P., Grosse-Kunstleve R., Jiang J., Kuszewski J., Nilges M., Pannu N., Read R., Rice L., Simonson T., and Warren G.. 1998. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54:905–921.
  • Chafin, D. R., Vitolo J. M., Henricksen L. A., Bambara R. A., and Hayes J. J.. 2000. Human DNA ligase I efficiently seals nicks in nucleosomes. EMBO J. 19:5492–5501.
  • Clemens, K. R., Liao X., Wolf V., Wright P. E., and Gottesfeld J. M.. 1992. Definition of the binding sites of individual Zn-fingers in the transcription factor IIIA-5S RNA gene complex. Proc. Natl. Acad. Sci. USA 89:10822–10826.
  • Del Rio, S., and Setzer D. R.. 1991. High yield purification of active transcription factor IIIA expressed in E. coli. Nucleic Acids Res. 19:6197–6203.
  • Engelke, D. R., Ng S.-Y., Shastry B. S., and Roeder R. G.. 1980. Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes. Cell 19:717–728.
  • Gottesfeld, J. M. 1987. DNA sequence-directed nucleosome reconstitution on 5S RNA genes of Xenopus laevis. Mol. Cell. Biol. 7:1612–1622.
  • Hayes, J., Tullius T. D., and Wolffe A. P.. 1989. A protein-protein interaction is essential for stable complex formation on a 5S RNA gene. J. Biol. Chem. 264:6009–6012.
  • Hayes, J. J., Clark D. J., and Wolffe A. P.. 1991. Histone contributions to the structure of DNA in the nucleosome. Proc. Natl. Acad. Sci. USA 88:6829–6833.
  • Hayes, J. J., and Clemens K. R.. 1992. Location of contacts between individual zinc fingers of Xenopus laevis transcription factor IIIA and the internal control region of a 5S RNA gene. Biochemistry 31:11600–11605.
  • Hayes, J. J., and Lee K. M.. 1997. In vitro reconstitution and analysis of mononucleosomes containing defined DNAs and proteins. Methods 12:2–9.
  • Hayes, J. J., and Tullius T. D.. 1992. The structure of the TFIIIA/5S DNA complex. J. Mol. Biol. 227:407–417.
  • Hayes, J. J., Tullius T. D., and Wolffe A. P.. 1990. The structure of DNA in a nucleosome. Proc. Natl. Acad. Sci. USA 87:7405–7409.
  • Hayes, J. J., and Wolffe A. P.. 1992. Histones H2A/H2B inhibit the interaction of transcription factor IIIA with the Xenopus borealis somatic 5S RNA gene in a nucleosome. Proc. Natl. Acad. Sci. USA 89:1229–1233.
  • Hayes, J. J., and Wolffe A. P.. 1992. The interaction of transcription factors with nucleosomal DNA. Bioessays 14:597–603.
  • Howe, L., Ranalli T. A., Allis C. D., and Ausio J.. 1998. Transcriptionally active Xenopus laevis somatic 5S ribosomal RNA genes are packaged with hyperacetylated histone H4, whereas transcriptionally silent oocyte genes are not. J. Biol. Chem. 273:20693–20696.
  • Jones, T., Zou J., Cowan S., and Kjeldgaard M.. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47:110–119.
  • Kassabov, S. R., Henry N. M., Zofall M., Tsukiyama T., and Bartholomew B.. 2002. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol. Cell. Biol. 22:7524–7534.
  • Lassar, A. B., Martin P. L., and Roeder R. G.. 1983. Transcription of class III genes: formation of preinitiation complexes. Science 222:740–748.
  • Lee, D. Y., Hayes J. J., Pruss D., and Wolffe A. P.. 1993. A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell 72:73–84.
  • Lee, K. M., Chafin D. R., and Hayes J. J.. 1999. Targeted cross-linking and DNA cleavage within model chromatin complexes. Methods Enzymol. 304:231–251.
  • Lee, K. M., and Hayes J. J.. 1997. The N-terminal tail of histone H2A binds to two distinct sites within the nucleosome core. Proc. Natl. Acad. Sci. USA 94:8959–8964.
  • 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 Å resolution. Nature 389:251–260.
  • Miller, J., McLachlan A. D., and Klug A.. 1985. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4:1609–1614.
  • Miller, J. A., and Widom J.. 2003. Collaborative competition mechanism for gene activation in vivo. Mol. Cell. Biol. 23:1623–1632.
  • Nolte, R. T., Conlin R. M., Harrison S. C., and Brown R. S.. 1998. Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. Proc. Natl. Acad. Sci. USA 95:2938–2943.
  • Pavletich, N. P., and Pabo C. O.. 1993. Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science 261:1701–1707.
  • Polach, K. J., Lowary P. T., and Widom J.. 2000. Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes. J. Mol. Biol. 298:211–233.
  • Polach, K. J., and Widom J.. 1995. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254:130–149.
  • Polach, K. J., and Widom J.. 1996. A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. J. Mol. Biol. 258:800–812.
  • Pruss, D., Bartholomew B., Persinger J., Hayes J., Arents G., Moudrianakis E. N., and Wolffe A. P.. 1996. An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres. Science 274:614–617.
  • Rhodes, D. 1985. Structural analysis of a triple complex between the histone octamer, a Xenopus gene for 5S RNA and transcription factor IIIA. EMBO J. 4:3473–3482.
  • Sakonju, S., and Brown D. D.. 1982. Contact points between a positive transcription factor and the Xenopus 5S RNA gene. Cell 31:395–405.
  • Simon, R. H., and Felsenfeld G.. 1979. A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite. Nucleic Acids Res. 6:689–696.
  • Simpson, R. T. 1991. Nucleosome positioning: occurrence, mechanisms, and functional consequences. Prog. Nucleic Acid Res. Mol. Biol. 40:143–184.
  • Smith, D. R., Jackson I. J., and Brown D. D.. 1984. Domains of the positive transcription factor specific for the Xenopus 5S RNA gene. Cell 37:645–652.
  • Thiriet, C., and Hayes J. J.. 1998. Functionally relevant histone-DNA interactions extend beyond the classically defined nucleosome core region. J. Biol. Chem. 273:21352–21358.
  • Tse, C., and Hansen J. C.. 1997. Hybrid trypsinized nucleosomal arrays: identification of multiple functional roles of the H2A/H2B and H3/H4 N-termini in chromatin fiber compaction. Biochemistry 36:11381–11388.
  • van Holde, K. E. 1989. Chromatin. Springer Verlag, New York, N.Y.
  • Vitolo, J. M., Thiriet C., and Hayes J. J.. 2000. The H3-H4 N-terminal tail domains are the primary mediators of transcription factor IIIA access to 5S DNA within a nucleosome. Mol. Cell. Biol. 20:2167–2175.
  • Vrana, K. E., Churchill M. E., Tullius T. D., and Brown D. D.. 1988. Mapping functional regions of transcription factor TFIIIA. Mol. Cell. Biol. 8:1684–1696.
  • Wolfe, S. A., Nekludova L., and Pabo C. O.. 2000. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29:183–212.
  • Wolffe, A. P. 1998. Chromatin structure and function, 3rd ed. Academic Press, San Diego, Calif.
  • Wolffe, A. P. 1988. Transcription fraction TFIIIC can regulate differential Xenopus 5S RNA gene transcription in vitro. EMBO J. 7:1071–1079.
  • Wolffe, A. P., and Brown D. D.. 1988. Developmental regulation of two 5S ribosomal RNA genes. Science 241:1626–1632.
  • Wolffe, A. P., and Hayes J. J.. 1999. Chromatin disruption and modification. Nucleic Acids Res. 27:711–720.
  • Wolffe, A. P., and Morse R. H.. 1990. The transcription complex of the Xenopus somatic 5 S RNA gene. A functional analysis of protein-DNA interactions outside of the internal control region. J. Biol. Chem. 265:4592–4599.
  • Wuttke, D. S., Foster M. P., Case D. A., Gottesfeld J. M., and Wright P. E.. 1997. Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity. J. Mol. Biol. 273:183–206.
  • Zheng, C., and Hayes J. J.. 2003. Intra- and inter-nucleosomal protein-DNA interactions of the core histone tail domains in a model system. J. Biol. Chem. 278:24217–24224.

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