Role of Histone N-Terminal Tails and Their Acetylation in Nucleosome Dynamics

REFERENCES

• Arents, G., Burlingame, R. W., Wang, B. C., Love, W. E., and Moudrianakis, E. N.. 1991. The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix. Proc. Natl. Acad. Sci. USA 88:10148–10152
   PubMed Web of Science ®Google Scholar
• Ausio, J., Dong, F., and van Holde, K. E.. 1989. Use of selectively trypsinized nucleosome core particles to analyze the role of the histone “tails” in the stabilization of the nucleosome. J. Mol. Biol. 206:451–463
   PubMed Web of Science ®Google Scholar
• Baer, B. W., and Rhodes, D.. 1983. Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes. Nature 301:482–488
   PubMed Web of Science ®Google Scholar
• Baneres, J. L., Martin, A., and Parello, J.. 1997. The N tails of histones H3 and H4 adopt a highly structured conformation in the nucleosome. J. Mol. Biol. 273:503–508
   PubMedGoogle Scholar
• Bates, D. L., Butler, P. J., Pearson, E. C., and Thomas, J. O.. 1981. Stability of the higher-order structure of chicken-erythrocyte chromatin in solution. Eur. J. Biochem. 119:469–476
   PubMedGoogle Scholar
• Burch, J. B., and Martinson, H. G.. 1980. The roles of H1, the histone core and DNA length in the unfolding of nucleosomes at low ionic strength. Nucleic Acids Res. 8:4969–4987
   PubMedGoogle Scholar
• Chen, H., Li, B., and Workman, J. L.. 1994. A histone-binding protein, nucleoplasmin, stimulates transcription factor binding to nucleosomes and factor-induced nucleosome disassembly. EMBO J. 13:380–390
   PubMedGoogle Scholar
• Chirinos, M., Hernandez, F., and Palacian, E.. 1998. Repressive effect on oligonucleosome transcription of the core histone tail domains. Biochemistry 37:7251–7259
   PubMedGoogle Scholar
• Clark, D. J., and Felsenfeld, G.. 1992. A nucleosome core is transferred out of the path of a transcribing polymerase. Cell 71:11–22
   PubMedGoogle Scholar
• Davie, J. R.. 1998. Covalent modifications of histones: expression from chromatin templates. Curr. Opin. Genet. Dev. 8:173–178
   PubMed Web of Science ®Google Scholar
• Duband-Goulet, I., Carot, V., Ulyanov, A. V., Douc-Rasy, S., and Prunell, A.. 1992. Chromatin reconstitution on small DNA rings. IV. DNA supercoiling and nucleosome sequence preference. J. Mol. Biol. 224:981–1001
   PubMedGoogle Scholar
• Dumuis-Kervabon, A., Encontre, I., Etienne, G., Jauregui-Adell, J., Mery, J., Mesnier, D., and Parello, J.. 1986. A chromatin core particle obtained by selective cleavage of histones by clostripain. EMBO J. 5:1735–1742
   PubMed Web of Science ®Google Scholar
• Encontre, I., and Parello, J.. 1988. Chromatin core particle obtained by selective cleavage of histones H3 and H4 by clostripain. J. Mol. Biol. 202:673–676
   PubMedGoogle Scholar
• Fletcher, T. M., and Hansen, J. C.. 1995. Core histone tail domains mediate oligonucleosome folding and nucleosomal DNA organization through distinct molecular mechanisms. J. Biol. Chem. 270:25359–25362
   PubMed Web of Science ®Google Scholar
• Garcia-Ramirez, M., Rocchini, C., and Ausio, J.. 1995. Modulation of chromatin folding by histone acetylation. J. Biol. Chem. 270:17923–17928
   PubMed Web of Science ®Google Scholar
• Hamiche, A., Carot, V., Alilat, M., De Lucia, F., O'Donohue, M. F., Revet, B., and Prunell, A.. 1996. Interaction of the histone (H3-H4)2 tetramer of the nucleosome with positively supercoiled DNA minicircles: potential flipping of the protein from a left- to a right-handed superhelical form. Proc. Natl. Acad. Sci. USA 93:7588–7593
   PubMed Web of Science ®Google Scholar
• Hamiche, A., and Richard-Foy, H.. 1998. The switch in the helical handedness of the histone (H3-H4)2 tetramer within a nucleoprotein particle requires a reorientation of the H3-H3 interface. J. Biol. Chem. 273:9261–9269
   PubMedGoogle Scholar
• Hamiche, A., Schultz, P., Ramakrishnan, V., Oudet, P., and Prunell, A.. 1996. Linker histone-dependent DNA structure in linear mononucleosomes. J. Mol. Biol. 257:30–42
   PubMedGoogle Scholar
• Hartzog, G. A., and Winston, F.. 1997. Nucleosomes and transcription: recent lessons from genetics. Curr. Opin. Genet. Dev. 7:192–198
   PubMedGoogle Scholar
• Hirschhorn, J. N., Brown, S. A., Clark, C. D., and Winston, F.. 1992. Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev. 6:2288–2298
   PubMed Web of Science ®Google Scholar
• Jackson, V.. 1990. In vivo studies on the dynamics of histone-DNA interaction: evidence for nucleosome dissolution during replication and transcription and a low level of dissolution independent of both. Biochemistry 29:719–731
   PubMed Web of Science ®Google Scholar
• Krajewski, W. A., and Becker, P. B.. 1998. Reconstitution of hyperacetylated, DNase I-sensitive chromatin characterized by high conformational flexibility of nucleosomal DNA. Proc. Natl. Acad. Sci. USA 95:1540–1545
   PubMedGoogle Scholar
• Lee, M. S., and Garrard, W. T.. 1991. Transcription-induced nucleosome ‘splitting’: an underlying structure for DNase I sensitive chromatin. EMBO J. 10:607–615
   PubMedGoogle Scholar
• Lenfant, F., Mann, R. K., Thomsen, B., Ling, X., and Grunstein, M.. 1996. All four core histone N-termini contain sequences required for the repression of basal transcription in yeast. EMBO J. 15:3974–3985
   PubMedGoogle Scholar
• Ling, X., Harkness, T. A., Schultz, M. C., Fisher-Adams, G., and Grunstein, M.. 1996. Yeast histone H3 and H4 amino termini are important for nucleosome assembly in vivo and in vitro: redundant and position-independent functions in assembly but not in gene regulation. Genes Dev. 10:686–699
   PubMedGoogle Scholar
• Louters, L., and Chalkley, R.. 1985. Exchange of histones H1, H2A, and H2B in vivo. Biochemistry 24:3080–3085
   PubMedGoogle Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Lutter, L. C., Halvorson, H. R., and Calladine, C. R.. 1996. Topological measurement of protein-induced DNA bend angles. J. Mol. Biol. 261:620–633
   PubMedGoogle Scholar
• Lutter, L. C., Judis, L., and Paretti, R. F.. 1992. Effects of histone acetylation on chromatin topology in vivo. Mol. Cell. Biol. 12:5004–5014
   PubMed Web of Science ®Google Scholar
• Nightingale, K. P., Wellinger, R. E., Sogo, J. M., and Becker, P. B.. 1998. Histone acetylation facilitates RNA polymerase II transcription of the Drosophila hsp26 gene in chromatin. EMBO J. 17:2865–2876
   PubMed Web of Science ®Google Scholar
• Norton, V. G., Imai, B. S., Yau, P., and Bradbury, E. M.. 1989. Histone acetylation reduces nucleosome core particle linking number change. Cell 57:449–457
   PubMed Web of Science ®Google Scholar
• Norton, V. G., Marvin, K. W., Yau, P., and Bradbury, E. M.. 1990. Nucleosome linking number change controlled by acetylation of histones H3 and H4. J. Biol. Chem. 265:19848–19852
   PubMed Web of Science ®Google Scholar
• O'Neill, T. E., Roberge, M., and Bradbury, E. M.. 1992. Nucleosome arrays inhibit both initiation and elongation of transcripts by bacteriophage T7 RNA polymerase. J. Mol. Biol. 223:67–78
   PubMedGoogle Scholar
• O'Neill, T. E., Smith, J. G., and Bradbury, E. M.. 1993. Histone octamer dissociation is not required for transcript elongation through arrays of nucleosome cores by phage T7 RNA polymerase in vitro. Proc. Natl. Acad. Sci. USA 90:6203–6207
   PubMedGoogle Scholar
• Orphanides, G., Wu, W. H., Lane, W. S., Hampsey, M., and Reinberg, D.. 1999. The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature 400:284–288
   PubMed Web of Science ®Google Scholar
• Panyim, S., and Chalkley, R.. 1969. A new histone found only in mammalian tissues with little cell division. Biochem. Biophys. Res. Commun. 37:1042–1049
   PubMed Web of Science ®Google Scholar
• Prunell, A.. 1998. A topological approach to nucleosome structure and dynamics: the linking number paradox and other issues. Biophys. J. 74:2531–2544
   PubMedGoogle Scholar
• Reeve, J. N., Sandman, K., and Daniels, C. J.. 1997. Archaeal histones, nucleosomes, and transcription initiation. Cell 89:999–1002
   PubMedGoogle Scholar
• Ruiz-Carrillo, A., and Jorcano, J. L.. 1979. An octamer of core histones in solution: central role of the H3-H4 tetramer in the self-assembly. Biochemistry 18:760–768
   PubMedGoogle Scholar
• Sathyanarayana, U. G., Freeman, L. A., Lee, M. S., and Garrard, W. T.. 1999. RNA polymerase-specific nucleosome disruption by transcription in vivo. J. Biol. Chem. 274:16431–16436
   PubMedGoogle Scholar
• Schuster, T., Han, M., and Grunstein, M.. 1986. Yeast histone H2A and H2B amino termini have interchangeable functions. Cell 45:445–451
   PubMedGoogle Scholar
• Sivolob, A., De Lucia, F., Alilat, M., and Prunell, A.. 2000. Nucleosome dynamics. VI. Histone tail regulation of tetrasome chiral transition. A relaxation study of tetrasomes on DNA minicircles. J. Mol. Biol. 295:55–69
   PubMedGoogle Scholar
• Stein, A., Whitlock, J. P.Jr., and Bina, M.. 1979. Acidic polypeptides can assemble both histones and chromatin in vitro at physiological ionic strength. Proc. Natl. Acad. Sci. USA 76:5000–5004
   PubMed Web of Science ®Google Scholar
• Studitsky, V. M., Clark, D. J., and Felsenfeld, G.. 1994. A histone octamer can step around a transcribing polymerase without leaving the template. Cell 76:371–382
   PubMed Web of Science ®Google Scholar
• Tse, C., Sera, T., Wolffe, A. P., and Hansen, J. C.. 1998. Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol. Cell. Biol. 18:4629–4638
   PubMed Web of Science ®Google Scholar
• Uberbacher, E. C., Ramakrishnan, V., Olins, D. E., and Bunick, G. J.. 1983. Neutron scattering studies of nucleosome structure at low ionic strength. Biochemistry 22:4916–4923
   PubMed Web of Science ®Google Scholar
• Van Holde, K. E.. 1989. Chromatin. Springer-Verlag, New York, N.Y
   Google Scholar
• Vettese-Dadey, M., Grant, P. A., Hebbes, T. R., Crane-Robinson, C., Allis, C. D., and Workman, J. L.. 1996. Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro. EMBO J. 15:2508–2518
   PubMed Web of Science ®Google Scholar
• Walker, J., Chen, T. A., Sterner, R., Berger, M., Winston, F., and Allfrey, V. G.. 1990. Affinity chromatography of mammalian and yeast nucleosomes. Two modes of binding of transcriptionally active mammalian nucleosomes to organomercurial-agarose columns, and contrasting behavior of the active nucleosomes of yeast. J. Biol. Chem. 265:5736–5746
   PubMed Web of Science ®Google Scholar
• Walter, P. P., Owen-Hughes, T. A., Cote, J., and Workman, J. L.. 1995. Stimulation of transcription factor binding and histone displacement by nucleosome assembly protein 1 and nucleoplasmin requires disruption of the histone octamer. Mol. Cell. Biol. 15:6178–6187
   PubMedGoogle Scholar
• White, J. H., Gallo, R. M., and Bauer, W. R.. 1992. Closed circular DNA as a probe for protein-induced structural changes. Trends Biochem. Sci. 17:7–12
   PubMed Web of Science ®Google Scholar
• Wolffe, A. P., and Kurumizaka, H.. 1998. The nucleosome: a powerful regulator of transcription. Prog. Nucleic Acid Res. Mol. Biol. 61:379–422
   PubMed Web of Science ®Google Scholar
• Zivanovic, Y., Duband-Goulet, I., Schultz, P., Stofer, E., Oudet, P., and Prunell, A.. 1990. Chromatin reconstitution on small DNA rings. III. Histone H5 dependence of DNA supercoiling in the nucleosome. J. Mol. Biol. 214:479–495
   PubMed Web of Science ®Google Scholar
• Zivanovic, Y., Goulet, I., and Prunell, A.. 1986. Properties of supercoiled DNA in gel electrophoresis. The V-like dependence of mobility on topological constraint. DNA-matrix interactions. J. Mol. Biol. 192:645–660
   PubMedGoogle Scholar