32
Views
53
CrossRef citations to date
0
Altmetric
Transcriptional Regulation

Effects of Histone Tail Domains on the Rate of Transcriptional Elongation through a Nucleosome

, , &
Pages 8866-8878 | Received 17 Jul 2000, Accepted 24 Aug 2000, Published online: 28 Mar 2023

REFERENCES

  • Anderson, J. D., and Widom, J.. 2000. Sequence- and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J. Mol. Biol. 296:979–987
  • 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
  • Ausio, J., and van Holde, K. E.. 1986. Histone hyperacetylation: its effects on nucleosome conformation and stability. Biochemistry 25:1421–1428
  • Bednar, J., Studitsky, V. M., Grigoryev, S. A., Felsenfeld, G., and Woodcock, C. L.. 1999. The nature of the nucleosomal barrier to transcription: direct observation of paused intermediates by electron cryomicroscopy. Mol. Cell. 4:377–386
  • Böhm, L., and Crane-Robinson, C.. 1984. Proteases as structural probes for chromatin: the domain structure of histones. Biosci. Rep. 4:365–386
  • Chirinos, M., Hernández, F., and Palacián, E.. 1998. Repressive effect on oligonucleosome transcription of the core histone tail domains. Biochemistry 37:7251–7259
  • Dong, F., Hansen, J. C., and van Holde, K. E.. 1990. DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequences in vitro. Proc. Natl. Acad. Sci. USA 87:5724–5728
  • 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
  • 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
  • Ericsson, C., Grossbach, U., Bjorkroth, B., and Daneholt, B.. 1990. Presence of histone H1 on an active balbiani ring gene. Cell 60:73–83
  • Feng, H.-P., Scherl, D. S., and Widom, J.. 1993. Lifetime of the histone octamer studied by continuous-flow quasielastic light scattering: test of a model for nucleosome transcription. Biochemistry 32:7824–7831
  • 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
  • Godde, J. S., Nakatani, Y., and Wolffe, A. P.. 1995. The amino-terminal tails of the core histones and the translational position of the TATA box determine TBP/TFIIA association with nucleosomal DNA. Nucleic Acids Res. 23:4557–4564
  • Grunstein, M.. 1997. Histone acetylation in chromatin structure and transcription. Nature 389:349–352
  • 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
  • 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
  • Kayne, P. S., Kim, U.-J., Han, M., Mullen, J. R., Yoshizaki, F., and Grunstein, M.. 1988. Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell 55:27–39
  • Kuo, M. H., and Allis, C. D.. 1998. Roles of histone acetyltransferases and deacetylases in gene regulation. Bioessays 20:615–626
  • 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
  • Lorch, Y., LaPointe, J. W., and Kornberg, R. D.. 1987. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell 49:203–210
  • Losa, R., and Brown, D. D.. 1987. A bacteriophage RNA polymerase transcribes in vitro through a nucleosome core without displacing it. Cell 50:801–808
  • Lowary, P. T., and Widom, J.. 1989. Higher order structure of Saccharomyces cerevisiae chromatin. Proc. Natl. Acad. Sci. USA 86:8266–8270
  • Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J.. 1997. Structure of the nucleosome core particle at 2.8Å resolution. Nature 389:251–260
  • Luger, K., Rechsteiner, T. J., Flaus, A. J., Waye, M. M. Y., and Richmond, T. J.. 1997. Characterization of nucleosome core particles containing histone proteins made in bacteria. J. Mol. Biol. 272:301–311
  • Luger, K., and Richmond, T. J.. 1998. DNA binding within the nucleosome core. Curr. Opin. Struct. Biol. 8:33–40
  • Luger, K., and Richmond, T. J.. 1998. The histone tails of the nucleosome. Curr. Opin. Genet. Dev. 8:140–146
  • Lutter, L. C.. 1989. Digestion of nucleosomes with deoxyribonucleases I and II. Methods Enzymol. 170:264–269
  • Lutter, L. C.. 1978. Kinetic analysis of deoxyribonuclease I cleavages in the nucleosome core: evidence for a DNA superhelix. J. Mol. Biol. 124:391–420
  • Nacheva, G. A., Guschin, D. Y., Preobrazhenskaya, O. V., Karpov, V. L., Ebralidse, K. K., and Mirzabekov, A. D.. 1989. Change in the pattern of histone binding to DNA upon transcriptional activation. Cell 58:27–36
  • Neubauer, B., and Horz, W.. 1989. Analysis of nucleosome positioning by in vitro reconstitution. Methods Enzymol. 170:630–644
  • Pereira, S. L., and Reeve, J. N.. 1998. Histones and nucleosomes in Archaea and Eukarya: a comparative analysis. Extremophiles 2:141–148
  • 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. 298:211–223
  • Protacio, R. U., Polach, K. J., and Widom, J.. 1997. Coupled enzymatic assays for the rate and mechanism of DNA site-exposure in a nucleosome. J. Mol. Biol. 274:708–721
  • Protacio, R. U., and Widom, J.. 1996. Nucleosome transcription studied in a real-time synchronous system: test of the lexosome model and direct determination of effects due to histone octamer. J. Mol. Biol. 256:458–472
  • Reeve, J. N., Sandman, K., and Daniels, C. J.. 1997. Archaeal histones, nucleosomes, and transcription initiation. Cell 89:999–1002
  • Schuster, T., Han, M., and Grunstein, M.. 1986. Yeast histone H2A and H2B amino termini have interchangeable functions. Cell 45:445–451
  • Shermoen, A. W., and O'Farrell, P. H.. 1992. Progression of the cell cycle through mitosis leads to abortion of nascent transcripts. Cell 67:303–310
  • Simpson, R. T., and Stafford, D. W.. 1983. Structural features of a phased nucleosome core particle. Proc. Natl. Acad. Sci. USA 80:51–55
  • Strahl, B. D., and Allis, C. D.. 2000. The language of covalent histone modifications. Nature 403:41–45
  • Struhl, K.. 1998. Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12:599–606
  • 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
  • Studitsky, V. M., Clark, D. J., and Felsenfeld, G.. 1995. Overcoming a nucleosomal barrier to transcription. Cell 83:19–27
  • Studitsky, V. M., Kassavetis, G. A., Geiduschek, E. P., and Felsenfeld, G.. 1997. Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase. Science 278:1960–1963
  • Tse, C., Sera, T., Wolffe, A., and Hansen, J.. 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
  • Turner, B. M.. 1998. Histone acetylation as an epigenetic determinant of long-term transcriptional competence. Cell Mol. Life Sci. 54:21–31
  • Ura, K., Kurumizaka, H., Dimitrov, S., Almouzni, G., and Wolffe, A. P.. 1997. Histone acetylation: influence on transcription, nucleosome mobility and positioning, and linker histone-dependent transcriptional repression. EMBO J. 16:2096–2107
  • 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
  • Vettese-Dadey, M., Walter, P., Chen, H., Juan, L.-J., and Workman, J. L.. 1994. Role of the histone amino termini in facilitated binding of a transcription factor, GAL4-AH, to nucleosome cores. Mol. Cell. Biol. 14:970–981
  • 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
  • Wallis, J. W., Rykowski, M., and Grunstein, M.. 1983. Yeast histone H2B containing large amino terminus deletions can function in vivo. Cell 35:711–719
  • Widom, J.. 1986. Physicochemical studies of the folding of the 100Å nucleosome filament into the 300Å filament. J. Mol. Biol. 190:411–424
  • Widom, J.. 1998. Structure, dynamics, and function of chromatin in vitro. Annu. Rev. Biophys. Biomol. Struct. 27:285–327
  • Wolffe, A.. Chromatin structure and function, 3rd ed. Academic Press, San Diego, Calif
  • Wolffe, A. P., and Hayes, J. J.. 1998. 1999. Chromatin disruption and modification. Nucleic Acids Res. 27:711–720
  • Workman, J. L., and Kingston, R. E.. 1998. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:545–579

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.