10
Views
23
CrossRef citations to date
0
Altmetric
Transcriptional Regulation

Nucleosomes Are Translationally Positioned on the Active Allele and Rotationally Positioned on the Inactive Allele of the HPRT Promoter

&
Pages 7682-7695 | Received 08 Jun 2001, Accepted 20 Aug 2001, Published online: 28 Mar 2023

REFERENCES

  • Becker, P. B., T. Tsukiyama, and C. Wu. 1994. Chromatin assembly extracts from Drosophila embryos. Methods Cell Biol. 44:207–223.
  • Belikov, S., B. Gelius, G. Almouzni, and O. Wrange. 2000. Hormone activation induces nucleosome positioning in vivo. EMBO J. 19:1023–1033.
  • Benezra, R., C. R. Cantor, and R. Axel. 1986. Nucleosomes are phased along the mouse beta-major globin gene in erythroid and nonerythroid cells. Cell 44:697–704.
  • Blomquist, P., S. Belikov, and O. Wrange. 1999. Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure. Nucleic Acids Res. 27:517–525.
  • Buckle, R., M. Balmer, A. Yenidunya, and J. Allan. 1991. The promoter and enhancer of the inactive chicken beta-globin gene contains precisely positioned nucleosomes. Nucleic Acids Res. 19:1219–1226.
  • Chen, C., M. C. Yang, and T. P. Yang. 2001. Evidence that silencing of the HPRT promoter by DNA methylation is mediated by critical CpG sites. J. Biol. Chem. 276:320–328.
  • Davey, C., S. Pennings, and J. Allan. 1997. CpG methylation remodels chromatin structure in vitro. J. Mol. Biol. 267:276–288.
  • Fedor, M. J., N. F. Lue, and R. D. Kornberg. 1988. Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J. Mol. Biol. 204:109–127.
  • Gartler, S. M., K. A. Dyer, and M. A. Goldman. 1992. Mammalian X chromosome inactivation 2, Academic Press, New York, N.Y
  • Gross, D. S., and W. T. Garrard. 1988. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57:159–197.
  • Hornstra, I. K., and T. P. Yang. 1994. High-resolution methylation analysis of the human hypoxanthine phosphoribosyltransferase gene 5′ region on the active and inactive X chromosomes: correlation with binding sites for transcription factors. Mol. Cell. Biol. 14:1419–1430.
  • Hornstra, I. K., and T. P. Yang. 1993. In vivo footprinting and genomic sequencing by ligation-mediated PCR. Anal. Biochem. 213:179–193.
  • Hornstra, I. K., and T. P. Yang. 1992. Multiple in vivo footprints are specific to the active allele of the X-linked human hypoxanthine phosphoribosyltransferase gene 5′ region: implications for X chromosome inactivation. Mol. Cell. Biol. 12:5345–5354.
  • Imbalzano, A. N., H. Kwon, M. R. Green, and R. E. Kingston. 1994. Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 370:481–485.
  • Kadonaga, J. T.. 1998. Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell 92:307–313.
  • Kim, S. H., J. C. Moores, D. David, J. G. Respess, D. J. Jolly, and T. Friedmann. 1986. The organization of the human HPRT gene. Nucleic Acids Res. 14:3103–3118.
  • Kontaraki, J., H. Chen, A. D. Riggs, and C. Bonifer. 2000. Chromatin fine structure profiles for a developmentally regulated gene: reorganization of the lysozyme locus before trans-activator binding and gene expression. Genes Dev. 14:2106–2122.
  • Kornberg, R. D., and Y. Lorch. 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285–294.
  • Kornberg, R. D., and L. Stryer. 1988. Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res. 16:6677–6690.
  • Krebs, J. E., and C. L. Peterson. 2000. Understanding “active” chromatin: a historical perspective of chromatin remodeling. Crit. Rev. Eukaryot. Gene Expr. 10:1–12.
  • Lee, H., and T. K. Archer. 1994. Nucleosome-mediated disruption of transcription factor-chromatin initiation complexes at the mouse mammary tumor virus long terminal repeat in vivo. Mol. Cell. Biol. 14:32–41.
  • Lee, M. S., and W. T. Garrard. 1991. Transcription-induced nucleosome 'splitting': an underlying structure for DNase I sensitive chromatin. EMBO J. 10:607–615.
  • Li, G., S. P. Chandler, A. P. Wolffe, and T. Hall. 1998. Architectural specificity in chromatin structure at the TATA box in vivo: nucleosome displacement upon β-phaseolin gene activation. Proc. Natl. Acad. Sci. USA 95:4772–4777.
  • Li, Q., and O. Wrange. 1995. Accessibility of a glucocorticoid response element in a nucleosome depends on its rotational positioning. Mol. Cell. Biol. 15:4375–4384.
  • Li, Q., O. Wrange, and P. Eriksson. 1997. The role of chromatin in transcriptional regulation. Int. J. Biochem. Cell Biol. 29:731–742.
  • Lin, D., and A. C. Chinault. 1988. Comparative study of DNase I sensitivity at the X-linked human HPRT locus. Somat. Cell Mol. Genet. 14:261–272.
  • Litt, M. D., R. S. Hansen, I. K. Hornstra, S. M. Gartler, and T. P. Yang. 1997. 5-Azadeoxycytidine-induced chromatin remodeling of the inactive X-linked HPRT gene promoter occurs prior to transcription factor binding and gene reactivation. J. Biol. Chem. 272:14921–14926.
  • Lorch, Y., J. W. LaPointe, and R. D. Kornberg. 1987. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell 49:203–210.
  • Lu, Q., L. L. Wallrath, and S. C. Elgin. 1995. The role of a positioned nucleosome at the Drosophila melanogaster hsp26 promoter. EMBO J. 14:4738–4746.
  • McPherson, C. E., E. Y. Shim, D. S. Friedman, and K. S. Zaret. 1993. An active tissue-specific enhancer and bound transcription factors existing in a precisely positioned nucleosomal array. Cell 75:387–398.
  • Noll, M.. 1974. Internal structure of the chromatin subunit. Nucleic Acids Res. 1:1573–1578.
  • Patel, P. I., P. E. Framson, C. T. Caskey, and A. C. Chinault. 1986. Fine structure of the human hypoxanthine phosphoribosyltransferase gene. Mol. Cell. Biol. 6:393–403.
  • Patel, S. A., D. M. Graunke, and R. O. Pieper. 1997. Aberrant silencing of the CpG island-containing human O6-methylguanine DNA methyltransferase gene is associated with the loss of nucleosome-like positioning. Mol. Cell. Biol. 17:5813–5822.
  • Pazin, M. J., P. Bhargava, E. P. Geiduschek, and J. T. Kadonaga. 1997. Nucleosome mobility and the maintenance of nucleosome positioning. Science 276:809–812.
  • Pazin, M. J., J. W. Hermann, and J. T. Kadonaga. 1998. Promoter structure and transcriptional activation with chromatin templates assembled in vitro. A single Gal4-VP16 dimer binds to chromatin or to DNA with comparable affinity. J. Biol. Chem. 273:34653–34660.
  • Pazin, M. J., R. T. Kamakaka, and J. T. Kadonaga. 1994. ATP-dependent nucleosome reconfiguration and transcriptional activation from preassembled chromatin templates. Science 266:2007–2011.
  • Pazin, M. J., P. L. Sheridan, K. Cannon, Z. Cao, J. G. Keck, J. T. Kadonaga, and K. A. Jones. 1996. NF-kappa B-mediated chromatin reconfiguration and transcriptional activation of the HIV-1 enhancer in vitro. Genes Dev. 10:37–49.
  • Pfeifer, G. P., and A. D. Riggs. 1991. Chromatin differences between active and inactive X chromosomes revealed by genomic footprinting of permeabilized cells using DNase I and ligation-mediated PCR. Genes Dev. 5:1102–1113.
  • Pina, B., D. Barettino, M. Truss, and M. Beato. 1990. Structural features of a regulatory nucleosome. J. Mol. Biol. 216:975–990.
  • Pina, B., U. Bruggemeier, and M. Beato. 1990. Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter. Cell 60:719–731.
  • Rincon Limas, D. E., F. Amaya Manzanares, M. L. Nino Rosales, Y. Yu, T. P. Yang, and P. I. Patel. 1995. Ubiquitous and neuronal DNA-binding proteins interact with a negative regulatory element of the human hypoxanthine phosphoribosyltransferase gene. Mol. Cell. Biol. 15:6561–6571.
  • Rincon Limas, D. E., D. A. Krueger, and P. I. Patel. 1991. Functional characterization of the human hypoxanthine phosphoribosyltransferase gene promoter: evidence for a negative regulatory element. Mol. Cell. Biol. 11:4157–4164.
  • Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
  • Sasaki, T., R. S. Hansen, and S. M. Gartler. 1992. Hemimethylation and hypersensitivity are early events in transcriptional reactivation of human inactive X-linked genes in a hamster × human somatic cell hybrid. Mol. Cell. Biol. 12:3819–3826.
  • Schild, C., F. X. Claret, W. Wahli, and A. P. Wolffe. 1993. A nucleosome-dependent static loop potentiates estrogen-regulated transcription from the Xenopus vitellogenin B1 promoter in vitro. EMBO J. 12:423–433.
  • Sewack, G. F., and U. Hansen. 1997. Nucleosome positioning and transcription-associated chromatin alterations on the human estrogen-responsive pS2 promoter. J. Biol. Chem. 272:31118–31129.
  • Shim, E. Y., C. Woodcock, and K. S. Zaret. 1998. Nucleosome positioning by the winged helix transcription factor HNF3. Genes Dev. 12:5–10.
  • Taylor, I. C., J. L. Workman, T. J. Schuetz, and R. E. Kingston. 1991. Facilitated binding of GAL4 and heat shock factor to nucleosomal templates: differential function of DNA-binding domains. Genes Dev. 5:1285–1298.
  • Tormanen, V. T., P. M. Swiderski, B. E. Kaplan, G. P. Pfeifer, and A. D. Riggs. 1992. Extension product capture improves genomic sequencing and DNase I footprinting by ligation-mediated PCR. Nucleic Acids Res. 20:5487–5488.
  • Travers, A., and H. Drew. 1997. DNA recognition and nucleosome organization. Biopolymers 44:423–433.
  • Truss, M., J. Bartsch, A. Schelbert, R. J. Hache, and M. Beato. 1995. Hormone induces binding of receptors and transcription factors to a rearranged nucleosome on the MMTV promoter in vivo. EMBO J. 14:1737–1751.
  • Truss, M., R. Candau, S. Chavez, and M. Beato. 1995. Transcriptional control by steroid hormones: the role of chromatin. Ciba Found. Symp. 191:7–17.
  • Venter, U., J. Svaren, J. Schmitz, A. Schmid, and W. Horz. 1994. A nucleosome precludes binding of the transcription factor Pho4 in vivo to a critical target site in the PHO5 promoter. EMBO J. 13:4848–4855.
  • Vettese-Dadey, M., P. Walter, H. Chen, L. J. Juan, and J. L. Workman. 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.
  • Widlak, P., R. B. Gaynor, and W. T. Garrard. 1997. In vitro chromatin assembly of the HIV-1 promoter. ATP-dependent polar repositioning of nucleosomes by Sp1 and NFkappaB. J. Biol. Chem. 272:17654–17661.
  • Wolf, S. F., and B. R. Migeon. 1985. Clusters of CpG dinucleotides implicated by nuclease hypersensitivity as control elements of housekeeping genes. Nature 314:467–469.
  • Wolffe, A. P.. 1992. New insights into chromatin function in transcriptional control. FASEB J. 6:3354–3361.
  • Wolffe, A. P.. 1994. Transcription: in tune with the histones. Cell 77:13–16.
  • Wong, J., Q. Li, B. Z. Levi, Y. B. Shi, and A. P. Wolffe. 1997. Structural and functional features of a specific nucleosome containing a recognition element for the thyroid hormone receptor. EMBO J. 16:7130–7145.
  • Workman, J. L., and R. E. Kingston. 1998. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:545–579.
  • Yang, T. P., and C. T. Caskey. 1987. Nuclease sensitivity of the mouse HPRT gene promoter region: differential sensitivity on the active and inactive X chromosomes. Mol. Cell. Biol. 7:2994–2998.
  • Yaniv, M., and S. Cereghini. 1986. Structure of transcriptionally active chromatin. CRC Crit. Rev. Biochem. 21:1–26.

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.