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. 1990 Dec 11;18(23):7015–7024. doi: 10.1093/nar/18.23.7015

Ultrastructure of transcriptionally competent chromatin.

L Locklear Jr 1, J A Ridsdale 1, D P Bazett-Jones 1, J R Davie 1
PMCID: PMC332764  PMID: 2263461

Abstract

We have examined a salt-soluble, transcriptionally competent gene-enriched fraction of chicken erythrocyte chromatin and compared it to bulk chromatin using the unique microanalytical capabilities of Electron Spectroscopic Imaging (ESI). The salt-soluble fraction is enriched 48 fold in beta-globin gene sequences and is also enriched in histones that are post-synthetically modified, including acetylation and ubiquitination. Differences between the two fractions are also apparent in the distribution of the two major forms of nucleoprotein structures, including (1) particles which present a circular profile and possess protein and DNA content nearly identical to that of the canonical nucleosome and account for 89% of particles in the bulk fraction but account for only 66% of the particles in the competent fraction, and (2) u-shaped particles which possess about 20% less protein mass than particles of circular profile and are about 10x more prevalent in the transcriptionally competent fraction than in the bulk. Additionally, elongated particles with protein and DNA content similar to the u-shaped objects are also seen in the competent fraction.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Baer B. W., Rhodes D. Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes. Nature. 1983 Feb 10;301(5900):482–488. doi: 10.1038/301482a0. [DOI] [PubMed] [Google Scholar]
  2. Bazett-Jones D. P., Brown M. L. Electron microscopy reveals that transcription factor TFIIIA bends 5S DNA. Mol Cell Biol. 1989 Jan;9(1):336–341. doi: 10.1128/mcb.9.1.336. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bazett-Jones D. P., Locklear L., Rattner J. B. Electron spectroscopic imaging of DNA. J Ultrastruct Mol Struct Res. 1988 Apr;99(1):48–58. doi: 10.1016/0889-1605(88)90032-8. [DOI] [PubMed] [Google Scholar]
  4. Bazett-Jones D. P., Ottensmeyer F. P. DNA organization in nucleosomes. Can J Biochem. 1982 Mar;60(3):364–370. doi: 10.1139/o82-043. [DOI] [PubMed] [Google Scholar]
  5. Bazett-Jones D. P. Phosphorus imaging of the 7-S ribonucleoprotein particle. J Ultrastruct Mol Struct Res. 1988 Apr;99(1):59–69. doi: 10.1016/0889-1605(88)90033-x. [DOI] [PubMed] [Google Scholar]
  6. Burlingame R. W., Love W. E., Wang B. C., Hamlin R., Nguyen H. X., Moudrianakis E. N. Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3.3 A. Science. 1985 May 3;228(4699):546–553. doi: 10.1126/science.3983639. [DOI] [PubMed] [Google Scholar]
  7. Drew H. R., Calladine C. R. Sequence-specific positioning of core histones on an 860 base-pair DNA. Experiment and theory. J Mol Biol. 1987 May 5;195(1):143–173. doi: 10.1016/0022-2836(87)90333-0. [DOI] [PubMed] [Google Scholar]
  8. Finch J. T., Lutter L. C., Rhodes D., Brown R. S., Rushton B., Levitt M., Klug A. Structure of nucleosome core particles of chromatin. Nature. 1977 Sep 1;269(5623):29–36. doi: 10.1038/269029a0. [DOI] [PubMed] [Google Scholar]
  9. Graziano V., Gerchman S. E., Ramakrishnan V. Reconstitution of chromatin higher-order structure from histone H5 and depleted chromatin. J Mol Biol. 1988 Oct 20;203(4):997–1007. doi: 10.1016/0022-2836(88)90124-6. [DOI] [PubMed] [Google Scholar]
  10. Harauz G., Ottensmeyer F. P. Nucleosome reconstruction via phosphorus mapping. Science. 1984 Nov 23;226(4677):936–940. doi: 10.1126/science.6505674. [DOI] [PubMed] [Google Scholar]
  11. Kefalas P., Gray F. C., Allan J. Precise nucleosome positioning in the promoter of the chicken beta A globin gene. Nucleic Acids Res. 1988 Jan 25;16(2):501–517. doi: 10.1093/nar/16.2.501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Korn A. P., Spitnik-Elson P., Elson D., Ottensmeyer F. P. Specific visualization of ribosomal RNA in the intact ribosome by electron spectroscopic imaging. Eur J Cell Biol. 1983 Sep;31(2):334–340. [PubMed] [Google Scholar]
  13. Langmore J. P., Wooley J. C. Chromatin architecture: investigation of a subunit of chromatin by dark field electron microscopy. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2691–2695. doi: 10.1073/pnas.72.7.2691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lin R., Leone J. W., Cook R. G., Allis C. D. Antibodies specific to acetylated histones document the existence of deposition- and transcription-related histone acetylation in Tetrahymena. J Cell Biol. 1989 May;108(5):1577–1588. doi: 10.1083/jcb.108.5.1577. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. McGhee J. D., Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. doi: 10.1146/annurev.bi.49.070180.005343. [DOI] [PubMed] [Google Scholar]
  16. Nacheva G. A., Guschin D. Y., Preobrazhenskaya O. V., Karpov V. L., Ebralidse K. K., Mirzabekov A. D. Change in the pattern of histone binding to DNA upon transcriptional activation. Cell. 1989 Jul 14;58(1):27–36. doi: 10.1016/0092-8674(89)90399-1. [DOI] [PubMed] [Google Scholar]
  17. Norton V. G., Imai B. S., Yau P., Bradbury E. M. Histone acetylation reduces nucleosome core particle linking number change. Cell. 1989 May 5;57(3):449–457. doi: 10.1016/0092-8674(89)90920-3. [DOI] [PubMed] [Google Scholar]
  18. Oliva R., Bazett-Jones D. P., Locklear L., Dixon G. H. Histone hyperacetylation can induce unfolding of the nucleosome core particle. Nucleic Acids Res. 1990 May 11;18(9):2739–2747. doi: 10.1093/nar/18.9.2739. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Oliva R., Bazett-Jones D., Mezquita C., Dixon G. H. Factors affecting nucleosome disassembly by protamines in vitro. Histone hyperacetylation and chromatin structure, time dependence, and the size of the sperm nuclear proteins. J Biol Chem. 1987 Dec 15;262(35):17016–17025. [PubMed] [Google Scholar]
  20. Oudet P., Gross-Bellard M., Chambon P. Electron microscopic and biochemical evidence that chromatin structure is a repeating unit. Cell. 1975 Apr;4(4):281–300. doi: 10.1016/0092-8674(75)90149-x. [DOI] [PubMed] [Google Scholar]
  21. Perry C. A., Annunziato A. T. Influence of histone acetylation on the solubility, H1 content and DNase I sensitivity of newly assembled chromatin. Nucleic Acids Res. 1989 Jun 12;17(11):4275–4291. doi: 10.1093/nar/17.11.4275. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Pfeffer U., Ferrari N., Vidali G. Availability of hyperacetylated H4 histone in intact nucleosomes to specific antibodies. J Biol Chem. 1986 Feb 25;261(6):2496–2498. [PubMed] [Google Scholar]
  23. Richmond T. J., Finch J. T., Rushton B., Rhodes D., Klug A. Structure of the nucleosome core particle at 7 A resolution. Nature. 1984 Oct 11;311(5986):532–537. doi: 10.1038/311532a0. [DOI] [PubMed] [Google Scholar]
  24. Ridsdale J. A., Davie J. R. Chicken erythrocyte polynucleosomes which are soluble at physiological ionic strength and contain linker histones are highly enriched in beta-globin gene sequences. Nucleic Acids Res. 1987 Feb 11;15(3):1081–1096. doi: 10.1093/nar/15.3.1081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ridsdale J. A., Hendzel M. J., Delcuve G. P., Davie J. R. Histone acetylation alters the capacity of the H1 histones to condense transcriptionally active/competent chromatin. J Biol Chem. 1990 Mar 25;265(9):5150–5156. [PubMed] [Google Scholar]
  26. Ridsdale J. A., Rattner J. B., Davie J. R. Erythroid-specific gene chromatin has an altered association with linker histones. Nucleic Acids Res. 1988 Jul 11;16(13):5915–5926. doi: 10.1093/nar/16.13.5915. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Sewell B. T., Bouloukos C., von Holt C. Formaldehyde and glutaraldehyde in the fixation of chromatin for electron microscopy. J Microsc. 1984 Oct;136(Pt 1):103–112. doi: 10.1111/j.1365-2818.1984.tb02550.x. [DOI] [PubMed] [Google Scholar]
  28. Smith R. M., Rill R. L. Mobile histone tails in nucleosomes. Assignments of mobile segments and investigations of their role in chromatin folding. J Biol Chem. 1989 Jun 25;264(18):10574–10581. [PubMed] [Google Scholar]
  29. Sun Y. L., Xu Y. Z., Bellard M., Chambon P. Digestion of the chicken beta-globin gene chromatin with micrococcal nuclease reveals the presence of an altered nucleosomal array characterized by an atypical ladder of DNA fragments. EMBO J. 1986 Feb;5(2):293–300. doi: 10.1002/j.1460-2075.1986.tb04212.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Walker J., Chen T. A., Sterner R., Berger M., Winston F., Allfrey V. G. 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. 1990 Apr 5;265(10):5736–5746. [PubMed] [Google Scholar]
  31. Weintraub H., Worcel A., Alberts B. A model for chromatin based upon two symmetrically paired half-nucleosomes. Cell. 1976 Nov;9(3):409–417. doi: 10.1016/0092-8674(76)90085-4. [DOI] [PubMed] [Google Scholar]
  32. Woodcock C. L., Frado L. L., Wall J. S. Composition of native and reconstituted chromatin particles: direct mass determination by scanning transmission electron microscopy. Proc Natl Acad Sci U S A. 1980 Aug;77(8):4818–4822. doi: 10.1073/pnas.77.8.4818. [DOI] [PMC free article] [PubMed] [Google Scholar]

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