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. 1978 Jan;25(1):175–186. doi: 10.1128/jvi.25.1.175-186.1978

Comparison of nuclease digestion of polyoma virus nucleoprotein complex and mouse chromatin.

B A Ponder, F Crew, L V Crawford
PMCID: PMC353914  PMID: 202734

Abstract

We digested polyoma virus nucleoprotein complex, isolated from disrupted virions, with micrococcal nuclease and DNase I. The results were compared with digestions of chromatin from mouse nuclei. The nucleosome "core" structures were similar, but the spacing of the nucleosomes in the isolated polymoma nucleoprotein complexes was irregular, whereas in mouse chromatin it was regular. The average nucleosome repeat length in each case was 190 to 200 base pairs. This figure suggests that, unless there are substantial stretches of free DNA, the polyoma nucleoprotein complex contains about 26 nucleosomes. The commonly used method of preparing the nucleoprotein complex by disruption of virions at pH 10.2 may lead to significant damage to the structure. Such damage may be more clearly revealed by the susceptibility of the DNA to nuclease digestion than by the usual criteria of sedimentation velocity and buoyant density.

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Selected References

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  1. Axel R. Cleavage of DNA in nuclei and chromatin with staphylococcal nuclease. Biochemistry. 1975 Jul;14(13):2921–2925. doi: 10.1021/bi00684a020. [DOI] [PubMed] [Google Scholar]
  2. Axel R., Melchior W., Jr, Sollner-Webb B., Felsenfeld G. Specific sites of interaction between histones and DNA in chromatin. Proc Natl Acad Sci U S A. 1974 Oct;71(10):4101–4105. doi: 10.1073/pnas.71.10.4101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bellard M., Oudet P., Germond J. E., Chambon P. Subunit structure of simian-virus-40 minichromosome. Eur J Biochem. 1976 Nov 15;70(2):543–553. doi: 10.1111/j.1432-1033.1976.tb11046.x. [DOI] [PubMed] [Google Scholar]
  4. Bonner W. M., Laskey R. A. A film detection method for tritium-labelled proteins and nucleic acids in polyacrylamide gels. Eur J Biochem. 1974 Jul 1;46(1):83–88. doi: 10.1111/j.1432-1033.1974.tb03599.x. [DOI] [PubMed] [Google Scholar]
  5. Camerini-Otero R. D., Sollner-Webb B., Felsenfeld G. The organization of histones and DNA in chromatin: evidence for an arginine-rich histone kernel. Cell. 1976 Jul;8(3):333–347. doi: 10.1016/0092-8674(76)90145-8. [DOI] [PubMed] [Google Scholar]
  6. Christiansen G., Landers T., Griffith J., Berg P. Characterization of components released by alkali disruption of simian virus 40. J Virol. 1977 Mar;21(3):1079–1084. doi: 10.1128/jvi.21.3.1079-1084.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cremisi C., Pignatti P. F., Croissant O., Yaniv M. Chromatin-like structures in polyoma virus and simian virus 10 lytic cycle. J Virol. 1975 Jan;17(1):204–211. doi: 10.1128/jvi.17.1.204-211.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Finch J. T., Klug A. Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci U S A. 1976 Jun;73(6):1897–1901. doi: 10.1073/pnas.73.6.1897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Finch J. T., Noll M., Kornberg R. D. Electron microscopy of defined lengths of chromatin. Proc Natl Acad Sci U S A. 1975 Sep;72(9):3320–3322. doi: 10.1073/pnas.72.9.3320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Frearson P. M., Crawford L. V. Polyoma virus basic proteins. J Gen Virol. 1972 Feb;14(2):141–155. doi: 10.1099/0022-1317-14-2-141. [DOI] [PubMed] [Google Scholar]
  11. Fried M., Griffin B. E. Organization of the genomes of polyoma virus and SV40. Adv Cancer Res. 1977;24:67–113. doi: 10.1016/s0065-230x(08)61013-1. [DOI] [PubMed] [Google Scholar]
  12. Friedmann T., David D. Structural roles of polyoma virus proteins. J Virol. 1972 Oct;10(4):776–782. doi: 10.1128/jvi.10.4.776-782.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Germond J. E., Hirt B., Oudet P., Gross-Bellark M., Chambon P. Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc Natl Acad Sci U S A. 1975 May;72(5):1843–1847. doi: 10.1073/pnas.72.5.1843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Green M. H., Miller H. I., Hendler S. Isolation of a polyoma-nucleoprotein complex from infected mouse-cell cultures. Proc Natl Acad Sci U S A. 1971 May;68(5):1032–1036. doi: 10.1073/pnas.68.5.1032. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Griffith J. D. Chromatin structure: deduced from a minichromosome. Science. 1975 Mar 28;187(4182):1202–1203. doi: 10.1126/science.187.4182.1202. [DOI] [PubMed] [Google Scholar]
  16. Hewish D. R., Burgoyne L. A. Chromatin sub-structure. The digestion of chromatin DNA at regularly spaced sites by a nuclear deoxyribonuclease. Biochem Biophys Res Commun. 1973 May 15;52(2):504–510. doi: 10.1016/0006-291x(73)90740-7. [DOI] [PubMed] [Google Scholar]
  17. Holmes D. S., Bonner J. Preparation, molecular weight, base composition, and secondary structure of giant nuclear ribonucleic acid. Biochemistry. 1973 Jun 5;12(12):2330–2338. doi: 10.1021/bi00736a023. [DOI] [PubMed] [Google Scholar]
  18. Huang E. S., Estes M. K., Pagano J. S. Structure and function of the polypeptides in simian virus 40. I. Existence of subviral deoxynucleoprotein complexes. J Virol. 1972 Jun;9(6):923–929. doi: 10.1128/jvi.9.6.923-929.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Keller W. Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4876–4880. doi: 10.1073/pnas.72.12.4876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kornberg R. D. Chromatin structure: a repeating unit of histones and DNA. Science. 1974 May 24;184(4139):868–871. doi: 10.1126/science.184.4139.868. [DOI] [PubMed] [Google Scholar]
  21. Kornberg R. D., Thomas J. O. Chromatin structure; oligomers of the histones. Science. 1974 May 24;184(4139):865–868. doi: 10.1126/science.184.4139.865. [DOI] [PubMed] [Google Scholar]
  22. Lacy E., Axel R. Analysis of DNA of isolated chromatin subunits. Proc Natl Acad Sci U S A. 1975 Oct;72(10):3978–3982. doi: 10.1073/pnas.72.10.3978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Laskey R. A., Mills A. D. Quantitative film detection of 3H and 14C in polyacrylamide gels by fluorography. Eur J Biochem. 1975 Aug 15;56(2):335–341. doi: 10.1111/j.1432-1033.1975.tb02238.x. [DOI] [PubMed] [Google Scholar]
  24. Loening U. E. The fractionation of high-molecular-weight ribonucleic acid by polyacrylamide-gel electrophoresis. Biochem J. 1967 Jan;102(1):251–257. doi: 10.1042/bj1020251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lohr D., Corden J., Tatchell K., Kovacic R. T., Van Holde K. E. Comparative subunit structure of HeLa, yeast, and chicken erythrocyte chromatin. Proc Natl Acad Sci U S A. 1977 Jan;74(1):79–83. doi: 10.1073/pnas.74.1.79. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Louie A. J. The organization of proteins in polyoma and cellular chromatin. Cold Spring Harb Symp Quant Biol. 1975;39(Pt 1):259–266. doi: 10.1101/sqb.1974.039.01.034. [DOI] [PubMed] [Google Scholar]
  27. Maniatis T., Jeffrey A., van deSande H. Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry. 1975 Aug 26;14(17):3787–3794. doi: 10.1021/bi00688a010. [DOI] [PubMed] [Google Scholar]
  28. McCann P. P., Martin R. G. Nuclease digestion of the DNA-protein complex from simian virus 40 virions. Biochim Biophys Acta. 1975 Jul 7;395(3):280–283. doi: 10.1016/0005-2787(75)90198-7. [DOI] [PubMed] [Google Scholar]
  29. McMillen J., Consigli R. A. Characterization of polyoma DNA-protein complexes. I. Electrophoretic identification of the proteins in a nucleoprotein complex isolated from polyoma-infected cells. J Virol. 1974 Dec;14(6):1326–1336. doi: 10.1128/jvi.14.6.1326-1336.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Meinke W., Hall M. R., Goldstein D. A. Proteins in intracellular simian virus 40 nucleoportein complexes: comparison with simian virus 40 core proteins. J Virol. 1975 Mar;15(3):439–448. doi: 10.1128/jvi.15.3.439-448.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Morris N. R. A comparison of the structure of chicken erythrocyte and chicken liver chromatin. Cell. 1976 Dec;9(4 Pt 1):627–632. doi: 10.1016/0092-8674(76)90045-3. [DOI] [PubMed] [Google Scholar]
  32. Morris N. R. Nucleosome structure in Aspergillus nidulans. Cell. 1976 Jul;8(3):357–363. doi: 10.1016/0092-8674(76)90147-1. [DOI] [PubMed] [Google Scholar]
  33. Noll M. Internal structure of the chromatin subunit. Nucleic Acids Res. 1974 Nov;1(11):1573–1578. doi: 10.1093/nar/1.11.1573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Noll M., Kornberg R. D. Action of micrococcal nuclease on chromatin and the location of histone H1. J Mol Biol. 1977 Jan 25;109(3):393–404. doi: 10.1016/s0022-2836(77)80019-3. [DOI] [PubMed] [Google Scholar]
  35. Noll M. Subunit structure of chromatin. Nature. 1974 Sep 20;251(5472):249–251. doi: 10.1038/251249a0. [DOI] [PubMed] [Google Scholar]
  36. Olins A. L., Olins D. E. Spheroid chromatin units (v bodies). Science. 1974 Jan 25;183(4122):330–332. doi: 10.1126/science.183.4122.330. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. Perry J. L., To C. M., Consigli R. A. Alkaline degradation of polyoma virus. J Gen Virol. 1969 Apr;4(3):403–411. doi: 10.1099/0022-1317-4-3-403. [DOI] [PubMed] [Google Scholar]
  39. Polisky B., McCarthy B. Location of histones on simian virus 40 DNA. Proc Natl Acad Sci U S A. 1975 Aug;72(8):2895–2899. doi: 10.1073/pnas.72.8.2895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Ponder B. A., Crawford L. V. The arrangement of nucleosomes in nucleoprotein complexes from polyoma virus and SV40. Cell. 1977 May;11(1):35–49. doi: 10.1016/0092-8674(77)90315-4. [DOI] [PubMed] [Google Scholar]
  41. Robberson D. L., Fried M. Sequence arrangements in clonal isolates of polyoma defective DNA. Proc Natl Acad Sci U S A. 1974 Sep;71(9):3497–3501. doi: 10.1073/pnas.71.9.3497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Schaffhausen B. S., Benjamin T. L. Deficiency in histone acetylation in nontransforming host range mutants of polyoma virus. Proc Natl Acad Sci U S A. 1976 Apr;73(4):1092–1096. doi: 10.1073/pnas.73.4.1092. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Shaw B. R., Herman T. M., Kovacic R. T., Beaudreau G. S., Van Holde K. E. Analysis of subunit organization in chicken erythrocyte chromatin. Proc Natl Acad Sci U S A. 1976 Feb;73(2):505–509. doi: 10.1073/pnas.73.2.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Sollner-Webb B., Felsenfeld G. A comparison of the digestion of nuclei and chromatin by staphylococcal nuclease. Biochemistry. 1975 Jul;14(13):2915–2920. doi: 10.1021/bi00684a019. [DOI] [PubMed] [Google Scholar]
  45. Staynov D. Z., Pinder J. C., Gratzer W. B. Molecular weight determination of nucleic acids by gel electrophoresis in non-aqueous solution. Nat New Biol. 1972 Jan 26;235(56):108–110. doi: 10.1038/newbio235108a0. [DOI] [PubMed] [Google Scholar]
  46. Varshavsky A. J., Bakayev V. V., Chumackov P. M., Georgiev G. P. Minichromosome of simian virus 40: presence of histone HI. Nucleic Acids Res. 1976 Aug;3(8):2101–2113. doi: 10.1093/nar/3.8.2101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Ward S., Wilson D. L., Gilliam J. J. Methods for fractionation and scintillation counting of radioisotope-labeled polyacrylamide gels. Anal Biochem. 1970 Nov;38(1):90–97. doi: 10.1016/0003-2697(70)90158-2. [DOI] [PubMed] [Google Scholar]

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