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. 1983 Jun 25;11(12):4035–4047. doi: 10.1093/nar/11.12.4035

A destabilized DNA conformation associated with tightly bound nuclear proteins in active genes of rat myoblast.

S A Leibovitch, M P Leibovitch, J Hillion, J Kruh, J Harel
PMCID: PMC326023  PMID: 6306573

Abstract

Purified nuclei from tissue cultured myoblasts were disrupted and centrifuged to equilibrium in a sarcosyl-caesium chloride gradient. A small portion (1.3% - 1.9%) of the non histone proteins (NHP) were banded with DNA in a high density region of the gradient. The DNA tightly bound to proteins representing about 0.6% of the total nuclear DNA was degraded after treating cell nuclei with S1 nuclease or DNAse I but resisted to mild micrococcal nuclease digestion. A large portion of the DNA sequences complementary to homologous RNA was concentrated in this DNA-proteins fraction. These finding suggest that a subset of NHP strongly associated to the active DNA regions play a role in the destabilisation of the double helical DNA during transcriptional processes.

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Selected References

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

  1. Been M. D., Champoux J. J. Breakage of single-stranded DNA by rat liver nicking-closing enzyme with the formation of a DNA-enzyme complex. Nucleic Acids Res. 1980 Dec 20;8(24):6129–6142. doi: 10.1093/nar/8.24.6129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bellard M., Gannon F., Chambon P. Nucleosome structure III: the structure and transcriptional activity of the chromatin containing the ovalbumin and globin genes in chick oviduct nuclei. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):779–791. doi: 10.1101/sqb.1978.042.01.078. [DOI] [PubMed] [Google Scholar]
  3. Berezney R., Coffey D. S. Nuclear protein matrix: association with newly synthesized DNA. Science. 1975 Jul 25;189(4199):291–293. doi: 10.1126/science.1145202. [DOI] [PubMed] [Google Scholar]
  4. Frenster J. H. Selective control of DNA helix openings during gene regulation. Cancer Res. 1976 Sep;36(9 Pt 2):3394–3398. [PubMed] [Google Scholar]
  5. Garel A., Axel R. Selective digestion of transcriptionally active ovalbumin genes from oviduct nuclei. Proc Natl Acad Sci U S A. 1976 Nov;73(11):3966–3970. doi: 10.1073/pnas.73.11.3966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Gould H. J., Maryanka D., Fey S. J., Cowling G. J., Allan J. The assay of globin gene transcription in reconstituted chromatin. Methods Cell Biol. 1978;19:387–422. doi: 10.1016/s0091-679x(08)60038-2. [DOI] [PubMed] [Google Scholar]
  7. Hanania N., Shaool D., Harel J. Isolation of a mouse DNA fraction which encodes more informational than non informational RNA sequences. Mol Biol Rep. 1982 Mar 31;8(2):91–96. doi: 10.1007/BF00778510. [DOI] [PubMed] [Google Scholar]
  8. James G. T., Yeoman L. C., Matsui S. i., Goldberg A. H., Busch H. Isolation and characterization of nonhistone chromosomal protein C-14 which stimulates RNA synthesis. Biochemistry. 1977 May 31;16(11):2384–2389. doi: 10.1021/bi00630a012. [DOI] [PubMed] [Google Scholar]
  9. Kafatos F. C., Jones C. W., Efstratiadis A. Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucleic Acids Res. 1979 Nov 24;7(6):1541–1552. doi: 10.1093/nar/7.6.1541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kitzis A., Leibovitch S. A., Leibovitch M. P., Tichonicky L., Harel J., Kruh J. The small chromatin fragments released by micrococcal nuclease from hepatoma tissue cultured cell nuclei are strongly enriched in coding DNA sequences and are related to an actively transcribed single-stranded DNA fraction. Biochim Biophys Acta. 1982 Apr 26;697(1):60–70. doi: 10.1016/0167-4781(82)90045-8. [DOI] [PubMed] [Google Scholar]
  11. Kuo M. T. Distribution of tightly bound proteins in the chicken ovalbumin gene region. Biochemistry. 1982 Jan 19;21(2):321–326. doi: 10.1021/bi00531a019. [DOI] [PubMed] [Google Scholar]
  12. Laemmli U. K., Cheng S. M., Adolph K. W., Paulson J. R., Brown J. A., Baumbach W. R. Metaphase chromosome structure: the role of nonhistone proteins. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 1):351–360. doi: 10.1101/sqb.1978.042.01.036. [DOI] [PubMed] [Google Scholar]
  13. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  14. Leibovitch M. P., Leibovitch S. A., Harel J., Kruh J. Changes in the frequency and diversity of messenger RNA populations in the course of myogenic differentiation. Eur J Biochem. 1979 Jul;97(2):321–326. doi: 10.1111/j.1432-1033.1979.tb13117.x. [DOI] [PubMed] [Google Scholar]
  15. Leibovitch M. P., Leibovitch S. A., Harel J., Kruh J. Effect of sodium butyrate on messenger RNA populations in myogenic cells in culture. Differentiation. 1982;22(2):106–112. doi: 10.1111/j.1432-0436.1982.tb01233.x. [DOI] [PubMed] [Google Scholar]
  16. Leibovitch M. P., Tichonicky L., Kruh J. Chromatin protein kinases and phosphoproteins during myoblast growth and differentiation. Biochem Biophys Res Commun. 1978 Mar 30;81(2):623–629. doi: 10.1016/0006-291x(78)91581-4. [DOI] [PubMed] [Google Scholar]
  17. Leibovitch S. A., Guillier M., Harel J. Accessibility of some regions of chromatin of leukemic chicken cells to single strand nuclease S1. Biochem Biophys Res Commun. 1981 Aug 14;101(3):719–726. doi: 10.1016/0006-291x(81)91810-6. [DOI] [PubMed] [Google Scholar]
  18. Leibovitch S. A., Harel J. Active DNA transcription sites released from the genome of normal embryonic chicken cells. Nucleic Acids Res. 1978 Mar;5(3):777–787. doi: 10.1093/nar/5.3.777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Leibovitch S. A., Leibovitch M. P., Kruh J., Harel J. Relationship between single-stranded DNA isolated from cultured muscular cells during differentiation and the transcription of messenger RNA. Eur J Biochem. 1979 Jul;97(2):327–333. doi: 10.1111/j.1432-1033.1979.tb13118.x. [DOI] [PubMed] [Google Scholar]
  20. Leibovitch S. A., Tapiero H., Harel J. Single-stranded DNA from oncornavirus-infected cells enriched in virus-specific DNA sequences. Proc Natl Acad Sci U S A. 1977 Sep;74(9):3720–3724. doi: 10.1073/pnas.74.9.3720. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Leibovitch S. A., Tichonicky L., Kruh J., Harel J. Single-strandedness of the majority of DNA sequences complementary to mRNA-coding sites isolated from rat hepatoma tissue cultured cells. Exp Cell Res. 1981 May;133(1):181–189. doi: 10.1016/0014-4827(81)90368-2. [DOI] [PubMed] [Google Scholar]
  22. Maniatis T., Jeffrey A., Kleid D. G. Nucleotide sequence of the rightward operator of phage lambda. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1184–1188. doi: 10.1073/pnas.72.3.1184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Minty A. J., Caravatti M., Robert B., Cohen A., Daubas P., Weydert A., Gros F., Buckingham M. E. Mouse actin messenger RNAs. Construction and characterization of a recombinant plasmid molecule containing a complementary DNA transcript of mouse alpha-actin mRNA. J Biol Chem. 1981 Jan 25;256(2):1008–1014. [PubMed] [Google Scholar]
  24. 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]
  25. Pardoll D. M., Vogelstein B., Coffey D. S. A fixed site of DNA replication in eucaryotic cells. Cell. 1980 Feb;19(2):527–536. doi: 10.1016/0092-8674(80)90527-9. [DOI] [PubMed] [Google Scholar]
  26. Patel G. L., Thompson P. E. Immunoreactive helix-destabilizing protein localized in transcriptionally active regions of Drosophila polytene chromosomes. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6749–6753. doi: 10.1073/pnas.77.11.6749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Razin S. V., Chernokhvostov V. V., Roodyn A. V., Zbarsky I. B., Georgiev G. P. Proteins tightly bound to DNA in the regions of DNA attachment to the skeletal structures of interphase nuclei and metaphase chromosomes. Cell. 1981 Nov;27(1 Pt 2):65–73. doi: 10.1016/0092-8674(81)90361-5. [DOI] [PubMed] [Google Scholar]
  28. Sargent T. D., Wu J. R., Sala-Trepat J. M., Wallace R. B., Reyes A. A., Bonner J. The rat serum albumin gene: analysis of cloned sequences. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3256–3260. doi: 10.1073/pnas.76.7.3256. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Tapiero H., Caneva R., Schildkraut C. L. Fractions of Chinese hamster DNA differing in their content of guanine+cytosine and evidence for the presence of single-stranded DNA. Biochim Biophys Acta. 1972 Jul 20;272(3):350–360. doi: 10.1016/0005-2787(72)90388-7. [DOI] [PubMed] [Google Scholar]
  30. Thomas J. O., Kornberg R. D. An octamer of histones in chromatin and free in solution. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2626–2630. doi: 10.1073/pnas.72.7.2626. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Thomas P. S. Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5201–5205. doi: 10.1073/pnas.77.9.5201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Weintraub H., Groudine M. Chromosomal subunits in active genes have an altered conformation. Science. 1976 Sep 3;193(4256):848–856. doi: 10.1126/science.948749. [DOI] [PubMed] [Google Scholar]

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