Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1976 Feb;3(2):299–314. doi: 10.1093/nar/3.2.299

Transcription of the nonrepeated fraction of "accessible" DNA in rat liver chromatin.

E A Arnold, K E Young
PMCID: PMC342902  PMID: 1257049

Abstract

The relationship between structure and function in eukaryotic chromatin has been studied in rat liver cells. To elucidate the functional significance of "accessible" DNA, the transcription of this DNA (prepared by titration of liver chromatin with poly-D-lysine) has been examined by RNA-DNA hybridization. The maximum extent to which nuclear RNA will hybridize to the nonrepeated fraction of "accessible" DNA has been measured and compared to the extent that whole chromatin DNA will hybridize. The results show that "accessible" DNA has the same number of sequences complementary to nuclear RNA as does total DNA. In addition DNA-DNA reassociation experiments indicate that there is only a small difference between the total unique sequence populations of "accessible" and total DNA. These results indicate that nonrepeated "accessible" DNA is not preferentially transcribed in the cell as is predicted by some models of chromatin structure.

Full text

PDF
299

Selected References

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

  1. Arnold E. A., Wahn U., Young K. E. Isolation and characterization of the DNA fraction of rat liver chromatin which binds polylysine. Nucleic Acids Res. 1975 May;2(5):667–681. doi: 10.1093/nar/2.5.667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arnold E. A., Young K. E. Heterogeneity of chromatin: fractionation of sonicated rat liver chromatin by partial precipitation with Mg2+. Arch Biochem Biophys. 1974 Sep;164(1):73–89. doi: 10.1016/0003-9861(74)90009-5. [DOI] [PubMed] [Google Scholar]
  3. Axel R., Cedar H., Felsenfeld G. Chromatin template activity and chromatin structure. Cold Spring Harb Symp Quant Biol. 1974;38:773–783. doi: 10.1101/sqb.1974.038.01.082. [DOI] [PubMed] [Google Scholar]
  4. Axel R., Cedar H., Felsenfield G. The structure of the globin genes in chromatin. Biochemistry. 1975 Jun 3;14(11):2489–2495. doi: 10.1021/bi00682a031. [DOI] [PubMed] [Google Scholar]
  5. Baldwin J. P., Boseley P. G., Bradbury E. M., Ibel K. The subunit structure of the eukaryotic chromosome. Nature. 1975 Jan 24;253(5489):245–249. doi: 10.1038/253245a0. [DOI] [PubMed] [Google Scholar]
  6. Baldwin J. P., Bradbury E. M., Butler-Browne G. S., Stephens R. M. Histone interactions with prokaryote DNA. FEBS Lett. 1973 Aug 15;34(2):133–136. doi: 10.1016/0014-5793(73)80774-4. [DOI] [PubMed] [Google Scholar]
  7. Billing R. J., Bonner J. The structure of chromatin as revealed by deoxyribonuclease digestion studies. Biochim Biophys Acta. 1972 Oct 27;281(3):453–462. doi: 10.1016/0005-2787(72)90462-5. [DOI] [PubMed] [Google Scholar]
  8. Britten R. J., Kohne D. E. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science. 1968 Aug 9;161(3841):529–540. doi: 10.1126/science.161.3841.529. [DOI] [PubMed] [Google Scholar]
  9. Clark R. J., Felsenfeld G. Structure of chromatin. Nat New Biol. 1971 Jan 27;229(4):101–106. doi: 10.1038/newbio229101a0. [DOI] [PubMed] [Google Scholar]
  10. Commerford S. L. Iodination of nucleic acids in vitro. Biochemistry. 1971 May 25;10(11):1993–2000. doi: 10.1021/bi00787a005. [DOI] [PubMed] [Google Scholar]
  11. Doenecke D., McCarthy B. J. The nature of protein association with chromatin. Biochemistry. 1975 Apr 8;14(7):1373–1378. doi: 10.1021/bi00678a005. [DOI] [PubMed] [Google Scholar]
  12. Elgin S. C., Weintraub H. Chromosomal proteins and chromatin structure. Annu Rev Biochem. 1975;44:725–774. doi: 10.1146/annurev.bi.44.070175.003453. [DOI] [PubMed] [Google Scholar]
  13. Grouse L., Chilton M. D., McCarthy B. J. Hybridization of ribonucleic acid with unique sequences of mouse deoxyribonucleic acid. Biochemistry. 1972 Feb 29;11(5):798–805. doi: 10.1021/bi00755a019. [DOI] [PubMed] [Google Scholar]
  14. Hyde J. E., Walker I. O. A model for chromatin sub-structure incorporating symmetry considerations of histone oligomers. Nucleic Acids Res. 1975 Mar;2(3):405–421. doi: 10.1093/nar/2.3.405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Itzhaki R. F. Accessible DNA in chromatin. Eur J Biochem. 1974 Aug 15;47(1):27–33. doi: 10.1111/j.1432-1033.1974.tb03664.x. [DOI] [PubMed] [Google Scholar]
  16. Itzhaki R. F., Cooper H. K. Similarity of chromatin from different tissues. J Mol Biol. 1973 Mar 25;75(1):119–128. doi: 10.1016/0022-2836(73)90533-0. [DOI] [PubMed] [Google Scholar]
  17. Itzhaki R. F. Studies on the accessibility of deoxyribonucleic acid in deoxyribonucleoprotein to cationic molecules. Biochem J. 1971 May;122(4):583–592. doi: 10.1042/bj1220583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kohne D. E. Isolation and characterization of bacterial ribosomal RNA cistrons. Biophys J. 1968 Oct;8(10):1104–1118. doi: 10.1016/S0006-3495(68)86542-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Leong J. A., Garapin A. C., Jackson N., Fanshier L., Levinson W., Bishop J. M. Virus-specific ribonucleic acid in cells producing rous sarcoma virus: detection and characterization. J Virol. 1972 Jun;9(6):891–902. doi: 10.1128/jvi.9.6.891-902.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Li H. J., Chang C. Polylysine binding to histone-bound regions in chromatin. Biochem Biophys Res Commun. 1972 May 26;47(4):883–887. doi: 10.1016/0006-291x(72)90575-x. [DOI] [PubMed] [Google Scholar]
  21. Marfey S. P., Li M. G. Relationship between tritiated poly-L-lysine binding and template activity of human chromosomes. Nature. 1974 Jun 7;249(457):559–560. doi: 10.1038/249559a0. [DOI] [PubMed] [Google Scholar]
  22. Noll M., Thomas J. O., Kornberg R. D. Preparation of native chromatin and damage caused by shearing. Science. 1975 Mar 28;187(4182):1203–1206. doi: 10.1126/science.187.4182.1203. [DOI] [PubMed] [Google Scholar]
  23. Oliver D., Chalkley R. Asymmetric distribution of histone on DNA: a model for nucleohistone primary structure. Biochemistry. 1974 Dec 3;13(25):5093–5098. doi: 10.1021/bi00722a006. [DOI] [PubMed] [Google Scholar]
  24. Orosz J. M., Wetmur J. G. In vitro iodination of DNA. Maximizing iodination while minimizing degradation; use of buoyant density shifts for DNA-DNA hybrid isolation. Biochemistry. 1974 Dec 31;13(27):5467–5473. doi: 10.1021/bi00724a003. [DOI] [PubMed] [Google Scholar]
  25. Reeck G. R., Simpson R. T., Sober H. A. Resolution of a spectrum of nucleoprotein species in sonicated chromatin. Proc Natl Acad Sci U S A. 1972 Aug;69(8):2317–2321. doi: 10.1073/pnas.69.8.2317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Simpson R. T. Interaction of a repotter molecule with chromatin. Evidence suggesting that the proteins of chromatin do not occupy the minor groove of deoxyribonucleic acid. Biochemistry. 1970 Nov 24;9(24):4814–4819. doi: 10.1021/bi00826a028. [DOI] [PubMed] [Google Scholar]
  27. Simpson R. T., Polacow I. Protein-DNA interactions in extended and condensed chromatin. Biochem Biophys Res Commun. 1973 Dec 19;55(4):1078–1084. doi: 10.1016/s0006-291x(73)80005-1. [DOI] [PubMed] [Google Scholar]
  28. Sutton W. D. A crude nuclease preparation suitable for use in DNA reassociation experiments. Biochim Biophys Acta. 1971 Jul 29;240(4):522–531. doi: 10.1016/0005-2787(71)90709-x. [DOI] [PubMed] [Google Scholar]
  29. Varshavsky A. J., Ilyin Y. V., Georgiev G. P. Very long stretches of free DNA in chromatin. Nature. 1974 Aug 16;250(467):602–606. doi: 10.1038/250602a0. [DOI] [PubMed] [Google Scholar]
  30. Wetmur J. G., Davidson N. Kinetics of renaturation of DNA. J Mol Biol. 1968 Feb 14;31(3):349–370. doi: 10.1016/0022-2836(68)90414-2. [DOI] [PubMed] [Google Scholar]
  31. Zimmerman S. B., Levin C. J. Do histones bind to a specific group of DNA sequences in chromatin? A test based on DNA ligase action on reconstituted chromatin. Biochem Biophys Res Commun. 1975 Jan 20;62(2):357–361. doi: 10.1016/s0006-291x(75)80146-x. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES