Skip to main content
NCBI home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1987 May;7(5):1612–1622. doi: 10.1128/mcb.7.5.1612

DNA sequence-directed nucleosome reconstitution on 5S RNA genes of Xenopus laevis.

J M Gottesfeld
PMCID: PMC365260  PMID: 3600640

Abstract

Nucleosomes were reconstituted in vitro with several singly end-labeled restriction fragments derived from a cloned somatic-type 5S RNA gene of Xenopus laevis and purified nucleosome core particles from Xenopus cultured cells or chicken erythrocytes. Nucleosome locations were determined by digestion of the reconstitutes with exonuclease III and DNase I and were the same for all fragments investigated, extending from 20 base pairs (bp) within the 5S gene to 80 bp beyond the 3' end of the gene. Both core particles and crude nuclear extracts gave equivalent results, suggesting that no factors other than the core histones are responsible for recognition of DNA sequence during reconstitution. The histone octamer and the 5S gene-specific transcription factor TFIIIA both bind to the same region and face of 5S DNA, and nucleosome reconstitution on the 5S gene excluded binding of TFIIIA. The helical repeat of somatic-type 5S DNA in solution was measured by the band shift method and was 10.5 to 10.6 bp per turn over the region of the TFIIIA-binding site. The difference in helical repeat between DNA in solution and on the surface of the nucleosome (10.0-bp spacing between DNase I cutting sites) may explain the linking number paradox.

Full text

PDF
1612

Images in this article

1615Image
on p.1615
1616Image
on p.1616
1616Image
on p.1616
1617Image
on p.1617
1618Image
on p.1618
1619Image
on p.1619

Selected References

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

  1. Bogenhagen D. F., Wormington W. M., Brown D. D. Stable transcription complexes of Xenopus 5S RNA genes: a means to maintain the differentiated state. Cell. 1982 Feb;28(2):413–421. doi: 10.1016/0092-8674(82)90359-2. [DOI] [PubMed] [Google Scholar]
  2. Böck H., Abler S., Zhang X. Y., Fritton H., Igo-Kemenes T. Positioning of nucleosomes in satellite I-containing chromatin of rat liver. J Mol Biol. 1984 Jun 15;176(1):131–154. doi: 10.1016/0022-2836(84)90385-1. [DOI] [PubMed] [Google Scholar]
  3. Chao M. V., Gralla J., Martinson H. G. DNA sequence directs placement of histone cores on restriction fragments during nucleosome formation. Biochemistry. 1979 Mar 20;18(6):1068–1074. doi: 10.1021/bi00573a021. [DOI] [PubMed] [Google Scholar]
  4. Crick F. H. Linking numbers and nucleosomes. Proc Natl Acad Sci U S A. 1976 Aug;73(8):2639–2643. doi: 10.1073/pnas.73.8.2639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dickerson R. E. Base sequence and helix structure variation in B and A DNA. J Mol Biol. 1983 May 25;166(3):419–441. doi: 10.1016/s0022-2836(83)80093-x. [DOI] [PubMed] [Google Scholar]
  6. Elgin S. C. DNAase I-hypersensitive sites of chromatin. Cell. 1981 Dec;27(3 Pt 2):413–415. doi: 10.1016/0092-8674(81)90381-0. [DOI] [PubMed] [Google Scholar]
  7. Emerson B. M., Lewis C. D., Felsenfeld G. Interaction of specific nuclear factors with the nuclease-hypersensitive region of the chicken adult beta-globin gene: nature of the binding domain. Cell. 1985 May;41(1):21–30. doi: 10.1016/0092-8674(85)90057-1. [DOI] [PubMed] [Google Scholar]
  8. Engelke D. R., Ng S. Y., Shastry B. S., Roeder R. G. Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes. Cell. 1980 Mar;19(3):717–728. doi: 10.1016/s0092-8674(80)80048-1. [DOI] [PubMed] [Google Scholar]
  9. Gottesfeld J. M., Bloomer L. S. Nonrandom alignment of nucleosomes on 5S RNA genes of X. laevis. Cell. 1980 Oct;21(3):751–760. doi: 10.1016/0092-8674(80)90438-9. [DOI] [PubMed] [Google Scholar]
  10. Gottesfeld J., Bloomer L. S. Assembly of transcriptionally active 5S RNA gene chromatin in vitro. Cell. 1982 Apr;28(4):781–791. doi: 10.1016/0092-8674(82)90057-5. [DOI] [PubMed] [Google Scholar]
  11. Klug A., Lutter L. C. The helical periodicity of DNA on the nucleosome. Nucleic Acids Res. 1981 Sep 11;9(17):4267–4283. doi: 10.1093/nar/9.17.4267. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Klug A., Rhodes D., Smith J., Finch J. T., Thomas J. O. A low resolution structure for the histone core of the nucleosome. Nature. 1980 Oct 9;287(5782):509–516. doi: 10.1038/287509a0. [DOI] [PubMed] [Google Scholar]
  13. Lutter L. C. Kinetic analysis of deoxyribonuclease I cleavages in the nucleosome core: evidence for a DNA superhelix. J Mol Biol. 1978 Sep 15;124(2):391–420. doi: 10.1016/0022-2836(78)90306-6. [DOI] [PubMed] [Google Scholar]
  14. Lutter L. C. Precise location of DNase I cutting sites in the nucleosome core determined by high resolution gel electrophoresis. Nucleic Acids Res. 1979 Jan;6(1):41–56. doi: 10.1093/nar/6.1.41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  16. McCall M., Brown T., Hunter W. N., Kennard O. The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA. Nature. 1986 Aug 14;322(6080):661–664. doi: 10.1038/322661a0. [DOI] [PubMed] [Google Scholar]
  17. Mengeritsky G., Trifonov E. N. Nucleotide sequence-directed mapping of the nucleosomes. Nucleic Acids Res. 1983 Jun 11;11(11):3833–3851. doi: 10.1093/nar/11.11.3833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Miller J., McLachlan A. D., Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun;4(6):1609–1614. doi: 10.1002/j.1460-2075.1985.tb03825.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Peck L. J., Wang J. C. Sequence dependence of the helical repeat of DNA in solution. Nature. 1981 Jul 23;292(5821):375–378. doi: 10.1038/292375a0. [DOI] [PubMed] [Google Scholar]
  20. Pelham H. R., Brown D. D. A specific transcription factor that can bind either the 5S RNA gene or 5S RNA. Proc Natl Acad Sci U S A. 1980 Jul;77(7):4170–4174. doi: 10.1073/pnas.77.7.4170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Peterson R. C., Doering J. L., Brown D. D. Characterization of two xenopus somatic 5S DNAs and one minor oocyte-specific 5S DNA. Cell. 1980 May;20(1):131–141. doi: 10.1016/0092-8674(80)90241-x. [DOI] [PubMed] [Google Scholar]
  22. Prunell A., Kornberg R. D., Lutter L., Klug A., Levitt M., Crick F. H. Periodicity of deoxyribonuclease I digestion of chromatin. Science. 1979 May 25;204(4395):855–858. doi: 10.1126/science.441739. [DOI] [PubMed] [Google Scholar]
  23. Prunell A., Kornberg R. D. Relation of nucleosomes to DNA sequences. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 1):103–108. doi: 10.1101/sqb.1978.042.01.011. [DOI] [PubMed] [Google Scholar]
  24. Ramsay N., Felsenfeld G., Rushton B. M., McGhee J. D. A 145-base pair DNA sequence that positions itself precisely and asymmetrically on the nucleosome core. EMBO J. 1984 Nov;3(11):2605–2611. doi: 10.1002/j.1460-2075.1984.tb02181.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Reynolds W. F., Gottesfeld J. M. 5S rRNA gene transcription factor IIIA alters the helical configuration of DNA. Proc Natl Acad Sci U S A. 1983 Apr;80(7):1862–1866. doi: 10.1073/pnas.80.7.1862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Rhodes D., Klug A. An underlying repeat in some transcriptional control sequences corresponding to half a double helical turn of DNA. Cell. 1986 Jul 4;46(1):123–132. doi: 10.1016/0092-8674(86)90866-4. [DOI] [PubMed] [Google Scholar]
  27. Rhodes D., Klug A. Helical periodicity of DNA determined by enzyme digestion. Nature. 1980 Aug 7;286(5773):573–578. doi: 10.1038/286573a0. [DOI] [PubMed] [Google Scholar]
  28. Rhodes D. Structural analysis of a triple complex between the histone octamer, a Xenopus gene for 5S RNA and transcription factor IIIA. EMBO J. 1985 Dec 16;4(13A):3473–3482. doi: 10.1002/j.1460-2075.1985.tb04106.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. 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]
  30. Sakonju S., Bogenhagen D. F., Brown D. D. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region. Cell. 1980 Jan;19(1):13–25. doi: 10.1016/0092-8674(80)90384-0. [DOI] [PubMed] [Google Scholar]
  31. Sakonju S., Brown D. D. Contact points between a positive transcription factor and the Xenopus 5S RNA gene. Cell. 1982 Dec;31(2 Pt 1):395–405. doi: 10.1016/0092-8674(82)90133-7. [DOI] [PubMed] [Google Scholar]
  32. Saragosti S., Moyne G., Yaniv M. Absence of nucleosomes in a fraction of SV40 chromatin between the origin of replication and the region coding for the late leader RNA. Cell. 1980 May;20(1):65–73. doi: 10.1016/0092-8674(80)90235-4. [DOI] [PubMed] [Google Scholar]
  33. Simpson R. T., Stafford D. W. Structural features of a phased nucleosome core particle. Proc Natl Acad Sci U S A. 1983 Jan;80(1):51–55. doi: 10.1073/pnas.80.1.51. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Simpson R. T., Thoma F., Brubaker J. M. Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones: a model system for study of higher order structure. Cell. 1985 Oct;42(3):799–808. doi: 10.1016/0092-8674(85)90276-4. [DOI] [PubMed] [Google Scholar]
  35. Simpson R. T., Whitlock J. P. Mapping DNAase l-susceptible sites in nucleosomes labeled at the 5' ends. Cell. 1976 Oct;9(2):347–353. doi: 10.1016/0092-8674(76)90124-0. [DOI] [PubMed] [Google Scholar]
  36. Sollner-Webb B., Felsenfeld G. Pancreatic DNAase cleavage sites in nuclei. Cell. 1977 Mar;10(3):537–547. doi: 10.1016/0092-8674(77)90040-x. [DOI] [PubMed] [Google Scholar]
  37. Wang J. C. The path of DNA in the nucleosome. Cell. 1982 Jul;29(3):724–726. doi: 10.1016/0092-8674(82)90433-0. [DOI] [PubMed] [Google Scholar]
  38. Young D., Carroll D. Regular arrangement of nucleosomes on 5S rRNA genes in Xenopus laevis. Mol Cell Biol. 1983 Apr;3(4):720–730. doi: 10.1128/mcb.3.4.720. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Zhurkin V. B. Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine-pyrimidine and pyrimidine-purine dimers. FEBS Lett. 1983 Jul 25;158(2):293–297. doi: 10.1016/0014-5793(83)80598-5. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES