Skip to main content
SpringerLink
Log in

Mapping of Nucleosome Positions in Yeast

  • Protocol
Chromatin Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 119))

  • 2038 Accesses

Abstract

The structural and functional subunits of chromatin are nucleosome cores. In a nucleosome core 145 bp of DNA are coiled around the outer surface of an octamer of histone proteins which consists of a tetramer of 2(H3·H4) and two H2A·H2B dimers (1). DNA extending from the nucleosome core to the next nucleosome is called linker DNA. It varies in length from about 20 to 90 bp in different organisms or tissues or between individual nucleosomes. Histone H1 may be associated with linker DNA at the site where the DNA leaves the nucleosome. While core histones are well conserved and present in all eukaryotic organisms, H1 is most variable and may even be missing in some organisms such as yeast Saccharomyces cerevisiae. Nucleosomes are built from many different DNA sequences and may contain histone variants (subtypes) and modified histones (e.g., acetylated) which can affect their structural and dynamic properties (reviewed in ref. 2).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. (1997) Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251–260.

    Article  PubMed  CAS  Google Scholar 

  2. Wolffe, A. (1995) Chromatin. Academic Press, San Diego, CA.

    Google Scholar 

  3. Simpson, R. T. (1991) Nucleosome positioning: occurrence, mechanisms, and functional consequences. Prog. Nucleic Acid Res. Mol. Biol. 40, 143–184.

    Article  PubMed  CAS  Google Scholar 

  4. Thoma, F. (1992) Nucleosome positioning. Biochimica et Biophysica Acta 1130, 1–19.

    PubMed  CAS  Google Scholar 

  5. Thoma, F. (1996) Mapping of nucleosome positions. Methods Enzymol. 274, 197–214.

    Article  PubMed  CAS  Google Scholar 

  6. Bellard, M., Dretzen, G., Giangrande, A., and Ramain, P. (1989) Nuclease digestion of transcriptionally active chromatin. Methods Enzymol. 170, 317–346.

    Article  PubMed  CAS  Google Scholar 

  7. Noll, M. and Kornberg, R. D. (1977) Action of micrococcal nuclease on chromatin and the location of histone H1. J. Mol. Biol. 109, 393–404.

    Article  PubMed  CAS  Google Scholar 

  8. Thoma, F., Bergman, L. W., and Simpson, R. T. (1984) Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease sensitive regions. J. Mol. Biol. 177, 715–733.

    Article  PubMed  CAS  Google Scholar 

  9. Lutter, L. C. (1979) Precise location of DNaseI cutting sites in the nucleosome core determined by high resolution gel electrophoresis. Nucleic Acids. Res. 6, 41–55.

    Article  PubMed  CAS  Google Scholar 

  10. Cartwright, I. L. and Elgin, S. C. R. (1989) Nonenzymatic cleavage of chromatin. Methods Enzymol. 170, 359–369.

    Article  PubMed  CAS  Google Scholar 

  11. Wu, C. (1980) The 5′ends of Drosophila heat shock genes in chromatin are hypersensitive to DNaseI. Nature 286, 854–860.

    Article  PubMed  CAS  Google Scholar 

  12. Nedospasov, S. A. and Georgiev, G. P. (1980) Non-random cleavage of SV-40 DNA in the compact minichromosome and free in solution by micrococcal nuclease. Biochem. Biophys. Res. Commun. 92, 532–539.

    Article  PubMed  CAS  Google Scholar 

  13. Wu, C. (1989) Analysis of hypersensitive sites in chromatin. Methods Enzymol. 170, 269–289.

    Article  PubMed  CAS  Google Scholar 

  14. Nedospasov, S. A., Shakhov, A. N., and Georgiev, G. P. (1989) Analysis of nucleosome positioning by indirect end-labeling and molecular cloning. Methods Enzymol. 170, 408–420.

    Article  PubMed  CAS  Google Scholar 

  15. Thoma, F. and Simpson, R. T. (1985) Local protein-DNA interactions may determine nucleosome positions on yeast plasmids. Nature 315, 250–252.

    Article  PubMed  CAS  Google Scholar 

  16. Thoma, F. (1986) Protein-DNA interactions and nuclease sensitive regions determine nucleosome positions on yeast plasmid chromatin. J. Mol. Biol. 190, 177–190.

    Article  PubMed  CAS  Google Scholar 

  17. Losa, R., Omari, S., and Thoma, F. (1990) Poly(dA)′poly(dT) rich sequence are not sufficient to exclude nucleosome formation in a constitutive yeast promoter. Nucleic Acids Res. 18, 3495–3502.

    Article  PubMed  CAS  Google Scholar 

  18. Bernardi, F., Zatchej, M., and Thoma, F. (1992) Species specific protein-DNA interactions may determine the chromatin units of genes in S. cerevisiae and in S. pombe. EMBO J. 11, 1177–1185.

    PubMed  CAS  Google Scholar 

  19. Thoma, F. and Zatchej, M. (1988) Chromatin folding modulates nucleosome positioning in yeast minichromosomes. Cell 55, 945–953.

    Article  PubMed  CAS  Google Scholar 

  20. Tanaka, S., Halter, D., Livingstone-Zatchej, M., Reszel, B., and Thoma, F. (1994) Transcription through the yeast origin of replication ARS1 ends at the ABFI binding site and affects extrachromosomal maintenance of minichromosomes. Nucleic Acids Res. 22, 3904–3910.

    Article  PubMed  CAS  Google Scholar 

  21. Pederson, D. S., Venkatesan, M., Thoma, F., and Simpson, R. T. (1986) Isolation of an episomal yeast gene and replication origin as chromatin. Proc. Natl. Acad. Sci. USA 83, 7206–7210.

    Article  PubMed  CAS  Google Scholar 

  22. Lohr, D. (1984) Organization of the GAL1-GAL10 intergenic control region chromatin. Nucleic Acids Res. 12, 8457–8474.

    Article  PubMed  CAS  Google Scholar 

  23. Almer, A., Rudolph, H., Hinnen, A., and Hörz, W. (1986) Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 5, 2689–2696.

    PubMed  CAS  Google Scholar 

  24. Buttinelli, M., DiMauro, E. D., and Negri, R. (1993) Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo. Proc. Natl. Acad. Sci. USA 90, 9315–9319.

    Article  PubMed  CAS  Google Scholar 

  25. Tanaka, S., Livingstone-Zatchej, M., and Thoma, F. (1996) Chromatin structure of the yeast URA3 gene at high resolution provides insight into structure and positioning of nucleosomes in the chromosomal context. J. Mol. Biol. 257, 919–934.

    Article  PubMed  CAS  Google Scholar 

  26. Suter, B., Livingstone-Zatchej, M., and Thoma, F. (1997) Chromatin structure modulates DNA repair by photolyase in vivo. EMBO J. 16, 2150–2160.

    Article  PubMed  CAS  Google Scholar 

  27. Diffley, J. F. X. and Cocker, J. H. (1992) Protein DNA interactions at a yeast replication origin. Nature 357, 169–172.

    Article  PubMed  CAS  Google Scholar 

  28. Fedor, M. J., Lue, N. F., and Kornberg, R. D. (1988) Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J. Mol. Biol. 204, 109–127.

    Article  PubMed  CAS  Google Scholar 

  29. Cavalli, G. and Thoma, F. (1993) Chromatin transitions during activation and repression of galactose-regulated genes in yeast. EMBO J. 12, 4603–4613.

    PubMed  CAS  Google Scholar 

  30. Cavalli, G., Bachmann, D., and Thoma, F. (1996) Inactivation of topoisomerases affect transcription dependent chromatin transitions in rDNA but not in a gene transcribed by RNA-polymerase II. EMBO J. 15, 590–597.

    PubMed  CAS  Google Scholar 

  31. Almer, A. and Hörz, W. (1986) Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus. EMBO J. 5, 2681–2687.

    PubMed  CAS  Google Scholar 

  32. Bernardi, F., Koller, T., and Thoma, F. (1991) The ade6-gene of the fission yeast Schizosaccharomyces pombe has the same chromatin structure in the chromosome and in plasmids. Yeast 7, 547–558.

    Article  PubMed  CAS  Google Scholar 

  33. Sherman, F., Fink, G. R., and Hicks, J. B. (1986) Laboratory Course Manual for Methods in Yeast Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institut für Zellbiologie, Eidgenossische Technische Hochschule, Hönggerberg, Zürich, Switzerland

    Magdalena Livingstone-Zatchej & Fritz Thoma

Authors
  1. Magdalena Livingstone-Zatchej
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fritz Thoma
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Adolf-Butenandt-Institut-Molekularbiologie, Ludwig-Maximilians-Universität, München, Germany

    Peter B. Becker

Rights and permissions

Reprints and permissions

Copyright information

© 1999 Humana Press Inc.

About this protocol

Cite this protocol

Livingstone-Zatchej, M., Thoma, F. (1999). Mapping of Nucleosome Positions in Yeast. In: Becker, P.B. (eds) Chromatin Protocols. Methods in Molecular Biology™, vol 119. Humana Press. https://doi.org/10.1385/1-59259-681-9:363

Download citation

  • DOI: https://doi.org/10.1385/1-59259-681-9:363

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-665-9

  • Online ISBN: 978-1-59259-681-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation