Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 May 25;21(10):2331–2338. doi: 10.1093/nar/21.10.2331

Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae.

R Dammann 1, R Lucchini 1, T Koller 1, J M Sogo 1
PMCID: PMC309528  PMID: 8506130

Abstract

The chromatin structure of yeast ribosomal DNA was analyzed in vivo by crosslinking intact cells with psoralen. We found that in exponentially growing cultures the regions coding for the 35S rRNA precursor fall into two distinct classes. One class was highly accessible to psoralen and associated with nascent RNAs, characteristic for transcriptionally active rRNA genes devoid of nucleosomes, whereas the other class showed a crosslinking pattern indistinguishable from that of bulk chromatin and was interpreted to represent the inactive rRNA gene copies. By crosslinking the same strain growing in complex or minimal medium, we have shown that yeast cells can modulate the proportion of active (non-nucleosomal) and inactive (nucleosomal) rRNA gene copies in response to variations in environmental conditions which suggests that yeast can regulate rRNA synthesis by varying the number of active gene copies, in contrast to the vertebrate cells studied so far. Whereas intergenic spacers flanking inactive rRNA gene copies are packaged in a regular nucleosomal array, spacers flanking active genes show an unusual crosslinking pattern suggesting a complex interaction of regulatory factors and histones with DNA.

Full text

PDF

Images in this article

2333Image
on p.2333
2333Image
on p.2333
2334Image
on p.2334
2335Image
on p.2335
2336Image
on p.2336
2336Image
on p.2336

Selected References

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

  1. Bell S. P., Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature. 1992 May 14;357(6374):128–134. doi: 10.1038/357128a0. [DOI] [PubMed] [Google Scholar]
  2. Bernardi F., Koller T., Thoma F. The ade6 gene of the fission yeast Schizosaccharomyces pombe has the same chromatin structure in the chromosome and in plasmids. Yeast. 1991 Aug-Sep;7(6):547–558. doi: 10.1002/yea.320070603. [DOI] [PubMed] [Google Scholar]
  3. Conconi A., Losa R., Koller T., Sogo J. M. Psoralen-crosslinking of soluble and of H1-depleted soluble rat liver chromatin. J Mol Biol. 1984 Oct 5;178(4):920–928. doi: 10.1016/0022-2836(84)90319-x. [DOI] [PubMed] [Google Scholar]
  4. Conconi A., Sogo J. M., Ryan C. A. Ribosomal gene clusters are uniquely proportioned between open and closed chromatin structures in both tomato leaf cells and exponentially growing suspension cultures. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5256–5260. doi: 10.1073/pnas.89.12.5256. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Conconi A., Widmer R. M., Koller T., Sogo J. M. Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell. 1989 Jun 2;57(5):753–761. doi: 10.1016/0092-8674(89)90790-3. [DOI] [PubMed] [Google Scholar]
  6. Elion E. A., Warner J. R. An RNA polymerase I enhancer in Saccharomyces cerevisiae. Mol Cell Biol. 1986 Jun;6(6):2089–2097. doi: 10.1128/mcb.6.6.2089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Elion E. A., Warner J. R. The major promoter element of rRNA transcription in yeast lies 2 kb upstream. Cell. 1984 Dec;39(3 Pt 2):663–673. doi: 10.1016/0092-8674(84)90473-2. [DOI] [PubMed] [Google Scholar]
  8. Godde J. S., Widom J. Chromatin structure of Schizosaccharomyces pombe. A nucleosome repeat length that is shorter than the chromatosomal DNA length. J Mol Biol. 1992 Aug 20;226(4):1009–1025. doi: 10.1016/0022-2836(92)91049-u. [DOI] [PubMed] [Google Scholar]
  9. Kief D. R., Warner J. R. Coordinate control of syntheses of ribosomal ribonucleic acid and ribosomal proteins during nutritional shift-up in Saccharomyces cerevisiae. Mol Cell Biol. 1981 Nov;1(11):1007–1015. doi: 10.1128/mcb.1.11.1007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kornberg R. D., Lorch Y. Chromatin structure and transcription. Annu Rev Cell Biol. 1992;8:563–587. doi: 10.1146/annurev.cb.08.110192.003023. [DOI] [PubMed] [Google Scholar]
  11. Kulkens T., van Heerikhuizen H., Klootwijk J., Oliemans J., Planta R. J. A yeast ribosomal DNA-binding protein that binds to the rDNA enhancer and also close to the site of Pol I transcription initiation is not important for enhancer functioning. Curr Genet. 1989 Dec;16(5-6):351–359. doi: 10.1007/BF00340714. [DOI] [PubMed] [Google Scholar]
  12. Kulkens T., van der Sande C. A., Dekker A. F., van Heerikhuizen H., Planta R. J. A system to study transcription by yeast RNA polymerase I within the chromosomal context: functional analysis of the ribosomal DNA enhancer and the RBP1/REB1 binding sites. EMBO J. 1992 Dec;11(12):4665–4674. doi: 10.1002/j.1460-2075.1992.tb05568.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Linskens M. H., Huberman J. A. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Nov;8(11):4927–4935. doi: 10.1128/mcb.8.11.4927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lohr D. Chromatin structure differs between coding and upstream flanking sequences of the yeast 35S ribosomal genes. Biochemistry. 1983 Feb 15;22(4):927–934. doi: 10.1021/bi00273a034. [DOI] [PubMed] [Google Scholar]
  15. Lohr D., Kovacic R. T., Van Holde K. E. Quantitative analysis of the digestion of yeast chromatin by staphylococcal nuclease. Biochemistry. 1977 Feb 8;16(3):463–471. doi: 10.1021/bi00622a020. [DOI] [PubMed] [Google Scholar]
  16. Lucchini R., Pauli U., Braun R., Koller T., Sogo J. M. Structure of the extrachromosomal ribosomal RNA chromatin of Physarum polycephalum. J Mol Biol. 1987 Aug 20;196(4):829–843. doi: 10.1016/0022-2836(87)90408-6. [DOI] [PubMed] [Google Scholar]
  17. Lucchini R., Sogo J. M. Different chromatin structures along the spacers flanking active and inactive Xenopus rRNA genes. Mol Cell Biol. 1992 Oct;12(10):4288–4296. doi: 10.1128/mcb.12.10.4288. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Morrow B. E., Johnson S. P., Warner J. R. Proteins that bind to the yeast rDNA enhancer. J Biol Chem. 1989 May 25;264(15):9061–9068. [PubMed] [Google Scholar]
  19. Morrow B. E., Johnson S. P., Warner J. R. The rRNA enhancer regulates rRNA transcription in Saccharomyces cerevisiae. Mol Cell Biol. 1993 Feb;13(2):1283–1289. doi: 10.1128/mcb.13.2.1283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Philippsen P., Thomas M., Kramer R. A., Davis R. W. Unique arrangement of coding sequences for 5 S, 5.8 S, 18 S and 25 S ribosomal RNA in Saccharomyces cerevisiae as determined by R-loop and hybridization analysis. J Mol Biol. 1978 Aug 15;123(3):387–404. doi: 10.1016/0022-2836(78)90086-4. [DOI] [PubMed] [Google Scholar]
  21. Planta R. J., Raué H. A. Control of ribosome biogenesis in yeast. Trends Genet. 1988 Mar;4(3):64–68. doi: 10.1016/0168-9525(88)90042-x. [DOI] [PubMed] [Google Scholar]
  22. Rattner J. B., Saunders C., Davie J. R., Hamkalo B. A. Ultrastructural organization of yeast chromatin. J Cell Biol. 1982 Apr;93(1):217–222. doi: 10.1083/jcb.93.1.217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Raué H. A., Planta R. J. Ribosome biogenesis in yeast. Prog Nucleic Acid Res Mol Biol. 1991;41:89–129. doi: 10.1016/s0079-6603(08)60007-0. [DOI] [PubMed] [Google Scholar]
  24. Reeder R. H. rRNA synthesis in the nucleolus. Trends Genet. 1990 Dec;6(12):390–395. doi: 10.1016/0168-9525(90)90298-k. [DOI] [PubMed] [Google Scholar]
  25. Saffer L. D., Miller O. L., Jr Electron microscopic study of Saccharomyces cerevisiae rDNA chromatin replication. Mol Cell Biol. 1986 Apr;6(4):1148–1157. doi: 10.1128/mcb.6.4.1148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Segall J. Assembly of a yeast 5 S RNA gene transcription complex. J Biol Chem. 1986 Sep 5;261(25):11578–11584. [PubMed] [Google Scholar]
  27. Skryabin K. G., Eldarov M. A., Larionov V. L., Bayev A. A., Klootwijk J., de Regt V. C., Veldman G. M., Planta R. J., Georgiev O. I., Hadjiolov A. A. Structure and function of the nontranscribed spacer regions of yeast rDNA. Nucleic Acids Res. 1984 Mar 26;12(6):2955–2968. doi: 10.1093/nar/12.6.2955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Sogo J. M., Ness P. J., Widmer R. M., Parish R. W., Koller T. Psoralen-crosslinking of DNA as a probe for the structure of active nucleolar chromatin. J Mol Biol. 1984 Oct 5;178(4):897–919. doi: 10.1016/0022-2836(84)90318-8. [DOI] [PubMed] [Google Scholar]
  29. Sogo J. M., Stahl H., Koller T., Knippers R. Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures. J Mol Biol. 1986 May 5;189(1):189–204. doi: 10.1016/0022-2836(86)90390-6. [DOI] [PubMed] [Google Scholar]
  30. Szostak J. W., Wu R. Insertion of a genetic marker into the ribosomal DNA of yeast. Plasmid. 1979 Oct;2(4):536–554. doi: 10.1016/0147-619x(79)90053-2. [DOI] [PubMed] [Google Scholar]
  31. Thoma F. Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin. J Mol Biol. 1986 Jul 20;190(2):177–190. doi: 10.1016/0022-2836(86)90291-3. [DOI] [PubMed] [Google Scholar]
  32. Warner J. R. Synthesis of ribosomes in Saccharomyces cerevisiae. Microbiol Rev. 1989 Jun;53(2):256–271. doi: 10.1128/mr.53.2.256-271.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Widmer R. M., Koller T., Sogo J. M. Analysis of the psoralen-crosslinking pattern in chromatin DNA by exonuclease digestion. Nucleic Acids Res. 1988 Jul 25;16(14B):7013–7024. doi: 10.1093/nar/16.14.7013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. van der Sande C. A., Kulkens T., Kramer A. B., de Wijs I. J., van Heerikhuizen H., Klootwijk J., Planta R. J. Termination of transcription by yeast RNA polymerase I. Nucleic Acids Res. 1989 Nov 25;17(22):9127–9146. doi: 10.1093/nar/17.22.9127. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES