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. 1998 Jul 1;333(Pt 1):65–69. doi: 10.1042/bj3330065

Changing nucleosome positions in vivo through modification of the DNA rotational information.

L Di Marcotullio 1, M Buttinelli 1, G Costanzo 1, E Di Mauro 1, R Negri 1
PMCID: PMC1219556  PMID: 9639563

Abstract

The effects of the rotational information of DNA in determining the in vivo localization of nucleosomal core particles (ncps) have been studied in the Saccharomyces cerevisiae 5 S rRNA repeat gene. The distribution of the phased series of flexibility signals present in this DNA has been altered by inserting in its centre a 25 bp tract. The effects of such alteration on the in vivo distribution of the helically phased, alternatively located ncps have been determined relative to a reference 21 bp insertion mutant. The results show that the answers provided in vitro and in vivo by the yeast 5 S rRNA gene sequence to specific modifications of the DNA rotational frame are similar, thus pointing to the relevance of DNA rotational information in vivo.

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Selected References

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

  1. Almer A., Rudolph H., Hinnen A., Hörz W. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 1986 Oct;5(10):2689–2696. doi: 10.1002/j.1460-2075.1986.tb04552.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Beato M., Eisfeld K. Transcription factor access to chromatin. Nucleic Acids Res. 1997 Sep 15;25(18):3559–3563. doi: 10.1093/nar/25.18.3559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Braun B. R., Riggs D. L., Kassavetis G. A., Geiduschek E. P. Multiple states of protein-DNA interaction in the assembly of transcription complexes on Saccharomyces cerevisiae 5S ribosomal RNA genes. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2530–2534. doi: 10.1073/pnas.86.8.2530. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Buttinelli M., Di Mauro E., Negri R. Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo. Proc Natl Acad Sci U S A. 1993 Oct 15;90(20):9315–9319. doi: 10.1073/pnas.90.20.9315. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Buttinelli M., Negri R., Di Marcotullio L., Di Mauro E. Changing nucleosome positions through modification of the DNA rotational information. Proc Natl Acad Sci U S A. 1995 Nov 7;92(23):10747–10751. doi: 10.1073/pnas.92.23.10747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Costanzo G., Di Mauro E., Negri R., Pereira G., Hollenberg C. Multiple overlapping positions of nucleosomes with single in vivo rotational setting in the Hansenula polymorpha RNA polymerase II MOX promoter. J Biol Chem. 1995 May 12;270(19):11091–11097. doi: 10.1074/jbc.270.19.11091. [DOI] [PubMed] [Google Scholar]
  7. Davey C., Pennings S., Allan J. CpG methylation remodels chromatin structure in vitro. J Mol Biol. 1997 Mar 28;267(2):276–288. doi: 10.1006/jmbi.1997.0899. [DOI] [PubMed] [Google Scholar]
  8. Davey C., Pennings S., Meersseman G., Wess T. J., Allan J. Periodicity of strong nucleosome positioning sites around the chicken adult beta-globin gene may encode regularly spaced chromatin. Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):11210–11214. doi: 10.1073/pnas.92.24.11210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Drew H. R., Travers A. A. DNA bending and its relation to nucleosome positioning. J Mol Biol. 1985 Dec 20;186(4):773–790. doi: 10.1016/0022-2836(85)90396-1. [DOI] [PubMed] [Google Scholar]
  10. Fragoso G., Hager G. L. Analysis of in vivo nucleosome positions by determination of nucleosome-linker boundaries in crosslinked chromatin. Methods. 1997 Feb;11(2):246–252. doi: 10.1006/meth.1996.0411. [DOI] [PubMed] [Google Scholar]
  11. Fragoso G., John S., Roberts M. S., Hager G. L. Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames. Genes Dev. 1995 Aug 1;9(15):1933–1947. doi: 10.1101/gad.9.15.1933. [DOI] [PubMed] [Google Scholar]
  12. Grunstein M. Histone function in transcription. Annu Rev Cell Biol. 1990;6:643–678. doi: 10.1146/annurev.cb.06.110190.003235. [DOI] [PubMed] [Google Scholar]
  13. Hansen J. C., Ausio J., Stanik V. H., van Holde K. E. Homogeneous reconstituted oligonucleosomes, evidence for salt-dependent folding in the absence of histone H1. Biochemistry. 1989 Nov 14;28(23):9129–9136. doi: 10.1021/bi00449a026. [DOI] [PubMed] [Google Scholar]
  14. Luger K., Mäder A. W., Richmond R. K., Sargent D. F., Richmond T. J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997 Sep 18;389(6648):251–260. doi: 10.1038/38444. [DOI] [PubMed] [Google Scholar]
  15. Meersseman G., Pennings S., Bradbury E. M. Mobile nucleosomes--a general behavior. EMBO J. 1992 Aug;11(8):2951–2959. doi: 10.1002/j.1460-2075.1992.tb05365.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Patterton H. G., Simpson R. T. Modified curved DNA that could allow local DNA underwinding at the nucleosomal pseudodyad fails to position a nucleosome in vivo. Nucleic Acids Res. 1995 Oct 25;23(20):4170–4179. doi: 10.1093/nar/23.20.4170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Pennings S., Meersseman G., Bradbury E. M. Mobility of positioned nucleosomes on 5 S rDNA. J Mol Biol. 1991 Jul 5;220(1):101–110. doi: 10.1016/0022-2836(91)90384-i. [DOI] [PubMed] [Google Scholar]
  18. Piña B., Barettino D., Truss M., Beato M. Structural features of a regulatory nucleosome. J Mol Biol. 1990 Dec 20;216(4):975–990. doi: 10.1016/S0022-2836(99)80015-1. [DOI] [PubMed] [Google Scholar]
  19. Piña B., Brüggemeier U., Beato M. Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter. Cell. 1990 Mar 9;60(5):719–731. doi: 10.1016/0092-8674(90)90087-u. [DOI] [PubMed] [Google Scholar]
  20. Rubbi L., Camilloni G., Caserta M., Di Mauro E., Venditti S. Chromatin structure of the Saccharomyces cerevisiae DNA topoisomerase I promoter in different growth phases. Biochem J. 1997 Dec 1;328(Pt 2):401–407. doi: 10.1042/bj3280401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Satchwell S. C., Drew H. R., Travers A. A. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol. 1986 Oct 20;191(4):659–675. doi: 10.1016/0022-2836(86)90452-3. [DOI] [PubMed] [Google Scholar]
  22. Shrader T. E., Crothers D. M. Artificial nucleosome positioning sequences. Proc Natl Acad Sci U S A. 1989 Oct;86(19):7418–7422. doi: 10.1073/pnas.86.19.7418. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Straka C., Hörz W. A functional role for nucleosomes in the repression of a yeast promoter. EMBO J. 1991 Feb;10(2):361–368. doi: 10.1002/j.1460-2075.1991.tb07957.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Tanaka S., Zatchej M., Thoma F. Artificial nucleosome positioning sequences tested in yeast minichromosomes: a strong rotational setting is not sufficient to position nucleosomes in vivo. EMBO J. 1992 Mar;11(3):1187–1193. doi: 10.1002/j.1460-2075.1992.tb05159.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Thoma F. Nucleosome positioning. Biochim Biophys Acta. 1992 Feb 28;1130(1):1–19. doi: 10.1016/0167-4781(92)90455-9. [DOI] [PubMed] [Google Scholar]
  26. Venditti P., Costanzo G., Negri R., Camilloni G. ABFI contributes to the chromatin organization of Saccharomyces cerevisiae ARS1 B-domain. Biochim Biophys Acta. 1994 Nov 22;1219(3):677–689. doi: 10.1016/0167-4781(94)90227-5. [DOI] [PubMed] [Google Scholar]
  27. Verdone L., Camilloni G., Di Mauro E., Caserta M. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol Cell Biol. 1996 May;16(5):1978–1988. doi: 10.1128/mcb.16.5.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Wallrath L. L., Lu Q., Granok H., Elgin S. C. Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. Bioessays. 1994 Mar;16(3):165–170. doi: 10.1002/bies.950160306. [DOI] [PubMed] [Google Scholar]
  29. Wolffe A. P. Nucleosome positioning and modification: chromatin structures that potentiate transcription. Trends Biochem Sci. 1994 Jun;19(6):240–244. doi: 10.1016/0968-0004(94)90148-1. [DOI] [PubMed] [Google Scholar]

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