Export file:

Format

  • RIS(for EndNote,Reference Manager,ProCite)
  • BibTex
  • Text

Content

  • Citation Only
  • Citation and Abstract

Columnar structure of SV40 minichromosome

Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel

Special Issues: Chromatin and Epigenetics

Like the sequence of the strongest 601 clone nucleosome of Lowary and Widom, the SV40 genome sequence contains tracks of YR dinucleotides separated by small integers of the 10.4n base series (10, 11, 21 and 30 bases). The tracks, however, substantially exceed the nucleosome DNA size and, thus, correspond to more extended structure - columnar chromatin. The micrococcal nuclease digests of the SV40 chromatin do not show uniquely positioned individual nucleosomes. This confirms the columnar structure of the minichromosome, as well as earlier electron microscopy studies.
  Figure/Table
  Supplementary
  Article Metrics

References

1. Griffith JD (1975) Chromatin structure: deduced from a minichromosome. Science 187: 1202-1203.    

2. Bellard M, Oudet P, Germond JE, et al. (1976) Subunit structure of simian-virus-40 minichromosome. Eur J Biochem 70: 543-553.    

3. Mengeritsky G, Trifonov EN (1984) Nucleotide sequence-directed mapping of the nucleosomes of SV40 chromatin. Cell Bioph 6: 1-9.    

4. Ambrose C, Lowman H, Rajadhyaksha A, et al. (1990) Location of nucleosomes in simian virus 40 chromatin. J Mol Biol 214: 875-884.    

5. Tatchell K, van Holde KE (1978) Compact oligomers and nucleosome phasing. Proc Natl Acad Sci USA 75: 3583-3587.

6. Fajkus J, Trifonov EN (2001) Columnar packing of telomeric nucleosomes. Biochem Biophys Res Comm 280: 961-963.    

7. Salih B, Trifonov EN (2015) Strong nucleosomes of A. thaliana concentrate in centromere regions. J Biomol Str Dyn 33: 10-13.

8. Salih B, Trifonov EN (2015). Strong nucleosomes reside in meiotic centromeres of C. elegans. J Biomol Str Dyn 33: 365-373.    

9. Nibhani R, Trifonov EN (2015) Reading sequence-directed computational nucleosome maps. J Biomol Str Dyn 33:1558-1566.    

10. Gu SG, Goszczynski B, McGhee JD, et al. (2013) Unusual DNA packaging characteristics in endoreduplicated Caenorhabditis elegans oocytes defined by in vivo accessibility to an endogenous nuclease activity. Epigenet Chromatin 6: 37.    

11. Ponder BAJ, Crawford LV (1977) Arrangement of nucleosomes in nucleoprotein complexes from polyoma-virus and SV40. Cell 11: 35-49.    

12. Zhang T, Talbert PB, Zhang W, et al. (2013) The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres. Proc Natl Acad Sci U S A 110: E4875-4883.

13. Rattner JB, Hamkalo BA (1978) Higher-order structure in metaphase chromosomes Chromosoma 69: 373-379.

14. Dubochet J, Adrian M, Schultz P, et al. (1986) Cryo-electron microscopy of vitrified SV40 minichromosomes: the liquid drop model. EMBO J 5: 519-528.

15. Wanner G, Formanek H (2000) A new chromosome model. J Struct Biol 132: 147-161.    

16. Karpov VL, Bavykin SG, Preobrazhenskaya OV, et al. (1982) Alignment of nucleosomes along DNA and organization of spacer DNA in drosophila chromatin. Nucl Acids Res 10: 4321-4337.    

17. Widom J (1992) A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Proc Natl Acad Sci U S A 89:1095-1099.

18. Rapoport AE, Frenkel ZM, Trifonov EN (2011) Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences. J Biomol Str Dyn 28: 567-574.    

19. Frenkel ZM, Bettecken T, Trifonov EN (2011) Nucleosome DNA sequence structure of isochores. BMC Genomics 12: 203.    

20. Tripathi V, Salih B, Trifonov EN (2015) Universal full-length nucleosome mapping sequence probe. J Biomol Str Dyn 33: 666-673.    

21. Lowary PT, Widom J (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence directed nucleosome positioning. J Mol Biol 276: 19-42.    

22. Trifonov EN, Nibhani R (2015) Review fifteen years of search for strong nucleosomes. Biopolymers, 103: 432-437.    

23. Nibhani R, Trifonov EN, TA-periodic (“601”-like) centromeric nucleosomes of A.thaliana. J Biomol Str Dyn [in press].

24. Vasudevan D, Chua EYD, Davey CA (2010) Crystal structures of nucleosome core particles containing the ‘601’ strong positioning sequence. J Mol Biol 403: 1-10.    

25. Zhurkin VB (1982) Periodicity in DNA primary structure and specific alignment of nucleosomes. Stud Biophys 87: 151-152.

26. Zhurkin VB (1983) Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine pyrimidine and pyrimidine purine dimers. FEBS Lett 158: 293-297.    

27. Zhurkin VB, Lysov YP, Ivanov VI (1979) Anisotropic flexibility of DNA and the nucleosomal structure. Nucl Acids Res 6: 1081-1096.    

28. Wang D, Ulyanov NB, Zhurkin VB (2010) Sequence-dependent kink-and-slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove. J Biomol Str Dyn 27: 843-859.    

29. McDowall AW, Smith JM, Dubochet J (1986) Cryo-electron microscopy of vitrified chromosomes in situ. EMBO J 5: 1395-1402.

30. Trifonov EN Nucleosome repeat lengths and columnar chromatin structure. J Biomol Str Dyn [in press].

Copyright Info: © 2015, Edward N Trifonov, licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution Licese (http://creativecommons.org/licenses/by/4.0)

Download full text in PDF

Export Citation

Article outline

Show full outline
Copyright © AIMS Press All Rights Reserved