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Analysis of Nucleosome Formation Potential and Conformational Properties of Human J1-J2 and D2-D1 Type Alpha Satellite DNA

  • A. KatokhinEmail author
  • V. Levitsky
  • D. Oshchepkov
  • A. Poplavsky
  • V. Trifonov
  • D. Furman
Chapter
  • 749 Downloads

Abstract

The structure-forming function of alpha satellites in arrangement of the centromeric heterochromatin implies the presence of certain contextual and conformational signals (codes) for compacting DNA of these regions into nucleosomes and chromatin structures of higher level. However, this aspect of informational content of alpha satellite primary DNA sequences yet requires further studies. Computer analysis of nucleosome formation potential (NFP) was performed using a sample of J1-J2 and D2-D1 type alpha satellites from the human genome. A number of regions with the context favorable for several variants of nucleosome positioning were detected. Statistical analysis of DNA conformational profiles, in particular, concerning the property Wedge, demonstrates a superposition of the context-dependent and CENP-B-dependent nucleosome positionings. The corresponding software packages are available at http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/ (RECON method) and http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/ (SITECON method).

Key words

alpha satellite DNA nucleosome positioning DNA conformational properties 

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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • A. Katokhin
    • 1
    Email author
  • V. Levitsky
    • 1
    • 2
  • D. Oshchepkov
    • 1
  • A. Poplavsky
    • 1
  • V. Trifonov
    • 1
  • D. Furman
    • 1
    • 2
  1. 1.Institute of Cytology and GeneticsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia

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