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Journal of Biomolecular Structure and Dynamics Volume 29, 2011 - Issue 3
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Original Articles

Nucleosome Positioning Patterns Derived from Human Apoptotic Nucleosomes

Zakharia M. Frenkel Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel; Department of Software Engineering, ORT Braude College, P.O. Box: 78, Karmiel, 21982, Israel
,
Edward N. Trifonov Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel; Department of Functional Genomics and Proteomics, Faculty of Science, Masaryk University, Kotlarska 2, CZ-61137, Brno, Czech Republic
,
Zeev Volkovich Department of Software Engineering, ORT Braude College, P.O. Box: 78, Karmiel, 21982, Israel
&
Thomas Bettecken CAGT-Center for Applied Genotyping, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, D-80804, Muenchen, Germany
Pages 577-583 | Received 14 Jun 2011, Published online: 11 Jul 2012

Abstract

This communication reports on the nucleosome positioning patterns (bendability matrices) for the human genome, derived from over 8 million nucleosome DNA sequences obtained from apoptotically digested lymphocytes. This digestion procedure is used here for the first time for the purpose of extraction and sequencing of the nucleosome DNA fragments. The dominant motifs suggested by the matrices of DNA bendability calculated for light and heavy isochores are significantly different. Both, however, are in full agreement with the linear description YRRRRRYYYYYR, and with earlier derivations by N-gram extensions. Thus, the choice of the nucleosome positioning patterns crucially depends on the G + C composition of the analyzed sequences.

Abbreviations

R=

purines (A or G)

Y=

pyrimidines (C or T)

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