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Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach

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  • Behrouz Eslami-Mossallam
  • Raoul D Schram
  • Marco Tompitak
  • John van Noort
  • Helmut Schiessel

Abstract

Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function.

Suggested Citation

  • Behrouz Eslami-Mossallam & Raoul D Schram & Marco Tompitak & John van Noort & Helmut Schiessel, 2016. "Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-14, June.
    • Handle: RePEc:plo:pone00:0156905
    DOI: 10.1371/journal.pone.0156905
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    References listed on IDEAS

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    2. Alon Diament & Ron Y. Pinter & Tamir Tuller, 2014. "Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
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    4. Eran Segal & Yvonne Fondufe-Mittendorf & Lingyi Chen & AnnChristine Thåström & Yair Field & Irene K. Moore & Ji-Ping Z. Wang & Jonathan Widom, 2006. "A genomic code for nucleosome positioning," Nature, Nature, vol. 442(7104), pages 772-778, August.
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