Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach
Behrouz Eslami-Mossallam, Raoul D. Schram, Marco Tompitak, John van Noort, Helmut Schiessel
Published: June 7, 2016http://dx.doi.org/10.1371/journal.pone.0156905
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.
Citation: Eslami-Mossallam B, Schram RD, Tompitak M, van Noort J, Schiessel H (2016) Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach. PLoS ONE 11(6): e0156905. doi:10.1371/journal.pone.0156905
Editor: Tamir Tuller, Tel Aviv University, ISRAEL
Received: December 22, 2015; Accepted: May 20, 2016; Published: June 7, 2016
Copyright: © 2016 Eslami-Mossallam et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper and its Supporting Information files.
Funding: This research is supported by the NanoFront consortium, a program of the Netherlands Organisation for Scientific Research (NWO) that is funded by the Dutch Ministry of Education, Culture and Science (OCW) and by the research programme of the Foundation for Fundamental Research on Matter (FOM), which is financially supported by NWO; and by the NWO-VICI program (JN). HS thanks the KITP at Santa Barbara for hospitality where part of this work has been performed and the National Science Foundation under Grant No. NSF PHY11-25915 for support.
Competing interests: The authors have declared that no competing interests exist.
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