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Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning

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Abstract

Nucleosome positioning plays an essential role in various fundamental cellular processes by modulating the accessibility of DNA to binding proteins. Understanding the mechanisms and precise recognition of nucleosome positioning along genomic sequences are substantially important for elucidating regulations of cellular processes such as DNA replication, recombination, and gene transcription. In this report, we present a knowledge-based model for calculation of deformational energy of nucleosomal DNA and apply the model to the prediction of nucleosome positioning along the genome of Saccharomyces cerevisiae accurately. The model successfully predicted genome-wide in vitro nucleosome positions. When combined with quadratic discriminant classifier, the model achieved an accuracy of 92.9 % in discriminating in vitro nucleosome forming sequences from nucleosome inhibiting sequences. Our result supports the debated notion that the nucleosome positioning in the genomic sequences is guided primarily by deformational properties of DNA.

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Abbreviations

MNase:

Micrococcal nuclease

NDRs:

Nucleosome-depleted regions

TSS:

Transcription start sites

TES:

Transcription end sites

ARS:

Autonomously replicating sequence

ACS:

ARS consensus sequences

ID:

Increment of diversity

QD:

Quadratic determinant

ORC:

Origin recognition complex

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Acknowledgments

We thank Yong-Qiang Xing for his helpful discussions. This work was supported by grants from the National Natural Science Foundation (61102162), Inner Mongolia Natural Science Foundation (2010MS0510), the Research Program of Higher Education of Inner Mongolia Autonomous Region (NJ10098), and the Innovation Fund of Inner Mongolia University of Science and Technology (2009NC005).

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Authors and Affiliations

  1. The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China

    Jian-Ying Wang, Jingyan Wang & Guoqing Liu

  2. School of Mathematics, Physics, and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China

    Jingyan Wang & Guoqing Liu

  3. State Key Laboratory for Utilization of Bayan Obo Multi-Metallic Resources, Inner Mongolia University of Science and Technology, Baotou, 014010, China

    Jian-Ying Wang

Authors
  1. Jian-Ying Wang
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  2. Jingyan Wang
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  3. Guoqing Liu
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Correspondence to Guoqing Liu.

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Responsible Editor: Dean A. Jackson.

This work was supported by grants from the National Natural Science Foundation (61102162) Inner Mongolia Natural Science Foundation (2010MS0510), the Research Program of Higher Education of Inner Mongolia Autonomous Region (NJ10098), and the Innovation Fund of Inner Mongolia University of Science and Technology (2009NC005).

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Wang, JY., Wang, J. & Liu, G. Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning. Chromosome Res 20, 889–902 (2012). https://doi.org/10.1007/s10577-012-9328-6

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  • DOI: https://doi.org/10.1007/s10577-012-9328-6

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