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Relationship between nucleosome positioning and DNA methylation

Author

Listed:
  • Ramakrishna K. Chodavarapu

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Suhua Feng

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA
    Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Yana V. Bernatavichute

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA
    Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Pao-Yang Chen

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Hume Stroud

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Yanchun Yu

    (University of Georgia, Athens, Georgia 30602, USA)

  • Jonathan A. Hetzel

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Frank Kuo

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Jin Kim

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Shawn J. Cokus

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA)

  • David Casero

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Maria Bernal

    (University of Heidelberg, BIOQUANT 23, R. 645, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany)

  • Peter Huijser

    (Max Planck Institute for Plant Breeding Research)

  • Amander T. Clark

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA
    Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California 90095, USA)

  • Ute Krämer

    (University of Heidelberg, BIOQUANT 23, R. 645, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany
    Present address: Department of Plant Physiology, University of Bochum, Universitaetsstrasse 150, D-44801 Bochum, Germany.)

  • Sabeeha S. Merchant

    (Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
    University of California, Los Angeles, Los Angeles, California 90095, USA)

  • Xiaoyu Zhang

    (University of Georgia, Athens, Georgia 30602, USA)

  • Steven E. Jacobsen

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA
    Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, California 90095, USA
    Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA)

  • Matteo Pellegrini

    (Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA
    Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA)

Abstract

Plant nucleosome positioning A genome-wide analysis in the plant Arabidopsis thaliana of the positioning of the nucleosomes — the nucleoprotein molecules that organize and control access to genomic DNA — combined with profiles of DNA methylation at single-base resolution, reveals 10-base periodicities in the DNA methylation status of nucleosome-bound DNA. The results suggest that nucleosome position influences DNA methylation patterning in the genome, and that DNA methyltransferases preferentially target nucleosome-bound DNA. Similar trends were observed in human nucleosomal DNA, indicating that the relationships between nucleosomes and DNA methyltransferases are conserved.

Suggested Citation

  • Ramakrishna K. Chodavarapu & Suhua Feng & Yana V. Bernatavichute & Pao-Yang Chen & Hume Stroud & Yanchun Yu & Jonathan A. Hetzel & Frank Kuo & Jin Kim & Shawn J. Cokus & David Casero & Maria Bernal & , 2010. "Relationship between nucleosome positioning and DNA methylation," Nature, Nature, vol. 466(7304), pages 388-392, July.
    • Handle: RePEc:nat:nature:v:466:y:2010:i:7304:d:10.1038_nature09147
    DOI: 10.1038/nature09147
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    Cited by:

    1. Xianfu Yi & Yu-Dong Cai & Zhisong He & WeiRen Cui & Xiangyin Kong, 2010. "Prediction of Nucleosome Positioning Based on Transcription Factor Binding Sites," PLOS ONE, Public Library of Science, vol. 5(9), pages 1-7, September.
    2. Yunyun An & Xin Zhao & Ziteng Zhang & Zhaohua Xia & Mengqi Yang & Li Ma & Yu Zhao & Gang Xu & Shunda Du & Xiang’an Wu & Shuowen Zhang & Xin Hong & Xin Jin & Kun Sun, 2023. "DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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