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Sequence features accurately predict genome-wide MeCP2 binding in vivo

Author

Listed:
  • H. Tomas Rube

    (Carl R. Woese Institute for Genomic Biology, University of Illinois
    University of Illinois
    Columbia University)

  • Wooje Lee

    (University of California School of Medicine
    Korea University)

  • Miroslav Hejna

    (Carl R. Woese Institute for Genomic Biology, University of Illinois
    University of Illinois)

  • Huaiyang Chen

    (University of California School of Medicine)

  • Dag H. Yasui

    (Genome Center, MIND Institute, University of California School of Medicine)

  • John F. Hess

    (University of California School of Medicine)

  • Janine M. LaSalle

    (Genome Center, MIND Institute, University of California School of Medicine)

  • Jun S. Song

    (Carl R. Woese Institute for Genomic Biology, University of Illinois
    University of Illinois
    University of Illinois
    University of California)

  • Qizhi Gong

    (University of California School of Medicine)

Abstract

Methyl-CpG binding protein 2 (MeCP2) is critical for proper brain development and expressed at near-histone levels in neurons, but the mechanism of its genomic localization remains poorly understood. Using high-resolution MeCP2-binding data, we show that DNA sequence features alone can predict binding with 88% accuracy. Integrating MeCP2 binding and DNA methylation in a probabilistic graphical model, we demonstrate that previously reported genome-wide association with methylation is in part due to MeCP2’s affinity to GC-rich chromatin, a result replicated using published data. Furthermore, MeCP2 co-localizes with nucleosomes. Finally, MeCP2 binding downstream of promoters correlates with increased expression in Mecp2-deficient neurons.

Suggested Citation

  • H. Tomas Rube & Wooje Lee & Miroslav Hejna & Huaiyang Chen & Dag H. Yasui & John F. Hess & Janine M. LaSalle & Jun S. Song & Qizhi Gong, 2016. "Sequence features accurately predict genome-wide MeCP2 binding in vivo," Nature Communications, Nature, vol. 7(1), pages 1-12, April.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms11025
    DOI: 10.1038/ncomms11025
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