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Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism

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  • Idelisse Ortiz Torres

    (University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
    Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA)

  • Kristopher M. Kuchenbecker

    (University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
    Biophysics Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA)

  • Chimno I. Nnadi

    (University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
    Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
    UCSF Medical Scientist Training Program, University of California)

  • Robert J. Fletterick

    (University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA)

  • Mark J. S. Kelly

    (University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA)

  • Danica Galonić Fujimori

    (University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
    University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA)

Abstract

The retinoblastoma binding protein KDM5A removes methyl marks from lysine 4 of histone H3 (H3K4). Misregulation of KDM5A contributes to the pathogenesis of lung and gastric cancers. In addition to its catalytic jumonji C domain, KDM5A contains three PHD reader domains, commonly recognized as chromatin recruitment modules. It is unknown whether any of these domains in KDM5A have functions beyond recruitment and whether they regulate the catalytic activity of the demethylase. Here using biochemical and nuclear magnetic resonance (NMR)-based structural studies, we show that the PHD1 preferentially recognizes unmethylated H3K4 histone tail, product of KDM5A-mediated demethylation of tri-methylated H3K4 (H3K4me3). Binding of unmodified H3 peptide to the PHD1 stimulates catalytic domain-mediated removal of methyl marks from H3K4me3 peptide and nucleosome substrates. This positive-feedback mechanism—enabled by the functional coupling between a reader and a catalytic domain in KDM5A—suggests a model for the spread of demethylation on chromatin.

Suggested Citation

  • Idelisse Ortiz Torres & Kristopher M. Kuchenbecker & Chimno I. Nnadi & Robert J. Fletterick & Mark J. S. Kelly & Danica Galonić Fujimori, 2015. "Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism," Nature Communications, Nature, vol. 6(1), pages 1-10, May.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7204
    DOI: 10.1038/ncomms7204
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