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Published on: August 1, 2017
Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism
Idelisse Ortiz Torres1, Kristopher M Kuchenbecker2, Chimno I Nnadi3
11] Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [2] Chemistry and Chemical Biology Graduate Program, 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.
Insights
KDM5A
Area of Science:
- Biochemistry
- Molecular Biology
- Epigenetics
Background:
- KDM5A (retinoblastoma binding protein) is a histone demethylase involved in lung and gastric cancers.
- KDM5A has a catalytic domain and three PHD reader domains, but their functions beyond recruitment are unclear.
- The role of KDM5A's reader domains in regulating its catalytic activity remains unknown.
Purpose of the Study:
- To investigate the function of KDM5A's PHD reader domains beyond chromatin recruitment.
- To determine if KDM5A's reader domains regulate its demethylase activity.
- To elucidate the mechanism of KDM5A's action on histone modifications.
Main Methods:
- Biochemical assays were employed to study KDM5A's activity.
- Nuclear magnetic resonance (NMR)-based structural studies provided insights into domain interactions.
- Studies utilized histone peptides and nucleosome substrates to assess demethylase activity.
Main Results:
- The PHD1 domain of KDM5A preferentially binds to unmethylated H3K4 histone tails.
- Binding of the unmodified H3 peptide to PHD1 enhances KDM5A's catalytic removal of methyl marks from H3K4me3.
- A positive-feedback loop is established through the functional coupling of KDM5A's reader and catalytic domains.
Conclusions:
- KDM5A's PHD1 domain plays a regulatory role in its catalytic activity, not just recruitment.
- A novel positive-feedback mechanism regulates KDM5A's demethylase activity.
- This mechanism suggests how KDM5A-mediated demethylation spreads across chromatin.
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