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

Idelisse Ortiz Torres,Kristopher M Kuchenbecker,Chimno I Nnadi,Mark J S Kelly,Danica Galonić Fujimori,Robert J Fletterick

doi:10.1038/ncomms7204

Idelisse Ortiz Torres, Kristopher M Kuchenbecker + Show 4 more

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https://doi.org/10.1038/ncomms7204

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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.

Highlights

The retinoblastoma binding protein KDM5A removes methyl marks from lysine 4 of histone H3 (H3K4)
Using unmethylated and methylated H3 tail peptides, we found that the PHD1 domain prefers the H3 peptide that contains unmethylated Lys[4] (H3K4me0), and shows the lowest affinity for the H3 tail peptide in which Lys[4] is tri-methylated (H3K4me[3]; Fig. 1c,d)
Dimethylation of R2, either symmetric (H3R2me2s) or asymmetric (H3R2me2a), reduces binding affinity by approximately fivefold (Fig. 1d). While methylation of both R2 and K4 influences peptide binding to the PHD1, methylation of lysine 9 has no effect on PHD1 binding (Supplementary Fig. 1)

Summary

Introduction

The retinoblastoma binding protein KDM5A removes methyl marks from lysine 4 of histone H3 (H3K4). Binding of unmodified H3 peptide to the PHD1 stimulates catalytic domain-mediated removal of methyl marks from H3K4me[3] 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. In the primary sequence of the demethylase, the PHD1 is positioned between the JmjN and JmjC domains, which have been postulated to form a composite active site in KDM5 histone demethylases[29,31,32] These observations suggest a potential role of the PHD1 domain in regulating the catalytic activity of KDM5A

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