Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications
Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications
CHD4 (chromodomain helicase DNA-binding protein 4) ATPase is a major subunit of the repressive NuRD (nucleosome remodelling and deacetylase) complex, which is involved in transcriptional regulation and development. CHD4 contains two PHD (plant homeodomain) fingers of unknown function. Here we show that the second PHD finger (PHD2) of CHD4 recognizes the N-terminus of histone H3 and that this interaction is facilitated by acetylation or methylation of Lys9 (H3K9ac and H3K9me respectively) but is inhibited by methylation of Lys4 (H3K4me) or acetylation of Ala1 (H3A1ac). An 18 μM binding affinity toward unmodified H3 rises to 0.6 μM for H3K9ac and to 0.9 μM for H3K9me3, whereas it drops to 2.0 mM for H3K4me3, as measured by tryptophan fluorescence and NMR. A peptide library screen further shows that phosphorylation of Thr3, Thr6 or Ser10 abolishes this interaction. A model of the PHD2–H3 complex, generated using a combination of NMR, data-driven docking and mutagenesis data, reveals an elongated site on the PHD2 surface where the H3 peptide is bound. Together our findings suggest that the PHD2 finger plays a role in targeting of the CHD4/NuRD complex to chromatin.
- University of Wisconsin–Madison United States
- University of Wisconsin–Oshkosh United States
- University of Sydney Australia
- University of Wisconsin System United States
- University of Colorado Denver United States
Homeodomain Proteins, Binding Sites, Biophysics, DNA Helicases, Acetylation, Histone-Lysine N-Methyltransferase, Autoantigens, Methylation, Models, Biological, Chromatin, Protein Structure, Tertiary, Substrate Specificity, Histones, Histone Methyltransferases, Humans, Hydrophobic and Hydrophilic Interactions, Histone Acetyltransferases, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Protein Binding
Homeodomain Proteins, Binding Sites, Biophysics, DNA Helicases, Acetylation, Histone-Lysine N-Methyltransferase, Autoantigens, Methylation, Models, Biological, Chromatin, Protein Structure, Tertiary, Substrate Specificity, Histones, Histone Methyltransferases, Humans, Hydrophobic and Hydrophilic Interactions, Histone Acetyltransferases, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Protein Binding
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