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The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B.

Zhang Y, Yang H, Guo X, Rong N, Song Y, Xu Y, Lan W, Zhang X, Liu M, Xu Y, Cao C - Protein Cell (2014)

Bottom Line: KDM5B is a histone H3K4me2/3 demethylase.The PHD1 domain of KDM5B is critical for demethylation, but the mechanism underlying the action of this domain is unclear.Our NMR structure of PHD1KDM5B in complex with H3K4me0 revealed that the binding mode is slightly different from that of other reported PHD fingers.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Bio-organic and Natural Product Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.

ABSTRACT
KDM5B is a histone H3K4me2/3 demethylase. The PHD1 domain of KDM5B is critical for demethylation, but the mechanism underlying the action of this domain is unclear. In this paper, we observed that PHD1KDM5B interacts with unmethylated H3K4me0. Our NMR structure of PHD1KDM5B in complex with H3K4me0 revealed that the binding mode is slightly different from that of other reported PHD fingers. The disruption of this interaction by double mutations on the residues in the interface (L325A/D328A) decreases the H3K4me2/3 demethylation activity of KDM5B in cells by approximately 50% and increases the transcriptional repression of tumor suppressor genes by approximately twofold. These findings imply that PHD1KDM5B may help maintain KDM5B at target genes to mediate the demethylation activities of KDM5B.

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PHD1KDM5Bspecifically binds to the tail of H3K4me0. (A) Mammalian KDM5 family members are highly similar in domain architecture and contain JmjN, ARID, Jmjc, zf-C5HC2 and PHD domains. (B) KDM5B variants described in the text. (C) In vitro binding assays for analysis of the binding of recombinant KDM5B variants to the unmodified histone H3K4 N-terminal tail. (D) PHD1KDM5B is sufficient for H3 tail binding. (E) The binding affinities of PHD1KDM5B to unmodified, mono-methylated, di-methylated or tri-methylated H3K4 peptides (residues 1–10) were measured through an ITC assay. The KD values are the means (± s.d.) of at least three experiments using varied peptide and protein concentrations
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Fig1: PHD1KDM5Bspecifically binds to the tail of H3K4me0. (A) Mammalian KDM5 family members are highly similar in domain architecture and contain JmjN, ARID, Jmjc, zf-C5HC2 and PHD domains. (B) KDM5B variants described in the text. (C) In vitro binding assays for analysis of the binding of recombinant KDM5B variants to the unmodified histone H3K4 N-terminal tail. (D) PHD1KDM5B is sufficient for H3 tail binding. (E) The binding affinities of PHD1KDM5B to unmodified, mono-methylated, di-methylated or tri-methylated H3K4 peptides (residues 1–10) were measured through an ITC assay. The KD values are the means (± s.d.) of at least three experiments using varied peptide and protein concentrations

Mentions: The members of the JARID1 subgroup are highly conserved from yeast to humans and contain a similar motif architecture, including JmjN, ARID (i.e., AT-rich interactive domain), JmjC, Zf-C5HC2 (i.e., zinc finger) and two or three PHD domains (denoted PHD1, PHD2 and PHD3 from the N-terminus to the C-terminus). A total of four members are found in mammals (Fig. 1A): JARID1A (also called RBP2 or KDM5A), JARID1B (also named PLU-1 or KDM5B), JARID1C (i.e., SMCX or KDM5C) and JARID1D (also known as SMCY orKDM5D). These members have been identified to be H3K4me2/3 demethylases (Christensen et al., 2007; Iwase et al., 2007; Klose et al., 2007; Lee et al., 2007; Tahiliani et al., 2007; Yamane et al., 2007). All of these proteins are key transcriptional co-repressors because they can remove the transcription-activating marker H3K4me3. KDM5B is involved in transcriptional repression and breast cancer cell proliferation (Yamane et al., 2007); thus, mechanistic studies on KDM5B demethylation are necessary and useful to understand the development of breast cancer. Notably, the deletion of the N-terminal PHD1 finger (i.e., PHD1KDM5B) of KDM5B results in the loss of enzymatic demethylase activity, implying that PHD1KDM5B is involved in H3K4me2/3 demethylation (Yamane et al., 2007). This observation is consistent with the fact that the N-terminal PHD1 finger of Lid (i.e., PHD1Lid), a homologue of KDM5B in Drosophila, is also required for the demethylase activity of H3K4me3, whereas the PHD2 and PHD3 of Lid are not (Li et al., 2010). However, the detailed mechanism underlying the function of PHD1KDM5B in the demethylation process remains unclear.Figure 1


The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B.

Zhang Y, Yang H, Guo X, Rong N, Song Y, Xu Y, Lan W, Zhang X, Liu M, Xu Y, Cao C - Protein Cell (2014)

PHD1KDM5Bspecifically binds to the tail of H3K4me0. (A) Mammalian KDM5 family members are highly similar in domain architecture and contain JmjN, ARID, Jmjc, zf-C5HC2 and PHD domains. (B) KDM5B variants described in the text. (C) In vitro binding assays for analysis of the binding of recombinant KDM5B variants to the unmodified histone H3K4 N-terminal tail. (D) PHD1KDM5B is sufficient for H3 tail binding. (E) The binding affinities of PHD1KDM5B to unmodified, mono-methylated, di-methylated or tri-methylated H3K4 peptides (residues 1–10) were measured through an ITC assay. The KD values are the means (± s.d.) of at least three experiments using varied peptide and protein concentrations
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Related In: Results  -  Collection

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Fig1: PHD1KDM5Bspecifically binds to the tail of H3K4me0. (A) Mammalian KDM5 family members are highly similar in domain architecture and contain JmjN, ARID, Jmjc, zf-C5HC2 and PHD domains. (B) KDM5B variants described in the text. (C) In vitro binding assays for analysis of the binding of recombinant KDM5B variants to the unmodified histone H3K4 N-terminal tail. (D) PHD1KDM5B is sufficient for H3 tail binding. (E) The binding affinities of PHD1KDM5B to unmodified, mono-methylated, di-methylated or tri-methylated H3K4 peptides (residues 1–10) were measured through an ITC assay. The KD values are the means (± s.d.) of at least three experiments using varied peptide and protein concentrations
Mentions: The members of the JARID1 subgroup are highly conserved from yeast to humans and contain a similar motif architecture, including JmjN, ARID (i.e., AT-rich interactive domain), JmjC, Zf-C5HC2 (i.e., zinc finger) and two or three PHD domains (denoted PHD1, PHD2 and PHD3 from the N-terminus to the C-terminus). A total of four members are found in mammals (Fig. 1A): JARID1A (also called RBP2 or KDM5A), JARID1B (also named PLU-1 or KDM5B), JARID1C (i.e., SMCX or KDM5C) and JARID1D (also known as SMCY orKDM5D). These members have been identified to be H3K4me2/3 demethylases (Christensen et al., 2007; Iwase et al., 2007; Klose et al., 2007; Lee et al., 2007; Tahiliani et al., 2007; Yamane et al., 2007). All of these proteins are key transcriptional co-repressors because they can remove the transcription-activating marker H3K4me3. KDM5B is involved in transcriptional repression and breast cancer cell proliferation (Yamane et al., 2007); thus, mechanistic studies on KDM5B demethylation are necessary and useful to understand the development of breast cancer. Notably, the deletion of the N-terminal PHD1 finger (i.e., PHD1KDM5B) of KDM5B results in the loss of enzymatic demethylase activity, implying that PHD1KDM5B is involved in H3K4me2/3 demethylation (Yamane et al., 2007). This observation is consistent with the fact that the N-terminal PHD1 finger of Lid (i.e., PHD1Lid), a homologue of KDM5B in Drosophila, is also required for the demethylase activity of H3K4me3, whereas the PHD2 and PHD3 of Lid are not (Li et al., 2010). However, the detailed mechanism underlying the function of PHD1KDM5B in the demethylation process remains unclear.Figure 1

Bottom Line: KDM5B is a histone H3K4me2/3 demethylase.The PHD1 domain of KDM5B is critical for demethylation, but the mechanism underlying the action of this domain is unclear.Our NMR structure of PHD1KDM5B in complex with H3K4me0 revealed that the binding mode is slightly different from that of other reported PHD fingers.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Bio-organic and Natural Product Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.

ABSTRACT
KDM5B is a histone H3K4me2/3 demethylase. The PHD1 domain of KDM5B is critical for demethylation, but the mechanism underlying the action of this domain is unclear. In this paper, we observed that PHD1KDM5B interacts with unmethylated H3K4me0. Our NMR structure of PHD1KDM5B in complex with H3K4me0 revealed that the binding mode is slightly different from that of other reported PHD fingers. The disruption of this interaction by double mutations on the residues in the interface (L325A/D328A) decreases the H3K4me2/3 demethylation activity of KDM5B in cells by approximately 50% and increases the transcriptional repression of tumor suppressor genes by approximately twofold. These findings imply that PHD1KDM5B may help maintain KDM5B at target genes to mediate the demethylation activities of KDM5B.

Show MeSH
Related in: MedlinePlus