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Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice.
PLoS Genet. 2013; 9(1):e1003239.PG

Abstract

Histone lysine methylation is an important epigenetic modification in regulating chromatin structure and gene expression. Histone H3 lysine 4 methylation (H3K4me), which can be in a mono-, di-, or trimethylated state, has been shown to play an important role in gene expression involved in plant developmental control and stress adaptation. However, the resetting mechanism of this epigenetic modification is not yet fully understood. In this work, we identified a JmjC domain-containing protein, JMJ703, as a histone lysine demethylase that specifically reverses all three forms of H3K4me in rice. Loss-of-function mutation of the gene affected stem elongation and plant growth, which may be related to increased expression of cytokinin oxidase genes in the mutant. Analysis of crystal structure of the catalytic core domain (c-JMJ703) of the protein revealed a general structural similarity with mammalian and yeast JMJD2 proteins that are H3K9 and H3K36 demethylases. However, several specific features were observed in the structure of c-JMJ703. Key residues that interact with cofactors Fe(II) and N-oxalylglycine and the methylated H3K4 substrate peptide were identified and were shown to be essential for the demethylase activity in vivo. Several key residues are specifically conserved in known H3K4 demethylases, suggesting that they may be involved in the specificity for H3K4 demethylation.

Authors+Show Affiliations

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23357881

Citation

Chen, Qingfeng, et al. "Structural Basis of a Histone H3 Lysine 4 Demethylase Required for Stem Elongation in Rice." PLoS Genetics, vol. 9, no. 1, 2013, pp. e1003239.
Chen Q, Chen X, Wang Q, et al. Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice. PLoS Genet. 2013;9(1):e1003239.
Chen, Q., Chen, X., Wang, Q., Zhang, F., Lou, Z., Zhang, Q., & Zhou, D. X. (2013). Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice. PLoS Genetics, 9(1), e1003239. https://doi.org/10.1371/journal.pgen.1003239
Chen Q, et al. Structural Basis of a Histone H3 Lysine 4 Demethylase Required for Stem Elongation in Rice. PLoS Genet. 2013;9(1):e1003239. PubMed PMID: 23357881.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice. AU - Chen,Qingfeng, AU - Chen,Xiangsong, AU - Wang,Quan, AU - Zhang,Faben, AU - Lou,Zhiyong, AU - Zhang,Qifa, AU - Zhou,Dao-Xiu, Y1 - 2013/01/24/ PY - 2012/04/09/received PY - 2012/11/27/accepted PY - 2013/1/30/entrez PY - 2013/1/30/pubmed PY - 2013/6/1/medline SP - e1003239 EP - e1003239 JF - PLoS genetics JO - PLoS Genet. VL - 9 IS - 1 N2 - Histone lysine methylation is an important epigenetic modification in regulating chromatin structure and gene expression. Histone H3 lysine 4 methylation (H3K4me), which can be in a mono-, di-, or trimethylated state, has been shown to play an important role in gene expression involved in plant developmental control and stress adaptation. However, the resetting mechanism of this epigenetic modification is not yet fully understood. In this work, we identified a JmjC domain-containing protein, JMJ703, as a histone lysine demethylase that specifically reverses all three forms of H3K4me in rice. Loss-of-function mutation of the gene affected stem elongation and plant growth, which may be related to increased expression of cytokinin oxidase genes in the mutant. Analysis of crystal structure of the catalytic core domain (c-JMJ703) of the protein revealed a general structural similarity with mammalian and yeast JMJD2 proteins that are H3K9 and H3K36 demethylases. However, several specific features were observed in the structure of c-JMJ703. Key residues that interact with cofactors Fe(II) and N-oxalylglycine and the methylated H3K4 substrate peptide were identified and were shown to be essential for the demethylase activity in vivo. Several key residues are specifically conserved in known H3K4 demethylases, suggesting that they may be involved in the specificity for H3K4 demethylation. SN - 1553-7404 UR - https://www.unboundmedicine.com/medline/citation/23357881/Structural_basis_of_a_histone_H3_lysine_4_demethylase_required_for_stem_elongation_in_rice_ L2 - https://dx.plos.org/10.1371/journal.pgen.1003239 DB - PRIME DP - Unbound Medicine ER -