Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE

In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate...

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Published in	Molecular cell Vol. 55; no. 3; pp. 495 - 504
Main Authors	Du, Jiamu, Johnson, Lianna M., Groth, Martin, Feng, Suhua, Hale, Christopher J., Li, Sisi, Vashisht, Ajay A., Gallego-Bartolome, Javier, Wohlschlegel, James A., Patel, Dinshaw J., Jacobsen, Steven E.
Format	Journal Article
Language	English
Published	United States Elsevier Inc 07.08.2014
Subjects	Arabidopsis Arabidopsis - chemistry Arabidopsis - genetics Arabidopsis - metabolism Arabidopsis Proteins - chemistry Arabidopsis Proteins - metabolism Binding Sites - genetics DNA DNA Methylation DNA, Plant - chemistry DNA, Plant - genetics Epigenesis, Genetic Gene Expression Regulation, Plant Genome, Plant Histone-Lysine N-Methyltransferase - chemistry Histone-Lysine N-Methyltransferase - metabolism histones Histones - physiology methyltransferases Models, Molecular mutants S-Adenosylhomocysteine - metabolism X-Ray Diffraction
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Abstract	In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide, and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1–15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights, complemented by functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation. [Display omitted] •Crystal structure of KYP in complex with mCHH DNA, SAH, and H3 peptide•Two-helix segment of KYP mediates relative alignment of SRA and SET domains•mCHH DNA and H3 tail are specifically recognized by SRA and SET domains, respectively•Structural model of KYP and CMT3-controlled DNA and histone methylation feedback loop Du et al. report on the structural and functional studies of a plant histone H3K9 methyltransferase, KRYPTONITE, in complex with mCHH DNA, H3 peptide, and SAH, revealing how this enzyme links DNA and histone methylation.
AbstractList	In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide, and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights, complemented by functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation. In Arabidopsis , CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights complemented by in vivo functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation. In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide, and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1–15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights, complemented by functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation. [Display omitted] •Crystal structure of KYP in complex with mCHH DNA, SAH, and H3 peptide•Two-helix segment of KYP mediates relative alignment of SRA and SET domains•mCHH DNA and H3 tail are specifically recognized by SRA and SET domains, respectively•Structural model of KYP and CMT3-controlled DNA and histone methylation feedback loop Du et al. report on the structural and functional studies of a plant histone H3K9 methyltransferase, KRYPTONITE, in complex with mCHH DNA, H3 peptide, and SAH, revealing how this enzyme links DNA and histone methylation. In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide, and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights, complemented by functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation.In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide, and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights, complemented by functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation.
Author	Johnson, Lianna M. Wohlschlegel, James A. Vashisht, Ajay A. Groth, Martin Li, Sisi Jacobsen, Steven E. Patel, Dinshaw J. Du, Jiamu Feng, Suhua Gallego-Bartolome, Javier Hale, Christopher J.
AuthorAffiliation	4 Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA 5 Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA 3 Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, CA 90095, USA 1 Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA 2 Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
AuthorAffiliation_xml	– name: 2 Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA – name: 5 Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA – name: 3 Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, CA 90095, USA – name: 1 Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA – name: 4 Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
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Snippet	In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3... In Arabidopsis , CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3...
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SubjectTerms	Arabidopsis Arabidopsis - chemistry Arabidopsis - genetics Arabidopsis - metabolism Arabidopsis Proteins - chemistry Arabidopsis Proteins - metabolism Binding Sites - genetics DNA DNA Methylation DNA, Plant - chemistry DNA, Plant - genetics Epigenesis, Genetic Gene Expression Regulation, Plant Genome, Plant Histone-Lysine N-Methyltransferase - chemistry Histone-Lysine N-Methyltransferase - metabolism histones Histones - physiology methyltransferases Models, Molecular mutants S-Adenosylhomocysteine - metabolism X-Ray Diffraction
Title	Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE
URI	https://dx.doi.org/10.1016/j.molcel.2014.06.009 https://www.ncbi.nlm.nih.gov/pubmed/25018018 https://www.proquest.com/docview/1552370220 https://www.proquest.com/docview/2000201811 https://pubmed.ncbi.nlm.nih.gov/PMC4127122
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