Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants
DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT...
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| Published in | Cell Vol. 151; no. 1; pp. 167 - 180 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
28.09.2012
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| Subjects | |
| Online Access | Get full text |
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| Abstract | DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification.
[Display omitted]
► CMT3 stably associates with H3K9me2-containing nucleosomes ► CMT3 has CHG MTase activity and is expressed in actively replicating cells ► Structural and ITC studies reveal that both BAH and chromo domains recognize H3K9me ► The dual-recognition model establishes mechanism targeting DNA methylation in plants
Two domains of the chromomethylase CMT3, which methylates CHG sites in Arabidopsis DNA, mediate the binding of CMT3 to dimethylated H3K9, explaining how H3K9me2 promotes DNA methylation at heterochromatic sites. |
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| AbstractList | DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2 and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homologue, ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both BAH- and chromo-domains. The structures reveal an aromatic cage within both BAH- and chromo-domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes, and show a complete loss of CMT3 activity
in vivo
. Our study establishes dual recognition of H3K9me2 marks by BAH- and chromo-domains, and reveals a novel mechanism of interplay between DNA methylation and histone modification. DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification. DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification.DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification. DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification. DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification. [Display omitted] ► CMT3 stably associates with H3K9me2-containing nucleosomes ► CMT3 has CHG MTase activity and is expressed in actively replicating cells ► Structural and ITC studies reveal that both BAH and chromo domains recognize H3K9me ► The dual-recognition model establishes mechanism targeting DNA methylation in plants Two domains of the chromomethylase CMT3, which methylates CHG sites in Arabidopsis DNA, mediate the binding of CMT3 to dimethylated H3K9, explaining how H3K9me2 promotes DNA methylation at heterochromatic sites. |
| Author | Tu, Andy Hetzel, Jonathan Vashisht, Ajay A. Pradhan, Sriharsa Stroud, Hume Du, Jiamu Chin, Hang Gyeong Caro, Elena Wohlschlegel, James A. Zhong, Xuehua Terragni, Jolyon Jacobsen, Steven E. Patel, Dinshaw J. Feng, Suhua Bernatavichute, Yana V. |
| AuthorAffiliation | 3 Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, 90095, USA 5 Howard Hughes Medical Institute and Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California, 90095, USA 4 New England Biolabs, Ipswich, Massachusetts, 01938, USA 1 Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA 2 Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, USA |
| AuthorAffiliation_xml | – name: 2 Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, 90095, USA – name: 3 Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, 90095, USA – name: 4 New England Biolabs, Ipswich, Massachusetts, 01938, USA – name: 5 Howard Hughes Medical Institute and Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California, 90095, USA – name: 1 Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA |
| Author_xml | – sequence: 1 givenname: Jiamu surname: Du fullname: Du, Jiamu organization: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA – sequence: 2 givenname: Xuehua surname: Zhong fullname: Zhong, Xuehua organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 3 givenname: Yana V. surname: Bernatavichute fullname: Bernatavichute, Yana V. organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 4 givenname: Hume surname: Stroud fullname: Stroud, Hume organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 5 givenname: Suhua surname: Feng fullname: Feng, Suhua organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 6 givenname: Elena surname: Caro fullname: Caro, Elena organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 7 givenname: Ajay A. surname: Vashisht fullname: Vashisht, Ajay A. organization: Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 8 givenname: Jolyon surname: Terragni fullname: Terragni, Jolyon organization: New England Biolabs, Ipswich, MA 01938, USA – sequence: 9 givenname: Hang Gyeong surname: Chin fullname: Chin, Hang Gyeong organization: New England Biolabs, Ipswich, MA 01938, USA – sequence: 10 givenname: Andy surname: Tu fullname: Tu, Andy organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 11 givenname: Jonathan surname: Hetzel fullname: Hetzel, Jonathan organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 12 givenname: James A. surname: Wohlschlegel fullname: Wohlschlegel, James A. organization: Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 13 givenname: Sriharsa surname: Pradhan fullname: Pradhan, Sriharsa organization: New England Biolabs, Ipswich, MA 01938, USA – sequence: 14 givenname: Dinshaw J. surname: Patel fullname: Patel, Dinshaw J. email: pateld@mskcc.org organization: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA – sequence: 15 givenname: Steven E. surname: Jacobsen fullname: Jacobsen, Steven E. email: jacobsen@ucla.edu organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23021223$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | Amino Acid Sequence Arabidopsis - genetics Arabidopsis - metabolism corn crystal structure Crystallography, X-Ray DNA (Cytosine-5-)-Methyltransferases - chemistry DNA (Cytosine-5-)-Methyltransferases - metabolism DNA Methylation DNA, Plant - metabolism epigenetics gene expression genome Heterochromatin - metabolism histones Histones - metabolism methylation Models, Molecular Molecular Sequence Data mutation nucleosomes Nucleosomes - metabolism peptides Sequence Alignment Zea mays - genetics Zea mays - metabolism |
| Title | Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants |
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