Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

Non-CG methylation is abundant in plants, but its functions are poorly understood. A new study has uncovered the contributions of each non-CG methyltransferase, including the poorly characterized methyltransferase CMT2, to DNA methylation patterning and gene silencing. The results suggest that non-C...

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Published in	Nature structural & molecular biology Vol. 21; no. 1; pp. 64 - 72
Main Authors	Stroud, Hume, Do, Truman, Du, Jiamu, Zhong, Xuehua, Feng, Suhua, Johnson, Lianna, Patel, Dinshaw J, Jacobsen, Steven E
Format	Journal Article
Language	English
Published	New York Nature Publishing Group US 01.01.2014 Nature Publishing Group
Subjects	631/208/176/1988 631/449 Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism Arabidopsis Proteins - physiology Arabidopsis thaliana Biochemistry Biological Microscopy Chromatin Deoxyribonucleic acid DNA DNA Methylation DNA, Plant Epigenesis, Genetic Epigenetic inheritance Epigenetics Genetic aspects Genetic research Life Sciences Membrane Biology Methylation Molecular biology Physiological aspects Protein Structure Proteins United States
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Abstract	Non-CG methylation is abundant in plants, but its functions are poorly understood. A new study has uncovered the contributions of each non-CG methyltransferase, including the poorly characterized methyltransferase CMT2, to DNA methylation patterning and gene silencing. The results suggest that non-CG methyltransferases participate in self-reinforcing loop mechanisms with histone H3 K9 methylation and small RNAs to control gene silencing throughout the Arabidopsis genome. DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however, its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana . We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo . CMT2 preferentially binds histone H3 Lys9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small-RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA.
AbstractList	Non-CG methylation is abundant in plants, but its functions are poorly understood. A new study has uncovered the contributions of each non-CG methyltransferase, including the poorly characterized methyltransferase CMT2, to DNA methylation patterning and gene silencing. The results suggest that non-CG methyltransferases participate in self-reinforcing loop mechanisms with histone H3 K9 methylation and small RNAs to control gene silencing throughout the Arabidopsis genome. DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however, its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana . We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo . CMT2 preferentially binds histone H3 Lys9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small-RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA. DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however, its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 preferentially binds histone H3 Lys9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small-RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA. DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however, its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 preferentially binds histone H3 Lys9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small-RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA. [PUBLICATION ABSTRACT] DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however, its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 preferentially binds histone H3 Lys9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small-RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA.DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however, its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 preferentially binds histone H3 Lys9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small-RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA.
Audience	Academic
Author	Patel, Dinshaw J Zhong, Xuehua Stroud, Hume Johnson, Lianna Du, Jiamu Jacobsen, Steven E Feng, Suhua Do, Truman
Author_xml	– sequence: 1 givenname: Hume surname: Stroud fullname: Stroud, Hume organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles – sequence: 2 givenname: Truman surname: Do fullname: Do, Truman organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles – sequence: 3 givenname: Jiamu surname: Du fullname: Du, Jiamu organization: Structural Biology Program, Memorial Sloan-Kettering Cancer Center – sequence: 4 givenname: Xuehua surname: Zhong fullname: Zhong, Xuehua organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Present address: Wisconsin Institute for Discovery, Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, USA – sequence: 5 givenname: Suhua surname: Feng fullname: Feng, Suhua organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Howard Hughes Medical Institute, University of California, Los Angeles – sequence: 6 givenname: Lianna surname: Johnson fullname: Johnson, Lianna organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles – sequence: 7 givenname: Dinshaw J surname: Patel fullname: Patel, Dinshaw J organization: Structural Biology Program, Memorial Sloan-Kettering Cancer Center – sequence: 8 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, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Howard Hughes Medical Institute, University of California, Los Angeles
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/24336224$$D View this record in MEDLINE/PubMed
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Snippet	Non-CG methylation is abundant in plants, but its functions are poorly understood. A new study has uncovered the contributions of each non-CG... DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS...
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SubjectTerms	631/208/176/1988 631/449 Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism Arabidopsis Proteins - physiology Arabidopsis thaliana Biochemistry Biological Microscopy Chromatin Deoxyribonucleic acid DNA DNA Methylation DNA, Plant Epigenesis, Genetic Epigenetic inheritance Epigenetics Genetic aspects Genetic research Life Sciences Membrane Biology Methylation Molecular biology Physiological aspects Protein Structure Proteins
Title	Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis
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