Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unkn...

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Published in	Cell Vol. 152; no. 1-2; pp. 352 - 364
Main Authors	Stroud, Hume, Greenberg, Maxim V.C., Feng, Suhua, Bernatavichute, Yana V., Jacobsen, Steven E.
Format	Journal Article
Language	English
Published	United States Elsevier Inc 17.01.2013 Elsevier
Subjects	Arabidopsis Arabidopsis - genetics Arabidopsis Proteins - metabolism CpG Islands data analysis DNA Methylation Gene Silencing genome Genome, Plant Genome-Wide Association Study Histones - metabolism Life Sciences mutants RNA Interference RNA Polymerase II - metabolism RNA Splicing Factors transposons
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Abstract	Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning. [Display omitted] ► Genome-wide single-nucleotide resolution methylation maps in 86 silencing mutants ► Complex interplays between different DNA methylation pathways ► Identification of novel regulators of DNA methylation A genome-wide study of DNA methylation in a comprehensive list of Arabidopsis mutants implicated in gene silencing and histone modification reveals that different pathways regulate DNA methylation site specifically, and the study uncovers new factors that regulate DNA methylation.
AbstractList	Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning. Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning. Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning. Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning. [Display omitted] ► Genome-wide single-nucleotide resolution methylation maps in 86 silencing mutants ► Complex interplays between different DNA methylation pathways ► Identification of novel regulators of DNA methylation A genome-wide study of DNA methylation in a comprehensive list of Arabidopsis mutants implicated in gene silencing and histone modification reveals that different pathways regulate DNA methylation site specifically, and the study uncovers new factors that regulate DNA methylation. Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning.Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning.
Author	Greenberg, Maxim V.C. Jacobsen, Steven E. Stroud, Hume Feng, Suhua Bernatavichute, Yana V.
AuthorAffiliation	3 Howard Hughes Medical Institute University of California, Los Angeles, Los Angeles, CA 90095, USA 2 Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Los Angeles, Los Angeles, CA 90095, USA 1 Department of Molecular, Cell and Developmental Biology, Los Angeles, Los Angeles, CA 90095, USA
AuthorAffiliation_xml	– name: 3 Howard Hughes Medical Institute University of California, Los Angeles, Los Angeles, CA 90095, USA – name: 2 Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Los Angeles, Los Angeles, CA 90095, USA – name: 1 Department of Molecular, Cell and Developmental Biology, Los Angeles, Los Angeles, CA 90095, USA
Author_xml	– sequence: 1 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: 2 givenname: Maxim V.C. surname: Greenberg fullname: Greenberg, Maxim V.C. organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 3 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: 4 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: 5 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/23313553$$D View this record in MEDLINE/PubMed https://hal.science/hal-03439061$$DView record in HAL
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Snippet	Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate...
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SubjectTerms	Arabidopsis Arabidopsis - genetics Arabidopsis Proteins - metabolism CpG Islands data analysis DNA Methylation Gene Silencing genome Genome, Plant Genome-Wide Association Study Histones - metabolism Life Sciences mutants RNA Interference RNA Polymerase II - metabolism RNA Splicing Factors transposons
Title	Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome
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