Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis

Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. Our genome-wide approach confirmed interactions that were previously observed by other methods as well as u...

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Published in	Molecular cell Vol. 55; no. 5; pp. 694 - 707
Main Authors	Feng, Suhua, Cokus, Shawn J., Schubert, Veit, Zhai, Jixian, Pellegrini, Matteo, Jacobsen, Steven E.
Format	Journal Article
Language	English
Published	United States Elsevier Inc 04.09.2014
Subjects	animals Arabidopsis - genetics Arabidopsis - metabolism Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism Arabidopsis Proteins - physiology Arabidopsis thaliana Chromatin - metabolism Chromatin - ultrastructure Chromosomes, Plant - chemistry Chromosomes, Plant - metabolism DNA, Plant - chemistry Epigenesis, Genetic - genetics epigenetics genome Genome, Plant Genomics - methods heterochromatin mutants Mutation Nucleic Acid Conformation topology
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Abstract	Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. Our genome-wide approach confirmed interactions that were previously observed by other methods as well as uncovered long-range interactions such as those among small heterochromatic regions embedded in euchromatic arms. We also found that interactions are correlated with various epigenetic marks that are localized in active or silenced chromatin. Arabidopsis chromosomes do not contain large local interactive domains that resemble the topological domains described in animals but, instead, contain relatively small interactive regions scattered around the genome that contain H3K27me3 or H3K9me2. We generated interaction maps in mutants that are defective in specific epigenetic pathways and found altered interaction patterns that correlate with changes in the epigenome. These analyses provide further insights into molecular mechanisms of epigenetic regulation of the genome. [Display omitted] •Chromatins interact through pericentromeres, telomeres, and adjacent regions•Interactive heterochromatic islands (IHIs) show strong long-range interactions•Interactions are correlated with epigenetic marks in active or silenced chromatins•Mutants in repressive epigenetic pathways alter chromatin-interaction patterns Using Hi-C analysis, Feng et al. show extensive interactions among regions of Arabidopsis chromatin. These interactions correlate with epigenetic marks, and mutants of epigenetic pathways affect interaction patterns.
AbstractList	Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. Our genome-wide approach confirmed interactions that were previously observed by other methods as well as uncovered long-range interactions such as those among small heterochromatic regions embedded in euchromatic arms. We also found that interactions are correlated with various epigenetic marks that are localized in active or silenced chromatin. Arabidopsis chromosomes do not contain large local interactive domains that resemble the topological domains described in animals but, instead, contain relatively small interactive regions scattered around the genome that contain H3K27me3 or H3K9me2. We generated interaction maps in mutants that are defective in specific epigenetic pathways and found altered interaction patterns that correlate with changes in the epigenome. These analyses provide further insights into molecular mechanisms of epigenetic regulation of the genome. Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. Our genome-wide approach confirmed interactions that were previously observed by other methods as well as uncovered long-range interactions such as those among small heterochromatic regions embedded in euchromatic arms. We also found that interactions are correlated with various epigenetic marks that are localized in active or silenced chromatin. Arabidopsis chromosomes do not contain large local interactive domains that resemble the topological domains described in animals but, instead, contain relatively small interactive regions scattered around the genome that contain H3K27me3 or H3K9me2. We generated interaction maps in mutants that are defective in specific epigenetic pathways and found altered interaction patterns that correlate with changes in the epigenome. These analyses provide further insights into molecular mechanisms of epigenetic regulation of the genome.Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. Our genome-wide approach confirmed interactions that were previously observed by other methods as well as uncovered long-range interactions such as those among small heterochromatic regions embedded in euchromatic arms. We also found that interactions are correlated with various epigenetic marks that are localized in active or silenced chromatin. Arabidopsis chromosomes do not contain large local interactive domains that resemble the topological domains described in animals but, instead, contain relatively small interactive regions scattered around the genome that contain H3K27me3 or H3K9me2. We generated interaction maps in mutants that are defective in specific epigenetic pathways and found altered interaction patterns that correlate with changes in the epigenome. These analyses provide further insights into molecular mechanisms of epigenetic regulation of the genome. Chromosomes form three-dimensional structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana . Our genome-wide approach confirmed interactions that were previously observed by other methods as well as uncovered previously unknown long-range interactions such as those among small heterochromatic regions embedded in euchromatic arms. We also found that interactions are correlated with various epigenetic marks that are localized in active or silenced chromatin. Arabidopsis chromosomes do not contain large local interactive domains that resemble the topological domains described in animals, but instead contain relatively small interactive regions scattered around the genome that contain H3K27me3 or H3K9me2. We generated interaction maps in mutants that are defective in specific epigenetic pathways and found altered interaction patterns that correlate with changes in the epigenome. These analyses provide further insights into molecular mechanisms of epigenetic regulation of the genome. Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. Our genome-wide approach confirmed interactions that were previously observed by other methods as well as uncovered long-range interactions such as those among small heterochromatic regions embedded in euchromatic arms. We also found that interactions are correlated with various epigenetic marks that are localized in active or silenced chromatin. Arabidopsis chromosomes do not contain large local interactive domains that resemble the topological domains described in animals but, instead, contain relatively small interactive regions scattered around the genome that contain H3K27me3 or H3K9me2. We generated interaction maps in mutants that are defective in specific epigenetic pathways and found altered interaction patterns that correlate with changes in the epigenome. These analyses provide further insights into molecular mechanisms of epigenetic regulation of the genome. [Display omitted] •Chromatins interact through pericentromeres, telomeres, and adjacent regions•Interactive heterochromatic islands (IHIs) show strong long-range interactions•Interactions are correlated with epigenetic marks in active or silenced chromatins•Mutants in repressive epigenetic pathways alter chromatin-interaction patterns Using Hi-C analysis, Feng et al. show extensive interactions among regions of Arabidopsis chromatin. These interactions correlate with epigenetic marks, and mutants of epigenetic pathways affect interaction patterns.
Author	Jacobsen, Steven E. Schubert, Veit Cokus, Shawn J. Zhai, Jixian Feng, Suhua Pellegrini, Matteo
AuthorAffiliation	1 Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA 4 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany 3 Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA 2 Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, CA 90095, USA
AuthorAffiliation_xml	– name: 2 Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, CA 90095, USA – name: 4 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany – name: 1 Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA – name: 3 Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
Author_xml	– sequence: 1 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: 2 givenname: Shawn J. surname: Cokus fullname: Cokus, Shawn J. organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 3 givenname: Veit surname: Schubert fullname: Schubert, Veit organization: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany – sequence: 4 givenname: Jixian surname: Zhai fullname: Zhai, Jixian organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 5 givenname: Matteo surname: Pellegrini fullname: Pellegrini, Matteo organization: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA – sequence: 6 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/25132175$$D View this record in MEDLINE/PubMed
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Snippet	Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction... Chromosomes form 3D structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global chromatin interaction... Chromosomes form three-dimensional structures that are critical to the regulation of cellular and genetic processes. Here, we present a study of global...
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SubjectTerms	animals Arabidopsis - genetics Arabidopsis - metabolism Arabidopsis Proteins - genetics Arabidopsis Proteins - metabolism Arabidopsis Proteins - physiology Arabidopsis thaliana Chromatin - metabolism Chromatin - ultrastructure Chromosomes, Plant - chemistry Chromosomes, Plant - metabolism DNA, Plant - chemistry Epigenesis, Genetic - genetics epigenetics genome Genome, Plant Genomics - methods heterochromatin mutants Mutation Nucleic Acid Conformation topology
Title	Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis
URI	https://dx.doi.org/10.1016/j.molcel.2014.07.008 https://www.ncbi.nlm.nih.gov/pubmed/25132175 https://www.proquest.com/docview/1560584265 https://www.proquest.com/docview/2000196210 https://pubmed.ncbi.nlm.nih.gov/PMC4347903
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