The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States
Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromati...
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| Published in | The Plant cell Vol. 26; no. 6; pp. 2351 - 2366 |
|---|---|
| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
American Society of Plant Biologists
01.06.2014
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS) to termination sites and two contain regulatory regions upstream of TSS. Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains. |
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| AbstractList | Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS) to termination sites and two contain regulatory regions upstream of TSS. Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains. Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS) to termination sites and two contain regulatory regions upstream of TSS. Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS) to termination sites and two contain regulatory regions upstream of TSS. Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains. A computational study of combinations of histone modifications and DNA features was developed to determine a high-resolution landscape of Arabidopsis chromatin states. The linear topography across the genome revealed the existence of chromatin motifs. This work provides a basis for studies on gene expression, e.g., bivalent H3K27me3/H3K4me3-containing regions, DNA replication, and epigenetics. A computational study of combinations of histone modifications and DNA features was developed to determine a high-resolution landscape of Arabidopsis chromatin states. The linear topography across the genome revealed the existence of chromatin motifs. This work provides a basis for studies on gene expression, e.g., bivalent H3K27me3/H3K4me3-containing regions, DNA replication, and epigenetics. Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites ( TSS ) to termination sites and two contain regulatory regions upstream of TSS . Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains. |
| Author | Gutierrez, Crisanto Mendez-Giraldez, Raul Peiró, Ramón Sequeira-Mendes, Joana Aragüez, Irene Jacobsen, Steven E. Zhang, Xiaoyu Bastolla, Ugo |
| Author_xml | – sequence: 1 givenname: Joana surname: Sequeira-Mendes fullname: Sequeira-Mendes, Joana – sequence: 2 givenname: Irene surname: Aragüez fullname: Aragüez, Irene – sequence: 3 givenname: Ramón surname: Peiró fullname: Peiró, Ramón – sequence: 4 givenname: Raul surname: Mendez-Giraldez fullname: Mendez-Giraldez, Raul – sequence: 5 givenname: Xiaoyu surname: Zhang fullname: Zhang, Xiaoyu – sequence: 6 givenname: Steven E. surname: Jacobsen fullname: Jacobsen, Steven E. – sequence: 7 givenname: Ugo surname: Bastolla fullname: Bastolla, Ugo – sequence: 8 givenname: Crisanto surname: Gutierrez fullname: Gutierrez, Crisanto |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24934173$$D View this record in MEDLINE/PubMed |
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| Copyright | 2014 American Society of Plant Biologists 2014 American Society of Plant Biologists. All rights reserved. 2014 American Society of Plant Biologists. All rights reserved. 2014 |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 www.plantcell.org/cgi/doi/10.1105/tpc.114.124578 Current address: Department of Plant Biology, University of Georgia, Athens, GA 30602-7271. Current address: Department of Biophysics and Biochemistry Genetic Medicine, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC 27599. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Crisanto Gutierrez (cgutierrez@cbm.csic.es). |
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| PublicationDate_xml | – month: 06 year: 2014 text: 2014-06-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | The Plant cell |
| PublicationTitleAlternate | Plant Cell |
| PublicationYear | 2014 |
| Publisher | American Society of Plant Biologists |
| Publisher_xml | – name: American Society of Plant Biologists |
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| Snippet | Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin... A computational study of combinations of histone modifications and DNA features was developed to determine a high-resolution landscape of Arabidopsis chromatin... A computational study of combinations of histone modifications and DNA features was developed to determine a high-resolution landscape of Arabidopsis chromatin... |
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| SubjectTerms | Antibodies Arabidopsis Chromatin DNA DNA replication epigenetics gene expression Genes genome Genomes Genomics Heterochromatin Histones Intergenic DNA landscapes Large-Scale Biology LARGE-SCALE BIOLOGY ARTICLE Nucleosomes Promoter regions topography |
| Title | The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States |
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