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Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional...

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Autores principales: Wang, Congmao, Liu, Chang, Roqueiro, Damian, Grimm, Dominik, Schwab, Rebecca, Becker, Claude, Lanz, Christa, Weigel, Detlef
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315298/
https://www.ncbi.nlm.nih.gov/pubmed/25367294
http://dx.doi.org/10.1101/gr.170332.113
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author Wang, Congmao
Liu, Chang
Roqueiro, Damian
Grimm, Dominik
Schwab, Rebecca
Becker, Claude
Lanz, Christa
Weigel, Detlef
author_facet Wang, Congmao
Liu, Chang
Roqueiro, Damian
Grimm, Dominik
Schwab, Rebecca
Becker, Claude
Lanz, Christa
Weigel, Detlef
author_sort Wang, Congmao
collection PubMed
description The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.
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spelling pubmed-43152982015-02-05 Genome-wide analysis of local chromatin packing in Arabidopsis thaliana Wang, Congmao Liu, Chang Roqueiro, Damian Grimm, Dominik Schwab, Rebecca Becker, Claude Lanz, Christa Weigel, Detlef Genome Res Research The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome. Cold Spring Harbor Laboratory Press 2015-02 /pmc/articles/PMC4315298/ /pubmed/25367294 http://dx.doi.org/10.1101/gr.170332.113 Text en © 2015 Wang et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0.
spellingShingle Research
Wang, Congmao
Liu, Chang
Roqueiro, Damian
Grimm, Dominik
Schwab, Rebecca
Becker, Claude
Lanz, Christa
Weigel, Detlef
Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
title Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
title_full Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
title_fullStr Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
title_full_unstemmed Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
title_short Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
title_sort genome-wide analysis of local chromatin packing in arabidopsis thaliana
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315298/
https://www.ncbi.nlm.nih.gov/pubmed/25367294
http://dx.doi.org/10.1101/gr.170332.113
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