Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 109, Issue 14, Pages 5370-5375Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1203145109
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Funding
- Ministry of Science and Education [BFU2009-9783, CSD2007-00057-B]
- Fundacion Ramon Areces
- Consejo Superior de Investigaciones Cientificas
- National Science Foundation [MCB-1121245]
- Fred Eiserling and Judith Lengyel Graduate Doctoral Fellowship
- Direct For Biological Sciences [1121245] Funding Source: National Science Foundation
- Div Of Molecular and Cellular Bioscience [1121245] Funding Source: National Science Foundation
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Nucleosomes package eukaryotic DNA and are composed of four different histone proteins, designated H3, H4, H2A, and H2B. Histone H3 has two main variants, H3.1 and H3.3, which show different genomic localization patterns in animals. We profiled H3.1 and H3.3 variants in the genome of the plant Arabidopsis thaliana and found that the localization of these variants shows broad similarity in plants and animals, along with some unique features. H3.1 was enriched in silent areas of the genome, including regions containing the repressive chromatin modifications H3 lysine 27 methylation, H3 lysine 9 methylation, and DNA methylation. In contrast, H3.3 was enriched in actively transcribed genes, especially peaking at the 3' end of genes, and correlated with histone modifications associated with gene activation, such as histone H3 lysine 4 methylation and H2B ubiquitylation, as well as RNA Pol II occupancy. Surprisingly, both H3.1 and H3.3 were enriched on defined origins of replication, as was overall nucleosome density, suggesting a novel characteristic of plant origins. Our results are broadly consistent with the hypothesis that H3.1 acts as the canonical histone that is incorporated during DNA replication, whereas H3.3 acts as the replacement histone that can be incorporated outside of S-phase during chromatin-disrupting processes like transcription.
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