Abstract
The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in Arabidopsis thaliana on a genome-wide scale using ChIP-seq of NRPE1, the largest catalytic subunit of Pol V. We found that Pol V is enriched at promoters and evolutionarily recent transposons. This localization pattern is highly correlated with Pol V-dependent DNA methylation and small RNA accumulation. We also show that genome-wide chromatin association of Pol V is dependent on all members of a putative chromatin-remodeling complex termed DDR. Our study presents a genome-wide view of Pol V occupancy and sheds light on the mechanistic basis of Pol V localization. Furthermore, these findings suggest a role for Pol V and RNA-directed DNA methylation in genome surveillance and in responding to genome evolution.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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Arabidopsis / genetics*
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Arabidopsis / metabolism
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Arabidopsis Proteins / analysis
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Arabidopsis Proteins / genetics
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Arabidopsis Proteins / metabolism*
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Chromatin / metabolism
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Chromosomal Proteins, Non-Histone / genetics
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Chromosomal Proteins, Non-Histone / metabolism*
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DNA Transposable Elements
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DNA-Binding Proteins / genetics
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DNA-Binding Proteins / metabolism*
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DNA-Directed RNA Polymerases / analysis
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DNA-Directed RNA Polymerases / genetics
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DNA-Directed RNA Polymerases / metabolism*
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Gene Expression Regulation, Plant*
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Gene Silencing
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Mutation
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Promoter Regions, Genetic
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Protein Subunits / analysis
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Protein Subunits / genetics
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Protein Subunits / metabolism
Substances
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Arabidopsis Proteins
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Chromatin
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Chromosomal Proteins, Non-Histone
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DMS3 protein, Arabidopsis
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DNA Transposable Elements
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DNA-Binding Proteins
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Protein Subunits
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RDM1 protein, Arabidopsis
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RNA polymerase V, Arabidopsis
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DNA-Directed RNA Polymerases
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DRD1 protein, Arabidopsis