Spatial and Functional Relationships Among Pol V-Associated Loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome

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Departmental Papers (Biology)
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DNA-dependent RNA polymerase
gene silencing
DNA methylation
epigenetics
short interfering RNA
RNA-directed DNA methylation
Biology
Genetics and Genomics
Nucleic Acids, Nucleotides, and Nucleosides
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Wierzbicki, Andrzej T
Cocklin, Ross
Mayampurath, Anoop
Lister, Ryan
Rowley, M. J
Ecker, Joseph R
Tang, Haixu
Pikaard, Craig S
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Multisubunit RNA polymerases IV and V (Pols IV and V) mediate RNA-directed DNA methylation and transcriptional silencing of retrotransposons and heterochromatic repeats in plants. We identified genomic sites of Pol V occupancy in parallel with siRNA deep sequencing and methylcytosine mapping, comparing wild-type plants with mutants defective for Pol IV, Pol V, or both Pols IV and V. Approximately 60% of Pol V-associated regions encompass regions of 24-nucleotide (nt) siRNA complementarity and cytosine methylation, consistent with cytosine methylation being guided by base-pairing of Pol IV-dependent siRNAs with Pol V transcripts. However, 27% of Pol V peaks do not overlap sites of 24-nt siRNA biogenesis or cytosine methylation, indicating that Pol V alone does not specify sites of cytosine methylation. Surprisingly, the number of methylated CHH motifs, a hallmark of RNA-directed de novo methylation, is similar in wild-type plants and Pol IV or Pol V mutants. In the mutants, methylation is lost at 50%–60% of the CHH sites that are methylated in the wild type but is gained at new CHH positions, primarily in pericentromeric regions. These results indicate that Pol IV and Pol V are not required for cytosine methyltransferase activity but shape the epigenome by guiding CHH methylation to specific genomic sites.

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2012-08-15
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At the time of this publication, Dr. Gregory was affiliated with the Salk Institute, but he is now a faculty member of the University of Pennsylvania.
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