期刊
GENES & DEVELOPMENT
卷 26, 期 16, 页码 1825-1836出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gad.197772.112
关键词
DNA-dependent RNA polymerase; gene silencing; DNA methylation; epigenetics; short interfering RNA; RNA-directed DNA methylation
资金
- National Institutes of Health grant [GM07759]
- Indiana University Competitive Research Grant
- National Science Foundation Grant [MCB 1120271]
- Ruth L. Kirschstein National Research Service Awards
- Direct For Biological Sciences [1120271] Funding Source: National Science Foundation
- Div Of Molecular and Cellular Bioscience [1120271] Funding Source: National Science Foundation
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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