Date of this Version
Genes & Development
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.
Copyright ©2012 Cold Spring Harbor Laboratory Press.
This article was published Open Access under a Creative Commons 4.0 International license.
DNA-dependent RNA polymerase, gene silencing, DNA methylation, epigenetics, short interfering RNA, RNA-directed DNA methylation
Wierzbicki, A. T., Cocklin, R., Mayampurath, A., Lister, R., Rowley, M. J., Gregory, B. D., Ecker, J. R., Tang, H., & Pikaard, C. S. (2012). Spatial and Functional Relationships Among Pol V-Associated Loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome. Genes & Development, 26 (16), 1825-1836. http://dx.doi.org/10.1101/gad.197772.112
Additional FilesSupplemental Fig 1_Spatial and functinal relationships among Pol V-associated loci.ps (1117 kB)
Supplemental Fig 2_Spatial and functional relationships among Pol V-associated loci.ps (1158 kB)
Supplemental Fig 3_Spatial and functional relationships among Pol V-associated loci.ps (1304 kB)
Supplemental Fig 4_Spatial and functional relationships among Pol V-associated loci.ps (1350 kB)
Supplemental_Figure_Legends_Spatial and functional relationships among Pol V-associated loci.docx (14 kB)
Table_S1_Spatial and functional relationships among Pol V-associated loci.xlsx (103 kB)
Tables_S2_Spatial and functional relationships among Pol V-associated loci.docx (36 kB)
Date Posted: 14 July 2017
This document has been peer reviewed.