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

Abstract

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 tomore » specific genomic sites.« less

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1097971
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Genes & Development, 26(16):1825-1836
Additional Journal Information:
Journal Name: Genes & Development, 26(16):1825-1836
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Wierzbicki, A. T., Cocklin, Ross, Mayampurath, Anoop, Lister, Ryan, Rowley, M. J., Gregory, Brian D., Ecker, Joseph R., Tang, Haixu, and Pikaard, Craig S. Spatial and Functional Relationships Among Pol V-Associated loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome. United States: N. p., 2012. Web. doi:10.1101/gad.197772.112.
Wierzbicki, A. T., Cocklin, Ross, Mayampurath, Anoop, Lister, Ryan, Rowley, M. J., Gregory, Brian D., Ecker, Joseph R., Tang, Haixu, & Pikaard, Craig S. Spatial and Functional Relationships Among Pol V-Associated loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome. United States. https://doi.org/10.1101/gad.197772.112
Wierzbicki, A. T., Cocklin, Ross, Mayampurath, Anoop, Lister, Ryan, Rowley, M. J., Gregory, Brian D., Ecker, Joseph R., Tang, Haixu, and Pikaard, Craig S. 2012. "Spatial and Functional Relationships Among Pol V-Associated loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome". United States. https://doi.org/10.1101/gad.197772.112.
@article{osti_1097971,
title = {Spatial and Functional Relationships Among Pol V-Associated loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome},
author = {Wierzbicki, A. T. and Cocklin, Ross and Mayampurath, Anoop and Lister, Ryan and Rowley, M. J. and Gregory, Brian D. and Ecker, Joseph R. and Tang, Haixu and Pikaard, Craig S.},
abstractNote = {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.},
doi = {10.1101/gad.197772.112},
url = {https://www.osti.gov/biblio/1097971}, journal = {Genes & Development, 26(16):1825-1836},
number = ,
volume = ,
place = {United States},
year = {Wed Aug 15 00:00:00 EDT 2012},
month = {Wed Aug 15 00:00:00 EDT 2012}
}