Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis.
DRD1 is a SWI/SNF-like protein that cooperates with a plant-specific RNA polymerase, Pol IVb, to facilitate RNA-directed de novo methylation and silencing of homologous DNA. Screens to identify endogenous targets of this pathway in Arabidopsis revealed intergenic regions and plant genes located primarily in euchromatin. Many putative targets are near retrotransposon LTRs or other intergenic sequences that encode short RNAs, which might epigenetically regulate adjacent genes. Consistent with this, derepression of a solo LTR in drd1 and pol IVb mutants was accompanied by reduced cytosine methylation and transcriptional upregulation of neighboring sequences. The solo LTR and several other LTRs that flank reactivated targets are associated with euchromatic histone modifications but little or no H3K9 dimethylation, a hallmark of constitutive heterochromatin. By contrast, LTRs of retrotransposons that remain silent in the mutants despite reduced cytosine methylation lack euchromatic marks and have H3K9 dimethylation. We propose that DRD1 and Pol IVb establish a basal level of silencing that can potentially be reversed in euchromatin, and further reinforced in heterochromatin by other proteins that induce more stable modifications.
Huettel
Bruno
B
Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria.
Kanno
Tatsuo
T
Daxinger
Lucia
L
Aufsatz
Werner
W
Matzke
Antonius J M
AJ
Matzke
Marjori
M
D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D019175:DNA Methylation; D019951:DNA Polymerase beta / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D015536:Down-Regulation / Q000235:genetics; D020869:Gene Expression Profiling; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D018749:RNA, Plant / Q000378:metabolism*; D020079:Terminal Repeat Sequences / Q000235:genetics; D015854:Up-Regulation / Q000235:genetics
D029681:Arabidopsis Proteins; D018749:RNA, Plant; D012321:DNA-Directed RNA Polymerases; C504888:DRD1 protein, Arabidopsis; D019951:DNA Polymerase beta