Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading.
Plants use siRNAs to target cytosine DNA methylation to both symmetrical CG and nonsymmetrical (CHG and CHH) sequence contexts. DNA methylation and siRNA clusters most frequently overlap with transposons in the Arabidopsis thaliana genome. However, a significant number of protein-coding genes also show promoter DNA methylation, and this can be used to silence their expression. Loss of the majority of non-CG DNA methylation in drm1 drm2 cmt3 triple mutants leads to developmental phenotypes. We identified the gene responsible for these phenotypes as SUPPRESSOR OF drm1 drm2 cmt3 (SDC), which encodes an F-box protein and possesses seven promoter tandem repeats. The SDC repeats show a unique silencing requirement for non-CG DNA methylation directed redundantly by histone methylation and siRNAs, and display spreading of siRNAs and methylation beyond the repeated region. In addition to revealing the complexity of DNA methylation control in A. thaliana, SDC has important implications for how plant genomes utilize gene silencing to repress endogenous genes.
Henderson
Ian R
IR
Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
Jacobsen
Steven E
SE
D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000502:physiology; D019175:DNA Methylation; D015257:DNA-Cytosine Methylases / Q000235:genetics; D044783:F-Box Proteins / Q000235:genetics* / Q000502:physiology; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing / Q000502:physiology; D016153:Genes, Suppressor; D008780:Methyltransferases / Q000235:genetics; D030821:Plants, Genetically Modified; D034741:RNA, Small Interfering / Q000378:metabolism*; D020080:Tandem Repeat Sequences / Q000502:physiology*; D014018:Tissue Distribution; D014170:Transformation, Genetic
D029681:Arabidopsis Proteins; D044783:F-Box Proteins; D034741:RNA, Small Interfering; C000602552:SDC protein, Arabidopsis; D015257:DNA-Cytosine Methylases; D008780:Methyltransferases; C429766:CMT3 protein, Arabidopsis; C470731:DRM1 protein, Arabidopsis; C470732:DRM2 protein, Arabidopsis