title: RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1.
abstract: Methylation of histone H3 lysine 9 (H3K9me) and small RNAs are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. Transposon-specific non-CpG methylation in plants is controlled by small RNAs and H3K9me. Although it is often assumed that small RNA directs H3K9me, interaction between small RNA and H3K9me has not been directly demonstrated in plants. We have previously shown that a mutation in the chromatin remodeling gene DDM1 (DECREASE IN DNA METHYLATION 1) induces a global decrease but a local increase of cytosine methylation and accumulation of small RNA at a locus called BONSAI. Here we show that de novo BONSAI methylation does not depend on RNAi but does depend on H3K9me. In mutants of H3K9 methyltransferase gene KRYPTONITE or the H3K9me-dependent DNA methyltransferase gene CHROMOMETHYALSE3, the ddm1-induced de novo cytosine methylation was abolished for all three contexts (CpG, CpHpG and CpHpH). Furthermore, RNAi mutants showed strong developmental defects when combined with the ddm1 mutation. Our results revealed unexpected interactions of epigenetic modifications that may be conserved among diverse eukaryotes.
authors.affiliation: Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Taku
authors.initials: T
authors.lastname: Sasaki
authors.forename: Akie
authors.initials: A
authors.lastname: Kobayashi
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Saze
authors.forename: Tetsuji
authors.initials: T
authors.lastname: Kakutani
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D019175:DNA Methylation; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D015257:DNA-Cytosine Methylases / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D056426:Genetic Loci; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D054817:Pollination; D034622:RNA Interference; D057945:Self-Fertilization; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; C118957:DDM1 protein, Arabidopsis; D018744:DNA, Plant; D004268:DNA-Binding Proteins; D006657:Histones; D014157:Transcription Factors; D015257:DNA-Cytosine Methylases; C429766:CMT3 protein, Arabidopsis; D011495:Histone-Lysine N-Methyltransferase; C471228:SUVH4 protein, Arabidopsis