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RNAi‐independent de novo DNA methylation revealed in Arabidopsis mutants of chromatin remodeling gene DDM1
Author(s) -
Sasaki Taku,
Kobayashi Akie,
Saze Hidetoshi,
Kakutani Tetsuji
Publication year - 2012
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2012.04911.x
Subject(s) - biology , rna directed dna methylation , dna methylation , histone methyltransferase , genetics , chromatin remodeling , methylation , epigenetics of physical exercise , epigenetics , histone methylation , chromatin , gene , gene expression
Summary 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.