Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis.
RNA-directed DNA methylation (RdDM) is a process in which 24 nucleotide (nt) small interfering RNAs (siRNAs) guide de novo cytosine methylation in the homologous genomic DNA region. Of several factors involving 24 nt siRNA accumulation, RNA-dependent RNA polymerase 2 (RDR2) is a key component, because accumulation of 24 nt siRNA disappears in the Arabidopsis rdr2 mutant. Here, we compared expression profiles among wild-type, rdr2-1 and ddc (drm1drm2cmt3), DNA methyltransferase triple mutant, using a whole genome tiling array to identify the candidate genes directly downregulated by RdDM-related 24 nt siRNAs. Of the transcripts upregulated in the mutants, we searched for those whose coding regions or flanking regions have siRNA-generating loci. We found upregulated expression of 18 transcripts with AGI codes and 19 predicted transcriptional units (TUs) with siRNA loci in both rdr2-1 and ddc. Our study provided important information for understanding the relationship between RdDM and the identified candidate genes.
Kurihara
Yukio
Y
Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan.
Matsui
Akihiro
A
Kawashima
Makiko
M
Kaminuma
Eli
E
Ishida
Junko
J
Morosawa
Taeko
T
Mochizuki
Yoshiki
Y
Kobayashi
Norio
N
Toyoda
Tetsuro
T
Shinozaki
Kazuo
K
Seki
Motoaki
M
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics; D015257:DNA-Cytosine Methylases / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D008780:Methyltransferases / Q000235:genetics; D018749:RNA, Plant / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000378:metabolism*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
D029681:Arabidopsis Proteins; C118957:DDM1 protein, Arabidopsis; D004268:DNA-Binding Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering; D014157:Transcription Factors; D015257:DNA-Cytosine Methylases; D008780:Methyltransferases; C429766:CMT3 protein, Arabidopsis; C470732:DRM2 protein, Arabidopsis; C519655:RDR2 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase