title: Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis.
abstract: 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.
authors.affiliation: 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.
authors.forename: Yukio
authors.initials: Y
authors.lastname: Kurihara
authors.forename: Akihiro
authors.initials: A
authors.lastname: Matsui
authors.forename: Makiko
authors.initials: M
authors.lastname: Kawashima
authors.forename: Eli
authors.initials: E
authors.lastname: Kaminuma
authors.forename: Junko
authors.initials: J
authors.lastname: Ishida
authors.forename: Taeko
authors.initials: T
authors.lastname: Morosawa
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Mochizuki
authors.forename: Norio
authors.initials: N
authors.lastname: Kobayashi
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Toyoda
authors.forename: Kazuo
authors.initials: K
authors.lastname: Shinozaki
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
mesh_terms: 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
chemical_list: 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