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.

[1]  S. Lerbs-Mache,et al.  Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. , 2005, Genes & development.

[2]  D. Zilberman,et al.  RNA Silencing Genes Control de Novo DNA Methylation , 2004, Science.

[3]  J. Paszkowski,et al.  Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis , 2003, Nature Genetics.

[4]  Marjori Matzke,et al.  Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation , 2003, Current Biology.

[5]  D. Bartel,et al.  A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. , 2006, Genes & development.

[6]  N. Fedoroff,et al.  Dynamic Regulation of ARGONAUTE4 within Multiple Nuclear Bodies in Arabidopsis thaliana , 2008, PLoS genetics.

[7]  Adam M. Gustafson,et al.  Genetic and Functional Diversification of Small RNA Pathways in Plants , 2004, PLoS biology.

[8]  David P. Kreil,et al.  Atypical RNA polymerase subunits required for RNA-directed DNA methylation , 2005, Nature Genetics.

[9]  M. Pellegrini,et al.  Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis , 2006, Cell.

[10]  James C. Carrington,et al.  Specialization and evolution of endogenous small RNA pathways , 2007, Nature Reviews Genetics.

[11]  Jason S. Cumbie,et al.  Genome-Wide Profiling and Analysis of Arabidopsis siRNAs , 2007, PLoS biology.

[12]  Xiaofeng Cao,et al.  ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation , 2003, Science.

[13]  D. Baulcombe,et al.  PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis , 2008, Proceedings of the National Academy of Sciences.

[14]  Masakazu Satou,et al.  Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. , 2008, Plant & cell physiology.

[15]  I. Henderson,et al.  RNAi, DRD1, and Histone Methylation Actively Target Developmentally Important Non-CG DNA Methylation in Arabidopsis , 2006, PLoS genetics.

[16]  C. Pikaard,et al.  Plant Nuclear RNA Polymerase IV Mediates siRNA and DNA Methylation-Dependent Heterochromatin Formation , 2005, Cell.

[17]  Kazuo Shinozaki,et al.  Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models. , 2005, The Plant journal : for cell and molecular biology.

[18]  J. Jurka,et al.  Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation , 2006, Nature.

[19]  D. Baulcombe,et al.  RNA Polymerase IV Directs Silencing of Endogenous DNA , 2005, Science.