Arabidopsis HDA6 Regulates Locus-Directed Heterochromatin Silencing in Cooperation with MET1
Figure 2
HDA6-mediated gene silencing requires MET1 but not RdDM pathway.
(A) A Venn diagram showing the small fraction of overlap between the AGI genes upregulated in axe1-5, compared with those in rdr2. The AGI genes identified as upregulated in rdr2 in a previous genome-wide transcriptional profiling experiment [43], were compared with the AGI genes upregulated in axe1-5 identified in this study. (B) Various mutants deficient in gene silencing, such as the chromatin modifying enzymes (hda6, met1, ddc, and kyp) and siRNA production (rdr2 and nrpd1) were examined for the activation of representative HDA6 target loci (AT3TE60310, At1g67105, At3g28899, AT3TE63935, AT3TE76225, AT4TE03410, AT5TE39590, At2g15555, At3g44070, At3g54730, At5g41660, G447 and G683) by RT-PCR analysis. ACT2 served as a control. The MET1 requirement for repression of HDA6 target loci is highlighted. (C) A Venn diagram showing the significant overlap between the AGI genes upregulated in axe1-5 and in met1-3 that were identified in genome-wide transcriptional profiling. (D) The DNA methylation status in wild-type Col-0 for the genes upregulated in axe1-5. The fraction of AGI genes associated with DNA methylation at more than 50% of methylated cytosines around TSS (−500 to +500 from TSS) was determined using publicly available datasets of methylcytosine immunoprecipitation [13]. (E) Cytosine methylation was investigated in each sequence context (CG, CHG, and CHH) in wild-type Col-0, met1-3, and ddc using publicly available datasets of cytosine methylation (methylC-seq, [13]). The percentages of methylated cytosines of the AGI genes upregulated in axe1-5 are shown.