Figure 1

DNA methylation in 45S rRNA gene repeats among Arabidopsis natural accessions. (A) A 10-kb rRNA gene repeat unit encoding the 18S, 5.8S, and 25S rRNAs. A bent arrow shows the location of the transcription start site, and the two hybridization probes (IGS and CR) are indicated below the monomer repeat unit as gray bars. (B) A representative genomic DNA blot analysis of Arabidopsis natural accessions using the CR probe. HpaII-digested genomic DNA was size fractionated by gel electrophoresis and transferred to a nylon membrane. The membrane was hybridized with radiolabeled CR probe corresponding to the 5.8S and 25S rRNA coding regions (see the map above). The hybridization signal indicates the extent of DNA methylation in the rRNA gene clusters; unmethylated fragments are cleaved by HpaII to small fragments (open box), whereas methylated genomic fragments remain uncleaved, or partially cleaved, and migrate as larger fragments (solid box). (C) Variation in CR DNA methylation among 88 Arabidopsis natural accessions. CR DNA methylation index (%) was calculated by measuring the percentage of hybridization signal in each lane that corresponded to restriction fragments >1 kb. Means and standard errors were calculated from at least three independent experiments.