Fig. 2.

AtSN1 as a model target of RNA-directed DNA methylation and transcriptional silencing. Schematic overview for the genomic region including SINE-like element AtSN1 located on chromosome 3 next to At3G44005. LTRs (bold grey arrows) flank the inner region (bold black arrow) that contains two putative promoter-like structures, Box A and Box B, and the internal region with homology to tRNA genes. Black dots indicate the region in which methylated cytosines are detected in wild type. Positions of primers used for amplification after bisulfite conversion bs-f and bs-r indicate the region analyzed for DNA methylation. The dotted arrow shows the putative extent of silenced transcript A, the black arrows indicate Pol V derived transcripts B and C. Positions of primers used for RT-PCR are marked by A-f, A-r; B-f, B-r; C-f, C-r