ABA induces methylation and reduces transcript levels.

(A) The difference in the levels of transcription (Transcription logFC) and DNA methylation (Methylation logFC) were determined from samples treated with ABA versus samples not treated with ABA for the A. thaliana genes NDF4 (At3g16250), SIG5 (At5g24120) and F12A4.4 (At1g35420). Transcript levels were determined by qRT-PCR and methylation profiles of upstream regions by bisulfite sequencing. For these experiments A. thaliana seedlings were treated with ABA for two days according to the protocol of Nishimura et al. [34]. (B) Changes in methylation and transcription in the crown gall tumor compared to mock-iocculated stems according to methylome (Methylation logFC) and transcriptome data (Transcription logFC) of a previous study [8]. Each data set is based on at least three independent biological replicates and the logarithmic of fold changes (logFC) were calculated from the mean values.