In a paper appearing in this week's PNAS Early Edition, a team led by investigators at the Salk Institute for Biological Studies in La Jolla, Calif., shows that, in response to salicylic acid exposure, transposon-associated differentially methylated regions in Arabidopsis thaliana that are accompanied by the upregulation of 21-nt siRNAs are often coupled to transcriptional changes of the transposon and/or the proximal gene.