Schematic of a PSI gene associated with two TEs. TE A represents TEs that are located distant from genes and are highly methylated, while TE B represents TEs that are close to genes and lowly methylated. Upon short term Pi deprivation, RNA polymerase II is recruited to Pi starvation-induced (PSI) genes, resulting in increased PSI gene expression. These high levels of RNA polymerase II could induce transcription of nearby and poorly methylated TEs, such as TE B, which could have deleterious effects upon the plant. As a consequence, upon prolonged Pi deprivation, TEs that are close to highly expressed stress-induced genes are hypermethylated, via a DCL3a-independent mechanism, thus preventing their transcription via RNA polymerase II. Black and white circles represent methylated and unmethylated cytosines, respectively. Thickness of the dashed lines represents the proportion of RNA polymerase II recruited to PSI genes or TEs.