Epigenetic management of self and non-self in plants

In plants, 24-nt small RNAs guide transcriptional gene silencing (TGS) while 21/22nt small RNAs guide post-transcriptional gene silencing (PTGS). These small RNAs are used to regulate the expression of a limited number of genes during development and in response to certain stresses. They are also used to control the movement of transposable elements and to counteract infection by pathogens. Transgenes generally have structures resembling that of endogenous genes (self), but integrate in the genome like transposable elements (dangerous self), and often carry sequences originating from pathogens (non-self). Transgenes are frequently targeted by TGS or PTGS, which allowed transgene-based genetic screens to decipher the underlying mechanisms. Nevertheless, despite being silenced like endogenous genes or transposable elements, transgenes exhibit a distinct epigenetic regulation. Moreover, contrasting the generally cell-autonomous silencing of endogenous genes and transposable elements, transgenes often undergo silencing in a systemic manner.