Plants are under constant genetic siege. From viruses and bacteria to transposable elements within their genomes, cells must contend with foreign genetic material. Besides these natural threats, modern biotechnology adds complexity by introducing transgenes to plants. While the integration of such DNA can enhance genetic diversity and confer desirable traits, its foreign origin is typically recognised by the plant cell as a signal of invasion and therefore targeted by the repressive mechanisms. Epigenetic silencing is a central strategy and involves the methylation of DNA and histones. A critical trigger of this silencing is the generation of small interfering RNAs (siRNAs). Although the role of siRNAs in maintaining epigenetic silencing is well established, the initial steps that lead to their production remain incompletely understood. This review discusses the key discoveries on how plant cells recognise foreign nucleic acids and initiate epigenetic silencing, contributing to our broader understanding of genome integrity and defence.
