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. 2022 Sep 30;66(5):635–646. doi: 10.1042/EBC20210082

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© 2022 The Author(s).

This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY). Open access for this article was enabled by the participation of University of Sheffield in an all-inclusive Read & Publish agreement with Portland Press and the Biochemical Society under a transformative agreement with JISC.

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Cis-regulation (left) occurs when an intronic TE controls alternative splicing or polyadenylation of the defence gene (A), or when the DNA methylation status of a nearby TE controls the chromatin density and transcriptional responsiveness of a defence gene (B). Trans-regulation (right) can be based on a variety of mechanisms. Post-transcriptional silencing of transcribed TEs by the RNA-induced silencing complex (RISC) can induce accumulation of 21/22-nt sRNAs via RDR6-dependent RNA-directed DNA methylation. This can induce nuclear activity of argonaute1 (AGO1), which stimulates defence gene expression through interaction with the SWI/SNF chromatin remodelling complex in a sRNA-dependent manner (C; [61]). Alternatively, transcription of hypomethylated TEs can increase accumulation of non-coding RNAs (lncRNAs) that scavenge defence-repressing microRNAs (miRNAs) through target mimicry (D; [63,64]). Finally, salicylic acid-binding microrchidia (MORC) proteins can mediate higher-order heterochromatic interactions in the genome [65,66], and so regulate the chromatin structure and expression of distal defence genes (E; [58]).