Figure 1.

The epigenetic regulatory mechanisms act coordinately in reprogramming gene expression when plants encounter biotic stress. The known factors in Arabidopsis that regulate the biotic stress involve small RNAs, RdDM, methylation and demethylation of DNA, histone modification, and chromatin remodelers, which are present here. (A) Small RNAs participate in conical and non-canonical RdDM pathways to regulate DNA methylation on TEs and defense-related genes. The RDR2- and DCL3-dependent hc-siRNAs are key components in PolIV-RDR2-DCL3-AGO4-PolV-DRM2, the conical RdDM pathway, which establish and reinforce DNA methylation at TEs and regulate the nearby defense response genes. The siRNAs derived from mRNA precursor, TE non-coding RNAs (TE ncRNAs), inverted repeats, or dsRNAs produced by RDR6 are processed by DCL2/4 also participate in establishing the DNA methylation and regulate the expression of defense-related genes. (B) Deposition of DNA methylation and on the NLRs, PRRs, or defense response genes leads to a transcriptionally suppressed status. Other components acting with the chromatin remodeler SWP73A (dark red oval) are not clear (unknown component is shown in gray oval). RdDM components including PolIV and PolV, DCLs, RDRs, AGO4/6, and DRD1 are shown in a dark green oval. DNA methyltransferases DRM2, MET1, and CMT3 are shown in a light green oval. SWI2/SNF2-like ATPases Decreased DNA Methylation 1 (DDM1), Swi2/Snf2-related 1 (SWR1), and Classy1 (CLSY1) are shown in an orange oval. The H3K9me2 reader EDM2 is shown in the light brown oval. Mutant plants that display a resistant phenotype to pathogen (such as Pst) relying on an SA-dependent response are surrounded with a red outline, whereas the blue outline indicates a more susceptible phenotype.