Polymorphic inverted repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana

Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response

“…Whether the structural nature of the Ea-IR transcript is sufficient to trigger the reported regulatory mechanism independently of the specific Ea-IR sequence or whether this IR has special properties in terms of recruiting specific elements of the DNA methylation machinery remains to be explored. However, the first scenario appears more likely, as we found that many IRs, regardless of their sequence, promote chromatin reorganization when expressed 34 . Still, it is possible that some sequence-specific DNA methyl readers can recognize methylated Ea-IR and fine-tune its regulatory function.…”

“…In this sense, while TEs are commonly silenced through the RNA-dependent DNA Methylation (RdDM) pathway that relies on the plant-specific RNA polymerases IV and V (Pol IV and Pol V) and the RNA-dependent RNA Polymerase 2 (RDR2) 36,37 , IRs can trigger DNA methylation by a non-canonical pathway as Pol II transcripts of IRs can fold into dsRNAs triggering sRNA production without the need of RDR2 38 . This turns IRs into autonomous elements that, when inserted near a gene, can be transcribed, triggering local RdDM, chromatin looping, and changes in gene expression 34 .Here we show that an IR that separates EFR from the myosin XI-k gene (Xlk), which associated with root organogenesis, ER dynamics, and fungal penetration 39-41 , controls EFR expression by shaping local chromatin topology. Mechanistically, the methylation of the IR induces the formation of a chromatin loop that represses EFR expression.…”

“…This provides an anchor point for the formation of short-range chromatin loops that influence the expression of neighboring genes 35 . Many IRs vary between A. thaliana accessions (with many accessions missing the entire IRs), causing differences in short-range chromatin interactions and gene expression 34 . Such variation in the gene-hosted IR content is significant because it can be associated with changes in phenotypic traits 34 .…”

“…Many IRs vary between A. thaliana accessions (with many accessions missing the entire IRs), causing differences in short-range chromatin interactions and gene expression 34 . Such variation in the gene-hosted IR content is significant because it can be associated with changes in phenotypic traits 34 . This points to IRs as powerful evolutionary agents that can epigenetically contribute to plant adaptation.…”

“…Because PRR RNA levels are known to be positively regulated ETI, this indicates that there are likely opportunities for fine-tuning PRR expression levels before and during pathogen attack 32 .Differences in gene expression can be caused in trans by accessionspecific transcriptional regulators or by cis-regulatory sequence variants. Recently, we found that the insertion of TE-derived inverted repeats (IRs) near genes changes the local chromatin organization, with profound impacts on the activity of neighboring loci 33,34 . Mechanistically, transcription of these IRs leads to the synthesis of 24-nt small RNAs and the methylation of the IRs.…”