Inverted repeat-derived small RNAs dynamically modulate the genome topology of the Sunflower HaWRKY6 transcription factor locus

Transposable elements (TE) are extremely abundant in complex plant genomes, such as sunflower. Small interfering RNAs (siRNAs) of 24 nucleotides in length control transposons activity in a process that involves de novo methylation of targeted loci DNA. Normally, this epigenetic modifications trigger nucleosome condensation and a permanent silencing of the affected loci. Here, we show that a TE-derived inverted repeat (IR) element, inserted near the Sunflower HaWRKY6 locus, dynamically regulates the expression of the gene by altering chromatin topology. This element, transcribed in antisense, is processed into 24 nucleotide siRNAs triggering DNA methylation on its own locus. This epigenetic marks act as an anchor point for the formation of tissue specific loops in the chromatin. In leaves, an intragenic loop is formed blocking HaWRKY6 transcription. While in cotyledons an alternative loop, encompassing the whole HaWRKY6 gene, allows for an efficient recycling of the RNA polymerase resulting in the enhanced transcription of the gene. In a self-buffered regulatory mechanism, the formation of this loop changes the promoter directionality reducing the transcription of the IR and ultimately releasing the loop. Our results provide evidence that TEs can act as active and dynamic regulatory elements within coding loci in a mechanism that combines the RNA silencing, epigenetic and chromatin remodeling machineries.