Regulation of chromatin topology and transcription by inverted repeatderived small RNAs

ARCE, AGUSTIN L.; WEIGEL, DETLEF; CAMBIAGNO, DAMIAN A.; CHANG LIU ; GAGLIARDI DELFINA

Puerto Varas

Conferencia; II MOLECULAR BIOSYSTEMS CONFERENCE. EUKARYOTIC GENE REGULATION & FUNCTIONAL GENOMICS; 2019

Small interfering RNAs (siRNAs) of 24 nucleotides in length are the most abundant type of small RNAs in plants. These siRNAs, derived from double-stranded RNA, play a critical role in controlling transposable elements (TEs) in a process known as transcriptional gene silencing (TGS). This process, which involves de novo methylation of targeted loci DNA, usually triggers nucleosome condensation and a permanent silencing of the affected loci. We found 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. The transcripts of this IR element are processed into 24-nt siRNAs, triggering DNA methylation on its locus. These epigenetic marks stabilize the formation of tissue-specific loops in the chromatin changing transcriptional activity, termination, and promoter directionality. Now, we have explored genome-wide in Arabidopsis how IR sequences nearby genes affect chromatin topology. We have also demonstrated that these TEderived elements can have evolutionary implication during adaptation by studying Arabidopsis ecotypes. Our results provide evidence that TEs can act as active and dynamic regulatory elements within coding loci in a mechanism that combines RNA silencing, epigenetic modification, and chromatin remodeling machinery.