Transposonic siRNA-producing Inverted Repeats as regulators of gene expression through chromatin looping in Arabidopsis thaliana

ARCE, AGUSTÍN L.; CAMBIAGNO, DAMIAN A.; MENCIA, REGINA; GAGLIARDI, DELFINA; WEIGEL, DETLEF; MANAVELLA, PABLO A.

Santa Fe

Congreso; XXXIII Argentinian meeting of Plant Physiology; 2021

Sociedad Argentina de Fisiología Vegetal

Transposons are known as genomic parasites and can account for morethan 80% of plant genomes. However, there are several reported casesin which their effects, mainly on gene expression, have an adaptiveor agronomic value. A transposon in the promoter of the sunflowerHaWRKY6 gene is involved in a complex regulatory mechanism. It is anelement with an inverted repeat (IR) which is transcribed andgenerates 24 nt siRNAs. These siRNAs target the IR region triggeringDNA methylation and serving as an anchoring point for two short rangechromatin loops. These loops regulate HaWRKY6 expression in a dynamicand tissue specific mode. We decided to explore similar mechanisms ofgene regulation in the Arabidopsis thaliana genome. We foundapproximately 1200 genes near IRs, of which we focused on 350presenting natural variation in transposonic IRs. We selected for thestudy Col-0 plants, mutants defective in DNA methylation and siRNAproduction, and two accessions with variation in IRs. On these plantswe performed a CaptureC assay (a targeted HiC) to investigate thechromatin topology in these loci and the potential role of the IRs inthe regulation of the genes. We further explored the mechanism bysimultaneously analyzing gene expression (RNA-Seq), siRNAs molecules(sRNA-Seq) and DNA methylation (BS-seq). Our results show that aproportion of the selected genes are potentially regulated at thechromatin level by the IR near them.p { margin-bottom: 0.1in; line-height: 115%; background: transparent }