Trinucleotide repeats are part of microsatellite repeats, and their expansion has been linked to several human genetic disorders. Repeat expansions in noncoding regions affect gene expression. However, the underlying mechanism of the repeat expansion-induced downregulation of gene expression remains unclear. One of the problems is the lack of an appropriate model to study. Arabidopsis is the first non-human model where a trinucleotide repeat expansion-associated phenotypic variation has been demonstrated (Surehkumar et al., Science,2009). The Bur-0 Arabidopsis strain harbors a triplet-repeat expansion associated with a growth defect linked to the downregulation of gene expression. Over the years, we have developed Arabidopsis as a natural model to uncover the molecular mechanisms associated with the repeat expansion-induced downregulation of gene expression. Recently, we discovered mechanisms by which repeat expansion leads to the accumulation of 24nt siRNAs via the RNA-directed DNA methylation (RdDM) pathway (Eimer et al., Cell, 2018) and SUMO protease FUG1 complex (Sureshkumar et al., Nature Plants, 2024, In press) induces epigenetic gene silencing at repeat expanded genetic loci harboring the expansion. I will be presenting our latest discoveries.