Silencing of retrotransposons in arabidopsis and reactivation by the ddm1 mutation

Gene silencing associated with repeated DNA sequences has been reported for many eukaryotes, including plants, However, its biological significance re mains to be determined. One important function that has been proposed is th e suppression of transposons. Here, we address transposon suppression by ex amining the behavior of the tobacco retrotransposon Tto1 and endogenous ret rotransposons in Arabidopsis. After an initial increase in copy number beca use of active transposition in the Arabidopsis genome, Tto1 became silent. The amount of transcript was reduced, and the inactivated Tto1 became methy lated. This silencing correlated with an increase in copy number. These phe nomena mimic repeat-induced gene silencing. The homozygous ddm1 (for decrea se in DNA methylation) mutation of Arabidopsis results in genomic DNA hypom ethylation and the release of silencing in repeated genes. To investigate t he role of DNA methylation and the gene-silencing machinery in the suppress ion of Tto1, we introduced the ddm1 mutation into an Arabidopsis line carry ing inactivated Tto1 copies. In the homozygous ddm1 background, Tto1 became hypomethylated and transcriptionally and transpositionally active. In addi tion, one of the newly isolated endogenous Arabidopsis retrotransposon fami lies, named Tar17, also became hypomethylated and transcriptionally active in the ddm1 mutant background, Our results suggest that the inactivation of retrotransposons and the silencing of repeated genes have mechanisms in co mmon.