Invasion of the Arabidopsis Genome by the Tobacco Retrotransposon Tnt1 Is Controlled by Reversible Transcriptional Gene Silencing  

Abstract

Long terminal repeat (LTR) retrotransposons are generally silent in plant genomes. However, they often constitute a large proportion of repeated sequences in plants. This suggests that their silencing is set up after a certain copy number is reached and/or that it can be released in some circumstances. We introduced the tobacco (Nicotiana tabacum) LTR retrotransposon Tnt1 into Arabidopsis (Arabidopsis thaliana), thus mimicking the horizontal transfer of a retrotransposon into a new host species and allowing us to study the regulatory mechanisms controlling its amplification. Tnt1 is transcriptionally silenced in Arabidopsis in a copy number-dependent manner. This silencing is associated with 24-nucleotide short-interfering RNAs targeting the promoter localized in the LTR region and with the non-CG site methylation of these sequences. Consequently, the silencing of Tnt1 is not released in methyltransferase1 mutants, in contrast to decrease in DNA methylation1 or polymerase IVa mutants. Stable reversion of Tnt1 silencing is obtained when the number of Tnt1 elements is reduced to two by genetic segregation. Our results support a model in which Tnt1 silencing in Arabidopsis occurs via an RNA-directed DNA methylation process. We further show that silencing can be partially overcome by some stresses.

Insertional Mutagenesis Using Tnt1 Retrotransposon in Potato

“…It was demonstrated in Arabidopsis that the transcription of Tnt1 was often silenced in plants containing numerous copies. The silencing of Tnt1 was associated with 24-nucleotide short-interfering RNAs targeting the promoter localized in the long terminal repeat region and with the non-CG site methylation of these sequences (Pérez-Hormaeche et al, 2008). Our data are in agreement with those in Arabidopsis.…”

Exogenous Transposable Elements Circumvent Identity-Based Silencing, Permitting the Dissection of Expression-Dependent Silencing

“…TE transgenes have been previously generated as tools for gene tagging and mutant generation (Raizada et al, 2001;Li et al, 2013). TE transgenes can be selected for activity, yet without selection for activity evidence suggests that they are recognized by host defense mechanisms and silenced by RdDM (Hirochika et al, 2000;Pérez-Hormaeche et al, 2008). Like TEs, silencing of newly integrated transgenes can occur through homology to the existing genome (Matzke et al, 2000(Matzke et al, , 1994, yet the detailed mechanism(s) of silencing establishment at the newly integrated TEs or transgenes is currently unknown.…”

Pol IV-Dependent siRNAs in Plants

“…Introduction of the tobacco TNT1 retrotransposon into Arabidopsis supports this hypothesis, as TNT1 proliferation attracts Pol IV and silences the element through RdDM (Perez-Hormaeche et al 2008). Recent deep sequencing of small RNAs also supports the genome-defense model by identifying thousands of TEs that generate p4-siRNAs (Kasschau et al 2007;Zhang et al 2007;Mosher et al 2008).…”