Endogenous targets of transcriptional gene silencing in arabidopsis

Transcriptional gene silencing (TGS) frequently inactivates foreign genes i ntegrated into plant genomes but very likely also suppresses an unknown sub set of chromosomal information. Accordingly, RNA analysis of mutants impair ed in silencing should uncover endogenous targets of this epigenetic regula tion. We compared transcripts from wild-type Arabidopsis carrying a silent transgene with RNA from an isogenic transgene-expressing TGS mutant. Two cD NA clones were identified representing endogenous RNA expressed only in the mutant. The synthesis of these RNAs was found to be released in several mu tants affected in TGS, implying that TGS in general and not a particular mu tation controls the transcriptional activity of their templates. Detailed a nalysis revealed that the two clones are part of longer transcripts termed TSI (for transcriptionally silent information). Two major classes of relate d TSI transcripts were found in a mutant cDNA library. They are synthesized from repeats present in heterochromatic pericentromeric regions of Arabido psis chromosomes. These repeats share sequence homology with the 3' termina l part of the putative retrotransposon Athila. However, the transcriptional activation does not include the transposon itself and does not promote its movement. There is no evidence for a general release of silencing from ret roelements. Thus, foreign genes in plants encounter the epigenetic control normally directed, at least in part, toward a subset of pericentromeric rep eats.