RNAi-dependent repression controls transposable elements in .

RNAi and repression play evolutionarily conserved and often coordinated roles in transcriptional silencing. Here, we show that, in the protozoan , germline-specific internally eliminated sequences (IESs)-many related to transposable elements (TEs)-become transcriptionally activated in mutants deficient in the RNAi-dependent repression pathway. Germline TE mobilization also dramatically increases in these mutants. The transition from noncoding RNA (ncRNA) to mRNA production accompanies transcriptional activation of TE-related sequences and vice versa for transcriptional silencing. The balance between ncRNA and mRNA production is potentially affected by cotranscriptional processing as well as RNAi and repression. We posit that interplay between RNAi and repression is a widely conserved phenomenon, whose ancestral role is epigenetic silencing of TEs.