A specialized TFIIB-like transcription factor is required for non-coding RNA directed DNA elimination

Transposable elements (TEs) are threats to genome stability and thus small RNA-mediated heterochromatinization suppresses the transcription of TEs. Paradoxically, transcription of non-coding RNA (ncRNA) from TEs is needed for the production of TE-targeting small RNAs and/or recruiting the silencing machinery to TEs. Hence, specialized RNA polymerase II (Pol II) transcription machinery is required for such unconventional transcription in different organisms. Indeed, the developmental stage-specific Mediator complex (Med)-associated proteins play essential roles in the ncRNA transcription from TE-related sequences in Tetrahymena. Yet it remains unknown how those Med-associated proteins are linked to the TE transcription by Pol II. Here, we report that Pol II is regulated by Emit3, a stage-specific, TFIIB-like protein specialized in TE transcription. Emit3 partners with the TFIIH complex and localizes to TE-dense regions within the meiotic MIC, particularly at sites marked by a G-rich genomic motif. Emit3 is essential for recruiting Pol II to chromatin, facilitating the transcription of TE-targeting ncRNAs, which serve as precursors to small RNAs. Deletion of EMIT3 disrupts Med association with chromatin and mislocalizes TFIIH. Conversely, Emit3's preferential localization to TE-rich loci partially depends on Med-associated proteins. Together, these findings suggest that Emit3, TFIIH, and Med-associated proteins coordinate to initiate ncRNA transcription, at least partly in a sequence-dependent manner.