LC-MS/MS analysis of immunoprecipitation samples of a Tetrahymena TFIIB-like protein Emit3 and the zinc-ribbon mutated Emit3

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, have found that Pol II is regulated by Emit3, a stage-specific, TFIIB-like protein specialized in TE transcription. Hence, to find out potential interactions, we did LC-MS/MS analysis for immunoprecipitation samples of Emit3 and the zinc-ribbon mutated Emit3.