TBP facilitates RNA Polymerase I transcription following mitosis

Abstract The TATA-box binding protein (TBP) is the sole transcription factor common in the initiation complexes of the three major eukaryotic RNA Polymerases (Pol I, II, and III). Decades of research have shown that TBP is essential for proper transcription by the three RNA Pols, though the emergence of TBP paralogs throughout evolution have expanded the complexity in RNA Pol initiation. We have previously shown that acute TBP depletion in mouse embryonic stem cells led to a global decrease in Pol III activity, consistent with the requirement of TBP in Pol III inititation. In contrast, Pol II transcription remained unaffected in the absence of TBP and its paralogs. In this report, we show that, in contrast to Pol II-transcribed genes, the TBP paralog TRF2 does not bind to Pol I promoters, and therefore cannot functionally replace TBP upon depletion. Importantly, acute TBP depletion has no major effect on Pol I occupancy or activity on ribosomal RNA genes, but TBP binding in mitosis leads to efficient Pol I reactivation following cell division. These findings provide a more nuanced role for TBP in Pol I transcription in murine embryonic stem cells. Significance The TATA-box binding protein (TBP) is a highly conserved and essential protein in eukaryotes. Decades of in vitro and yeast research have established its role in the initiation of the three main eukaryotic RNA polymerases. However, the ability to rapidly deplete proteins in vivo is revealing more nuance in the function of TBP in mammalian cells. Using this technology, we reassess the role of TBP in RNA Polymerase I (Pol I) transcription in mouse embryonic stem cells. We find that neither TBP nor its paralog TRF2 are required for Pol I recruitment or activity, but TBP binding during mitosis promotes efficient reactivation after cell division. Overall, these findings provide new evidence into the complex function of TBP in eukaryotic transcription.