Fig. 5: Model for the TBPL1- and PAF1-dependent regulation and roles of Pol II, Pol I, and their ncRNAs at the rDNA IGS.

a At the IGS of wild-type cells grown under standard conditions, TBPL1 at TCT motif-containing IGS sites promotes sense Pol I and antisense Pol II recruitment (i) for the synthesis of sincRNAs and asincRNAs, respectively. Downstream of Pol II transcription initiation, PAF1 promotes the release of Pol II from a natural pause site at IGS20 (ii). Pol II promotes a natural R-loop shield for Pol I (iii). Thus, TBPL1 and PAF1 promote the maintenance of baseline sincRNA levels through different processes. b TBPL1 deficiency reduces the recruitment and function of Pol I and Pol II at the IGS, decreasing the levels of intergenic ncRNAs and abrogating nucleolar structure and function. c Loss of PAF1 induces excessive Pol II pausing at IGS20, leading to total Pol II buildup, depletion of elongating Pol II, and the emergence of unscheduled R-loops, limiting the recruitment of Pol I and its ability to synthesize the baseline levels of sincRNAs needed to ensure nucleolar organization and rRNA biogenesis. d Overall impact of sincRNA levels on nucleolar structure and function.