Ribosomal DNA promoter recognition is determined in vivo by cooperation between UBTF1 and SL1 and is compromised in the UBTF-E210K neuroregression syndrome

Transcription of the ~200 mouse and human ribosomal RNA genes (rDNA) by RNA Polymerase I (RPI/PolR1) accounts for 80% of total cellular RNA, around 35% of all nuclear RNA synthesis, and determines the cytoplasmic ribosome complement. It is therefore a major factor controlling cell growth and its misfunction has been implicated in hypertrophic and developmental disorders. Activation of each rDNA repeat requires nucleosome replacement by the architectural multi-HMGbox factor UBTF to create a 15.7 kbp nucleosome free region (NFR). Formation of this NFR is also essential for recruitment of the TBP-TAF(I) factor SL1 and for preinitiation complex (PIC) formation at the gene and enhancer-associated promoters of the rDNA. However, these promoters show little sequence commonality and neither UBTF nor SL1 display significant DNA sequence binding specificity, making what drives PIC formation a mystery. Here we show that cooperation between SL1 and the longer UBTF1 splice variant generates the specificity required for rDNA promoter recognition in cell. We find that conditional deletion of the TAF1B subunit of SL1 causes a striking depletion of UBTF at both rDNA promoters but not elsewhere across the rDNA. We also find that while both UBTF1 and -2 variants bind throughout the rDNA NFR, only UBTF1 is present with SL1 at the promoters. The data strongly suggest an induced-fit model of RPI promoter recognition in which UBTF1 plays an architectural role. Interestingly, a recurrent UBTF-E210K mutation and the cause of a pediatric neurodegeneration syndrome provides indirect support for this model. E210K knock-in cells show enhanced levels of the UBTF1 splice variant and a concomitant increase in active rDNA copies. In contrast, they also display reduced rDNA transcription and promoter recruitment of SL1. We suggest the underlying cause of the UBTF-E210K syndrome is therefore a reduction in cooperative UBTF1-SL1 promoter recruitment that may be partially compensated by enhanced rDNA activation. Author summaryThe 200 Ribosomal RNA gene copies (the rDNA) account for 80% of total cellular RNA and determine the cell's ribosome complement and hence also its capacity to synthesize proteins. As a consequence, these genes directly control cell growth and their misfunction leads both to hypertrophic and developmental disorders. However, it is still unclear what determines the choice of which rDNA copies are activated and how this relates to the formation of the transcription preinitiation complex. Our study, based on the conditional deletion of TAF1B, a subunit of the TBP complex SL1, reveals how the DNA sequence non-specific HMGbox factor UBTF plays a sequence-specific role in SL1 recruitment and preinitiation complex formation. We further show how this role is degraded by a mutation that is the cause of the E210K recurrent pediatric neuroregression syndrome. The data suggest an induced-fit model of preinitiation complex formation in which UBTF creates a DNA folding that is specifically recognized by SL1.

Automated summary

The translation discusses the cellular mechanisms involved in the transcription of mouse and human ribosomal RNA genes, the cooperative relationship between UBTF and SL1 in cell growth and gene activation, and the impact of gene mutations on gene expression and cellular development.