Evolutionary variability of these TAFs determine their species-specific functions and that of RPI transcription, and for example human or mouse SL1 complexes are not functionally exchangeable ( 16– 18). SL1 consists of the TATA-box Binding Protein (TBP) and the RPI specific TBP Associated Factors, TAFIA to D. The basal factors of the mammalian RPI transcription machinery include Selectivity Factor 1 (SL1), the multi-HMGbox factor UBTF/UBF and the RPI-associated initiation factor RRN3 ( 8, 14, 15) ( Figure 1A). Further, we show that this UBTF function is compromised by an E210K mutation recently linked to a recurrent human pediatric neuroregression syndrome ( 6, 11– 13). Here we show that despite having little or no inherent DNA sequence selectivity, the multi-HMGbox Upstream Binding Factor (UBF/UBTF) plays a crucial role in targeting RPI preinitiation complex formation to the rDNA promoters in vivo. However, what directs the RPI transcription machinery exclusively to the rDNA and how it is specifically recruited to both the major 47S pre-rRNA promoter and enhancer element despite these having little or no DNA sequence commonality are still not understood. The functional uniqueness of the RPI machinery provides an obvious target for novel therapeutic approaches ( 10). This strict correspondence of gene and polymerase has resulted in the rapid coevolution of rDNA promoters with basal factors, leading to a high degree of species specificity of the RPI transcription machinery ( 7– 9).
Transcription of the several hundred tandemly repeated and essentially identical rRNA genes, the rDNA, is undertaken exclusively by RNA Polymerase I (RPI, Pol1, PolR1) and a set of basal transcription factors dedicated to this task. To develop treatment strategies for these diseases it is important that we command an understanding of how these genes are transcribed and regulated. Dysregulation of rRNA genes is also the cause of a large range of developmental and neurological disorders that are often also associated with cancer ( 2– 6). As such, transcription of these genes is a major determinant of cell growth, cell cycle progression and cell survival and an essential factor in the formation of hypertrophic diseases such as cancer ( 1). The ribosomal RNA (rRNA) genes encode the catalytic and structural RNAs of the ribosome as a single 47S precursor. 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. In contrast, they also display reduced rDNA transcription and promoter recruitment of SL1. E210K knock-in cells show enhanced levels of the UBTF1 splice variant and a concomitant increase in active rDNA copies. Interestingly, a recurrent UBTF-E210K mutation and the cause of a pediatric neurodegeneration syndrome provides indirect support for this model. The data strongly suggest an induced-fit model of RPI promoter recognition in which UBTF1 plays an architectural role. We also find that while both UBTF1 and −2 variants bind throughout the rDNA NFR, only UBTF1 is present with SL1 at the promoters. We find that conditional deletion of the Taf1b subunit of SL1 causes a striking depletion UBTF at both rDNA promoters but not elsewhere across the rDNA. Here we show that cooperation between SL1 and the longer UBTF1 splice variant generates the specificity required for rDNA promoter recognition in cell. 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.
/figure/unnamed-chunk-3-1.png "magicplot pro combining figures")
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.
MAGICPLOT PRO COMBINING FIGURES FREE
Activation of each rDNA repeat requires nucleosome replacement by the architectural multi-HMGbox factor UBTF to create a 15kbp nucleosome free region (NFR). It is therefore a major factor controlling cell growth and its misfunction has been implicated in hypertrophic and developmental disorders. 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.
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