The nuclei of all eukaryotic cells contain three RNA polymerases (designated I, II and III). These enzymes catalyze the formation of the phosphodiester bond that links nucleotides together to form a linear chain. RNA polymerase moves stepwise along the DNA, unwinding the DNA helix just ahead of the active site for polymerization, to expose a new region of the template strand for complementary base pairing. In this way, the growing RNA chain is extended one nucleotide at a time in the 5' to 3' direction. Each eukaryotic RNA polymerase catalyzes transcription of genes encoding different classes of RNA. RNA polymerase I is dedicated to the synthesis of pre ribosomal RNA (rRNA). The primary pre-rRNA transcript is processed into the 18S, 5.8S, and 28S rRNAs in vertebrates or their functional equivalents in other eukaryotes.
RNA polymerase I transcribes the gene for rRNA from a single type of promoter. The transcript includes the sequences of both large and small rRNAs, which are later released by cleavage and processing. The promoter in human cells consists of a bipartite sequence in the region preceding the start point. The 'core promoter element' which is essential for transcription surrounds the start point, extending from -45 to +20, and is sufficient for transcription initiation. However, its efficiency is increased by the presence of a ~50bp long upstream control element (UCE), which extends from -180 to -107. Both regions have an unusual composition for a promoter, being rich in GC base pairs. RNA polymerase I requires ancillary factors; upstream binding factor (UBF) is a single polypeptide that binds to a GC-rich element in the core promoter. SL1 is a multimeric protein composed of TBP and three TAFI units. UBF itself does not bind stably to rDNA but rapidly associates and dissociates. SL1 interacts with the rDNA promoter independently and stably and significantly reduces the rate of dissociation of UBF from the rDNA promoter. Once both factors are bound, RNA polymerase I can bind to the core promoter, completing assembly of the initiation complex.