4. RNA polymerase I has a bipartite promoter

20.4 RNA polymerase I has a bipartite promoter

Figure 20.4 Transcription units for RNA polymerase I have a core promoter separated by ~70 bp from the upstream control element. UBF1 binds to both regions, after which SL1 can bind. RNA polymerase I then binds to the core promoter. The nature of the interaction between the factors bound at the upstream control element and those at the core promoter is not known.

RNA polymerase I transcribes only the genes for ribosomal RNA, from a single type of promoter. The transcript includes the sequences of both large and small rRNAs, which are later released by cleavages and processing. There are many copies of the transcription unit, alternating with nontranscribed spacers, and organized in a cluster as discussed in 4 Clusters and repeats. The organization of the promoter, and the events involved in initiation, are illustrated in Figure 20.4.

The promoter has been best characterized in human cells, in which it consists of a bipartite sequence in the region preceding the startpoint. The core promoter surrounds the startpoint, extending from V45 to +20, and is sufficient for transcription to initiate. However, its efficiency is very much increased by the upstream control element (UCE), which extends from V180 to V107. Both regions have an unusual composition for a promoter, being rich in G PC base pairs; and they are ~85% identical.

RNA polymerase I requires two ancillary factors. UBF1 is a single polypeptide that binds to a G PC-rich element in the core promoter and UCE. Factor SL1 does not by itself have specificity for the promoter, but once UBF1 has bound, SL1 can bind cooperatively to extend the region of DNA that is covered. Once both factors are bound, RNA polymerase I can bind to the core promoter to initiate transcription. We assume that factors bound at the core promoter interact directly with RNA polymerase I, but we do not know how binding of the same factors at the UCE stimulates initiation in the core region. (We see later that action at a distance involving enhancers is a prominent feature of initiation at promoters for RNA polymerase II, in which it has been investigated in more detail.)

SL1 consists of 4 proteins. One of them, called TBP, is a factor that is required also for initiation by RNA polymerases II and III. We discuss its role in initiation by those polymerases shortly. TBP does not bind directly to G PC-rich DNA, so DNA-binding is probably the responsibility of the other components of SL1. It is likely that TBP interacts with RNA polymerase, possibly with a common subunit or a feature that has been conserved among polymerases.

The behavior of SL1 resembles a bacterial sigma factor. As an isolated protein complex, it does not bind specifically to the promoter, but in conjunction with other components, specific promoter regions are bound. It may have primary responsibility for ensuring that the RNA polymerase is properly localized at the startpoint. We see shortly that a comparable function is provided for RNA polymerases II and III by a factor that consists of TBP associated with other proteins. So a common feature in initiation by all three polymerases is a reliance on a "positioning" factor that consists of TBP associated with proteins that are specific for each type of promoter.