What Is an RNA Promoter?

An RNA promoter is a sequence of nucleotides preceding a gene that encodes ribonucleic acid (RNA). This sequence is located in the deoxyribonucleic acid (DNA) of a cell, and, like all promoters, an RNA promoter helps facilitate gene transcription. The difference between this type of promoter and other types of promoters is that, while many genes following a promoter encode memory RNA (mRNA), genes following an RNA promoter code for ribosomal RNA (rRNA), used in the ribosomes to help translate mRNA into proteins. RNA promoters are found in the genetic information of all eukaryotic cells, so all organisms except for bacteria and viruses have them. This promoter can be recognized by proteins that bind to both its nucleotide sequence and the enzyme responsible for transcription, speeding up the rate at which transcription takes place.

The RNA promoter provides its function by providing a binding site for RNA polymerase I, the enzyme that transcribes rRNA, as well as associated transcription factors. The promoter sequence on the DNA is different than most genes, which use a thymine and adenine series of nucleotides called a TATA box. The RNA promoter, instead, has a sequence called an upstream control sequence (UCS) that is recognized by a protein called upstream binding factor (UBF). After they are bound, a larger protein complex, called transcription initiation factor-IB (TIF-IB). TIF-IB consists of the TATA binding protein (TBP) used in other promoters, as well as other transcription factor enzymes. The other enzymes present help TBP bind to the UBF, since, as mentioned above, there is no TATA box on rRNA coding sequences of DNA for it to bind to.

After the TIF-IB complex is bound upstream from the gene coding for rRNA, it is phosphorylated, which activates the complex and allows it to recruit and bind RNA polymerase I. This is the only enzyme that is able to transcribe DNA sequence coding for rRNA, and as such, the only polymerase type to make use of the RNA promoter. It binds to a part of the promoter complex that consists of the protein TBP associated factor-IA, and then, in turn, can bind to the DNA sequence downstream from the promoter complex that codes for rRNA. Through this promoter, RNA polymerase I can find the necessary DNA sequences to transcribe much more quickly than if it had to locate these sequences on their own, so this promoter is a means of regulating the rate of rRNA transcription.