A promoter is a region of DNA where transcription of a gene initiates. Promoters are adjacent and typically upstream (5’) of the sense strand of the regulated gene. Promoters are a vital component of expression vectors because they control the attachment of RNA polymerase to DNA and are directly responsible for the amount of transcript generated.
The promoter region controls when and where the RNA polymerase will attach to DNA so transcription can commence. DNA sequences called response elements are located within promoter regions, and they provide a stable binding site for RNA polymerase and transcription factors. Transcription factors are proteins which recruit RNA polymerase and control and regulate the transcription of DNA into mRNA.
Promoter binding is very different in bacteria compared to eukaryotes. In bacteria, RNA polymerase only requires the associated protein sigma factor to bind the promoter. On the other hand, the process in eukaryotes is much more complex. Eukaryotes require a minimum of seven transcription factors in order for the binding of RNA polymerase II (eukaryote-specific RNA polymerase) to the promoter.
Both in bacteria and eukaryotes, the promoter is controlled by various DNA regulatory sequences including enhancers, boundary elements, insulators, and silencers. Transcription is tightly controlled in every cell.
There are three main portions that make up a promoter: core promoter, proximal promoter, and distal promoter.
The core promoter region is located most proximally and contains the RNA polymerase binding site, TATA box, and transcription start site (TSS). RNA polymerase will bind to this core promoter region stably and transcription of the template strand can initiate. The TATA box is a DNA sequence (5'-TATAAA-3) within the core promoter region where general transcription factor proteins and histones can bind. Histone binding will prevent the initiation of transcription whereas transcription factors will drive the onset of transcription. The most 3' portion of the core promoter is the TSS which is where transcription literally is initiated.
However, only eukaryotes and archaea contain this TATA box. Prokaryotes contain something called the Pribnow box which usually consists of the six nucleotides TATAAT. There are three types of RNA polymerases that all encode different molecules when a gene is transcribed. RNA polymerase I encodes for ribosomal RNA (rRNA) which is a main component of a cell’s ribosome structure. RNA polymerase II encodes for messenger RNA (mRNA) when a gene is transcribed which is the RNA responsible for providing a stable template for the translation of a protein. Finally, RNA polymerase III transcribes genes encoding for transfer RNA tRNA, an adaptor molecule that is responsible for bringing the triplet codon to the ribosome when proteins are being formed. No matter which RNA polymerase molecule it is, the promoter is the location where it will bind to initiate transcription of a gene.
Further upstream from the core promoter you will find the proximal promoter which contains many primary regulatory elements. The proximal promoter is found approximately 250 base pairs upstream from the TSS and it is the site where general transcription factors bind.
The final portion of the promoter region is called the distal promoter which is anything further upstream from the gene. The distal promoter also contains transcription factor binding sites, but mostly contains regulatory elements.
Promoters in prokaryotic organisms are two short DNA sequences located at the -10 (10bp 5' or upstream) and -35 positions from the transcription start site (TSS). Their equivalent to the eukaryotic TATA box, the Pribnow box (TATAAT) is located at the -10 position and is essential for transcription initiation. The -35 position, simply titled the -35 element, typically consists of the sequence TTGACA and this element controls the rate of transcription. Prokaryotic cells contain sigma factors which assist the RNA polymerase in binding to the promoter region. Each sigma factor recognizes different core promoter sequences.
Eukaryotic Promoters are much more complex and diverse than prokaryotic promoters. Eukaryotic promoters span a wide range of DNA sequences. It is not unusual to have several regulatory elements such as enhancers several kilo bases away from the TSS. Eukaryotic Promoters are so complex in structure that the DNA tends to fold back on itself which explains how a lot of regulatory sequences can effect transcription while being physically located far from the initiation transcription site. The TATA-binding protein binds the TATA box and helps in the subsequent binding of the RNA polymerase. A transcription complex is constructed from the RNA polymerase and several transcription factor proteins.