Promoter
In genetics, a promoter is a DNA sequence that enables a gene to be transcribed. The promoter is recognized by RNA polymerase, which then initiates transcription.
The perfect promoter is called a canonical sequence.
Promoter elements
- Core promoter
- Transcription Start Site (TSS)
- Approximately -35 to +35
- A binding site for RNA polymerase
- RNA-polymerase I: transcribes genes encoding ribosomal RNA
- RNA-polymerase II: transcribes genes encoding mRNA and certain small nuclear RNAs
- RNA-polymerase III: transcribes genes encoding tRNAs and other small RNAs
- General transcription factor binding sites
- Proximal promoter
- Approximately -250 to +250
- Specific transcription factor binding sites
- Distal promoter
- Anything further downstream (still within the gene area)
- Enhancer
- Short regulatory elements positioned several kilobases upstream or downstream of the core promoter
- Silencers, Boundary/Insulators
Promoter sequences
Prokaryotic promoters
In prokaryotes, the promoter consists of two short sequences at -10 and -35 position upstream of the gene, that is, prior to the gene in the direction of transcription. The sequence at -10 is called the Pribnow box and usually consists of the six nucleotides TATAAT. The Pribnow box is absolutely essential to start transcription in prokaryotes. The other sequence at -35 usually consists of the six nucleotides TTGACA. Its presence allows a very high transcription rate.
<-- upstream downstream -->
5'-XXXXXXXPPPPPXXXXXXPPPPPXXXXGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGXXXX-3'
-35 -10 Gene to be transcribed
Probability of occurrence of each nucleotide
T A T A A T
77% 76% 60% 61% 56% 82%
T T G A C A
69% 79% 61% 56% 54% 54%
Eukaryotic promoters
See Michael Levine and Robert Tjian. "Transcription regulation and animal diversity". Nature 424, 147 - 151 (10 July 2003)
Binding
The binding of a promoter sequence (P) to a sigma factor-RNAP complex (R) is a two step process:
- R+P ↔ RP(closed). K = 10E7
- RP(closed) --> RP(open). K = 10E-2
