Structural Features of Specific DNA Binding Sites
Since RNA polymerase must interact at the promoter site of all genes, you might expect that all genes would have a similar nucleotide sequence in the promoter region. This is found to be true for both prokaryotic and eukaryotic genes. You would expect, however, that all transcription factors would not have identical DNA binding sequences. The sequences of DNA just upstream of the start site of the gene that binds protein (RNA polymerase, transcription factors, etc) are called promoters. The table below shows the common DNA sequence motif called the Pribnow or TATA box found at around -10 base pairs upstream from the start site, and another at -35. Proteins bind to these sites and facilitate binding of RNA polymerase, leading to gene transcription.
Prokaryotic Promoter Sequences
|Spacer||-10 Region||Spacer||RNA start|
The TATA box in prokaryotes is also known as the Pribnow box. A similar sequence is found in eukaryotes (consensus TATAAA) located about 25 nucleotides upstream from the transcription start site. It is also called the Goldstein-Hogness box.
- Jmol: TATA Box Binding Protein
In addition, in eukaryotes, sequences further upstream called response elements bind specific proteins (such as CREB or cyclic AMP response element binding protein) to further control gene transcription.
Eukaryotic Response Elements (RE)s
|Consensus||DNA bound||Factor||Size (daltons)|
|Heat Shock||HSE||CNNGAANNTCCNNG||27 bp||HSTF||93,000|
|Phorbol Ester||TRE||TGACTCA||22 bp||AP1||39,000|
|Hypoxia Inducible Factor||826 aa|
|Peroxisome Proliferator Activated Receptor (PPAR)||PPRE||aGG_CAAAGGT(CG)A||PPAR||59,000|
|Steroid (general) (progesterone, androgen, mineralcorticoids, glucocorticoids)|| |
- Eukaryotic Promoter Database - annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally
"The multi-subunit general transcription apparatus: identification of tissue-specific and gene-selective subunits. Diversified metazoan transcription initiation complexes. a, The eukaryotic transcriptional apparatus can be subdivided into three broad classes of multi-subunit ensembles that include the RNA polymerase II core complex and associated general transcription factors (TFIIA, -B,-D,-E,-F and -H), multi-subunit cofactors (mediator, CRSP, TRAP, ARC/DRIP, and so on) and various chromatin modifying or remodelling complexes (SWI/SNF, PBAF, ACF, NURF and RSF). b, c, Metazoan organisms have evolved multiple gene-selective and tissue-specific TFIID-like assemblies by using alternative TAFs (TBP-associated factors such as the ovarian-specific TAF105) as well as TRFs (TBP-related factors such as TRF2 in Drosophila and mice) to mediate the formation of specialized RNA polymerase initiation complexes that direct the transcription of tissue-specific and gene-selective programmes of expression." (Nature reference in figure above.)
Proteins can interact specifically with DNA through electrostatic, H-bond, and hydrophobic interactions. AT and GC base pairs have available H bond donors and acceptors which are exposed in the major and minor groove of the ds DNA helix, allowing specific protein-DNA interactions.