Adjacent genes (RNA-coding as well as protein-coding) are often separated by an
insulator which helps them avoid cross-talk between each other's promoters and enhancers (and/or silencers).
Transcription start site
This is where a molecule of
RNA polymerase II (pol II, also known as RNAP II) binds. Pol II is a complex of 12 different proteins (shown in the figure in yellow with small colored circles superimposed on it).
The start site is where
transcription of the gene into RNA begins.
The basal promoter
The basal promoter contains a sequence of 7 bases (TATAAAA) called the TATA box. It is bound by a large complex of some 50 different proteins, including:
Transcription Factor IID (TFIID) which is a complex of
TATA-binding protein (TBP), which recognizes and binds to the TATA box
14 other protein factors which bind to TBP — and each other — but not to the DNA.
Transcription Factor IIB (TFIIB) which binds both the DNA and pol II.
The basal or core promoter is found in all protein-coding genes. This is in sharp contrast to the upstream promoter whose structure and associated binding factors differ from gene to gene.
Although the figure is drawn as a straight line, the binding of transcription factors to each other probably draws the DNA of the promoter into a loop.
Many different genes and many different types of cells share the same transcription factors — not only those that bind at the basal promoter but even some of those that bind upstream. What turns on a particular gene in a particular cell is probably the unique combination of promoter sites and the transcription factors that are chosen.
An analogy
The rows of lock boxes in a bank provide a useful analogy.
To open any particular box in the room requires two keys:
your key, whose pattern of notches fits only the lock of the box assigned to you (= the upstream promoter), but which cannot unlock the box without
a key carried by a bank employee that can activate the unlocking mechanism of any box (= the basal promoter) but cannot by itself open any box.
