Promoter elements that are not required for transcription initiation, but influence the
level, rate, timing or tissue specificity of transcription are theCAAT box(CCAAT), and
gene-specific response elements. The CAAT box is generally located at sites 2 70 to
2 80. The gene-specific response elements vary in their sequence and location within the
promoter. A third type ofcis-regulatory element is anenhancer, the location of which
varies from gene to gene. Unlike a promoter element, an enhancer can function even at
long distances (.1kb) upstream or downstream of the transcriptional start site (Khoury
and Gruss 1983), and its orientation can be inverted without losing its function. The
CAAT box, gene-specific response elements, and enhancers carry out their functions by
binding specific transcription factors (Fig. 6.7).
6.3.2 Transcription Factors
Transcription factorsare regulatory proteins that bind to DNA and to other regulatory pro-
teins to effect gene expression, as described above. Thus, there are transcription factor
genes whose expression affects the regulation of other genes. In order to carry out their
functions, they generally have specific portions, or domains. There are two main
domains in transcription factors, aDNA binding domain and atrans-acting domain.
TheDNA binding domaindoes just that; it allows the transcription factor to bind directly
to a DNAcis-regulatory element. DNA binding domains are characterized by specific
structures or motifs. For example, some DNA binding domains have a helix–turn–
helix motif, a zinc-finger motif, or a leucine zipper motif. Thetrans-acting domainof a
transcription factor allows it to bind to RNAP II or to other transcription factors, thus
allowing protein–protein interactions. So, with two such domains, a transcription factor
Figure 6.7.Regulation of transcription. Thecis-acting elements are segments of DNA that regulate
transcription; these segments may be adjacent to the gene such as the promoter (CAAT box) and
thecis-acting gene-specific response elements, or they may be distant to the gene such as enhancers.
Thetrans-acting elements are transcription factors and other regulatory proteins that may associate
with the promoter, other proteins, or both. See color insert.
6.3. TRANSCRIPTION 143