Geoscience Reference
In-Depth Information
core promoter or proximal promoter through a mechanism that
involves looping out the intervening DNA. The core promoter ele-
ments (CPEs) are the region at the beginning of a gene that serves
as the docking site for the basic transcriptional machinery and pre-
initiation complex (PIC) assembly, and defines the position of the
transcription start site (TSS) as well as the direction of transcrip-
tion (Smale and Kadonaga, 2003; Maston et al., 2006; Sandelin
et al., 2007). The core promoter includes DNA elements that can
extend up to 40 bp upstream and/or downstream of the transcrip-
tion start site (TSS) (Kadonaga, 2002). The first described CPE
was the TATA box, the binding site for the TBP subunit of TFIID.
In addition to the TATA box, core promoters can be composed
of numerous other elements, including initiator element (INR),
downstream promoter element (DPE), downstream core element
(DCE), TFIIB-recognition element (BRE) and motif ten element
(MTE) (Thomas and Chiang, 2006) (Figure 13.2).
The proximal promoter is defined as the region immediately
upstream (up to a few hundred base pairs) from the core promoter
(Figure 13.2), and typically contains multiple binding sites for acti-
vators (Juven-Gershon and Kadonaga, 2010). The
cis
-elements to
which general transcription factors bind are located in this region.
These regulatory motifs can promote or suppress the binding of
the core promoter components involved in the basal transcrip-
tion complex. Sequence-specific DNA-binding transcription fac-
tors are capable of activating or repressing transcription. They
cause genes to be selectively expressed in response to a certain
environmental condition in a particular cell. Other transcription
factors and co-regulators are specific in their activity and typi-
cally bind to promoters of genes that are regulated in response to
some stimulus such as a pathogen or an environmental condition.
Distal (upstream) regulatory elements can include enhanc-
ers, silencers, insulators, and locus control regions. It is located
up to thousands of base pairs away from the TSS, downstream
of the gene, and also in the introns of the gene (Juven-Gershon
and Kadonaga, 2010). Conceivably, the transcription factors
that bind to these elements also bind to the basal transcription
complex by bending the DNA into a loop and thus, acting as the
transcription. These sequences can suppress or enhance tran-
scription significantly and the strand on which they occur does
not act on their influence. They are also responsible for tissue-
specific expression as are elements in the proximal promoter,
which often consist of repeats of the same elements as in the
proximal promoter. Enhancers can act as the transcription of
more than one gene, both by changing the chromatin structure
and by interacting with the PIC.
