112 6 Constitutive and Regulated Promoters in Yeast
to several physiological stimuli, converging transcription initiation on the TSS(s)
defined by the core promoter [28, 29].
Transcription factors bind the upstream element on specific and well‐defined
DNA motifs called transcription factor binding sites (TFBSs). TFBSs are neces-
sary and sufficient to confer regulation to a promoter [31].
In yeast, the most frequently observed mechanism of transcription initiation
stimulation is activation by recruitment [32]. Transcription activators bind
TFBSs located in the UAS. Their role merely consists of indicating the DNA
region that needs to be transcribed. The binding of the transcription activator to
its TFBS triggers the recruitment of the coactivators SAGA and TFIID, which in
turn localize TBP to the core promoter. This array of protein–protein interac-
tions results in the PIC assembly.
An important hint about the mechanism of activation by recruitment comes
from the observation that DNA-binding and transcription activation activities of
yeast transcription activators are functionally and physically separable. In fact,
yeast activators display a modular structure containing, among others, a DNA‐
binding domain and an activation domain [33]. Truncations retaining either the
DNA‐binding or activation portion fail to initiate transcription. However, reas-
sociation of these two portions restores function [34–36].
The modular structure of yeast transcription activators implies possible regu-
lation of the mechanism of activation by recruitment. Masking the DNA‐binding
or activation activity by protein–protein interactions results in the failure of
transcription initiation. The activity of the general repressor complex Cyc8–Tup1
consists in binding and covering the activation domains of target transcription
activators. This interaction causes transcription initiation inhibition, even
though the transcription activator is bound to its TFBS. Unmasking the activa-
tion domain by abolishing the interactions with Cyc8–Tup1 results in the
recruitment of the transcriptional machinery [37].
In eukaryotes, DNA is not directly accessible, since it is wrapped around his-
tones to form nucleosomes (reviewed in [38]). Nucleosomes provide a general
inhibitory function that reduces basal transcription initiation of all genes
(reviewed in [39]). As histones have a general affinity for DNA, nucleosomes
form at random positions along DNA [40]. DNA‐binding proteins that recog-
nize specific binding sites compete with histones to interact with DNA (reviewed
in [41]). However, the specific interaction of a DNA‐binding protein to its bind-
ing site produces a physical barrier on the DNA that forces nucleosomes to
phase around this point [40, 42]. In some promoters, nucleosome phasing may
have an indirect role in transcription initiation stimulation by enhancing the
accessibility of the TFBS of the transcription activator [42]. After the binding of
the transcription activator, the nucleosomes must be displaced to assemble the
PIC and start transcription. Therefore, the transcriptional machinery recruits
factors involved in nucleosome remodeling [11]. The efficiency of nucleosome
clearance is influenced by the propensity of DNA to be wrapped into nucle-
osomes [43]. The homopolymeric dA:dT sequences frequently observed in the
UASs interact weakly with the histones and therefore cause the inefficient
formation of nucleosomes in the region. This results in easier nucleosome
clearance and stronger transcription [44]. Therefore, composition, length, and