6.2 Yeast Promoters 111provides transcription initiation start sites (TSSs) defined by the consensus
sequence A(Arich) 5 NPyA(A/T)NN(Arich) 6. In this consensus, A is the first
transcribed nucleotide, N can be any nucleotide, and Py can be only a pyrimi-
dine [18, 19]. As most yeast core promoters contain several TSSs, several tran-
script isoforms are usually produced from each promoter [20]. The core
promoter is a platform for RNA polymerase II recruitment [21]. RNA polymer-
ase II requires the assistance of general transcription factors to bind the pro-
moter and become competent for transcription initiation. The general
transcription factor called TATA‐binding protein (TBP) recognizes the TATA
element, a DNA sequence enriched for T and A [22], placed at variable dis-
tances upstream of the TSS(s) [18, 19]. The interaction between TBP and the
TATA element triggers the stepwise recruitment of RNA polymerase II and
other general transcription factors at the core promoter [22]. This results in the
formation of the pre‐initiation complex (PIC) , which is necessary to start tran-
scription [12, 14]. Since the interaction between TBP and the TATA element
directly triggers PIC assembly, the strength of this binding influences the over-
all transcription initiation efficiency. Therefore, the TATA element can be con-
sidered as a module acting as a scaling factor within the core promoter: strong
TATA elements result in strong promoters; weak TATA elements result in
weak promoters [23]. After PIC formation, RNA polymerase II searches the
TSS(s) by scanning the template strand [24]. While RNA synthesis is not
required for the scanning process, the selection of the TSS requires transcrip-
tion. Indeed, limiting RNA polymerase II function leads to selection of TSS(s)
further downstream [25]. The region between the TATA element and the
TSS(s) is usually enriched in Ts, while downstream of the TSS(s), A is the pre-
ponderant nucleotide [26]. In strong promoters this biased nucleotide distri-
bution is more evident than in weak promoters, suggesting that this feature
could have an influence on transcription initiation efficiency by probably facil-
itating the identification of the TSS(s) during scanning [27].
The upstream element confers regulation by recruiting transcription factors
[13]. Elements stimulating transcription initiation are called upstream activation
sequences (UASs) and have some common features. First, their regulation
depends on physiological stimuli [3, 16]. Second, their orientation does not affect
their performance [28, 29]. Third, the distance between UASs and core promoter
does not usually influence transcription initiation frequency [4, 28]. Fourth,
UASs do not regulate transcription when they are placed downstream of the
TATA element [28].
The observation that the UAS orientation and the distance from the TATA
element do not influence transcription suggests that the UAS activity is inde-
pendent of the core promoter; that is, these two regions do not interact with the
same sets of proteins [30]. The distinct roles of core promoter and upstream ele-
ment were demonstrated by constructing the first synthetic hybrid promoter,
where the original UAS of a promoter was substituted with one of a second pro-
moter. The resulting construct initiated transcription from the natural TSS of the
first promoter but showed the typical regulation of the second [3]. This inde-
pendence underscores the modular structure of yeast promoters, suggesting the
possibility to combine several upstream elements. The resulting promoter reacts