Abstract
In Saccharomyces cerevisiae, the core promoters of class II genes contain either TATA or TATA-like elements to direct accurate transcriptional initiation. Genome-wide analyses show that the consensus sequence of the TATA element is TATAWAWR (8 bp), whereas TATA-like elements carry one or two mismatches to this consensus. The fact that several functionally distinct TATA sequences have been identified indicates that these elements may function, at least to some extent, in a gene-specific manner. The purpose of the present study was to identify functional TATA sequences enriched in one particular core promoter and compare them with the TATA or TATA-like elements that serve as the pre-initiation complex (PIC) assembly sites on the yeast genome. For this purpose, we conducted a randomized screen of the TATA element in the CYC1 promoter by using a novel reporter assay system and identified several hundreds of unique sequences that were tentatively classified into nine groups. The results indicated that the 7 bp TATA element (i.e., TATAWAD) and several sets of TATA-like sequences are preferred specifically by this promoter. Furthermore, we find that the most frequently isolated TATA-like sequence, i.e., TATTTAAA, is actually utilized as a functional core promoter element for the endogenous genes, e.g., ADE5,7 and ADE6. Collectively, these results indicate that the sequence requirements for the functional TATA or TATA-like elements in one particular core promoter are not as stringent. However, the variation of these sequences differs significantly from that of the PIC assembly sites on the genome, presumably depending on promoter structures and reflecting the gene-specific function of these sequences.
Highlights
In eukaryotes, transcription is highly regulated by the physical interactions between transcriptional regulators that bind to the upstream activating sequence (UAS in budding yeast) or the enhancer and a cohort of transcription factors that assemble on the core promoter to form the pre-initiation complex (PIC)
Our previous study showed that VTC1 could be used as a reporter for gene expression in yeast cells through the quantification of polyP using magnetic resonance spectroscopy (MRS) and/or magnetic resonance imaging (MRI) [33]
We devised a convenient method based on the same reporter gene system and the measurement of polyP amounts by staining with toluidine blue (TB) dye
Summary
Transcription is highly regulated by the physical interactions between transcriptional regulators that bind to the upstream activating sequence (UAS in budding yeast) or the enhancer (in higher eukaryote) and a cohort of transcription factors that assemble on the core promoter to form the pre-initiation complex (PIC) (reviewed in [1, 2]). The core promoter region contains a variety of functionally distinct small DNA segments (termed “core promoter elements”) such as the TATA element, BREu/d, Inr/sINR, TCT motif, DPE, MTE, bridge element, DCE, and XCPE1/2 (reviewed in [3,4,5]) Most of these elements are recognized by general transcription factors (GTFs), including TFIIB or TFIID [6]. Dorsal, a key regulator of the dorsal-ventral gene regulatory network in Drosophila, preferentially activates the DPE-containing core promoter over the TATA-containing core promoter [14] The latter two observations might be accounted for by a recent finding that the DPE-containing core promoter is recognized by TBP-containing TFIID [15], and by TRF2 (TBP-related factor 2)-containing complexes [16]. It is likely that the core transcriptional machinery recruited by a given transcriptional regulator could become fully competent only when it is recruited to the core promoter with an appropriate structure
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
