Identification and Distinct Regulation of Yeast TATA Box-Containing Genes

Basehoar, Andrew D.; Zanton, Sara J.; Pugh, B. Franklin

doi:10.1016/s0092-8674(04)00205-3

Cited by 601 publications

(807 citation statements)

References 57 publications

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“…These preset promoters tend to be underrepresented for TATA boxes and tend to have a strong nucleosome-depleted region at a stereotypical position relative to the transcriptional start site, a promoter architecture that has been termed "type II" (Field et al, 2008). Previous work has characterized TATA-less promoters as enriched in constitutively expressed housekeeping genes (Basehoar et al, 2004), but the work reported here clearly demonstrates that individual TATA-less preset promoters are capable of dramatic gene expression changes.…”

Section: Preset Promotersmentioning

confidence: 67%

“…We observed that genes containing TATA boxes, which constitute ϳ20% of all genes in yeast (Basehoar et al, 2004), were unusual in several respects. First, as noted previously (Ioshikhes et al, 2006;Albert et al, 2007;Mavrich et al, 2008), we found that, although the 5Ј NDRs in non-TATA containing promoters were all 200 base pairs wide and stereotypically centered 100 base pairs upstream of the TSS, the NDRs in promoters with TATA boxes were of the same size as those at non-TATA promoters but were dispersed over a much wider region, with each gene containing an individually positioned NDR.…”

Section: Promoters Containing Tata Boxes Are More Likely To Undergo Nmentioning

confidence: 90%

“…As a consequence, TATA box-containing promoters exhibit a much higher correlation between transcriptional change and nucleosome remodeling than do promoters lacking TATA boxes. Pugh and coworkers noted previously that TATA boxes are enriched in the promoters of genes induced by starvation and other cell stresses and that these genes are particularly dependent on chromatin modification activities (Basehoar et al, 2004). We can now appreciate this dependency as a consequence of the significant proportion of TATA-containing promoters, relative to TATA-less promoters, that undergo nucleosome remodeling during transcriptional reprogramming.…”

Section: Remodeling Promotersmentioning

confidence: 90%

“…The correlation between promoter log ratio MNase hybridization intensity change and transcriptional change for genes lacking a TATA box is weak (r ϭ 0.23). However, the correlation (Basehoar et al, 2004). For each subgroup, the average nucleosome occupancy at every nucleotide around the TSS was calculated before glucose addition (solid line) and 20 min after glucose addition (dashed line) and the values plotted relative to the position of the nucleotide from the TSS.…”

Section: Promoters Containing Tata Boxes Are More Likely To Undergo Nmentioning

confidence: 99%

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Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

Zawadzki

Morozov

Broach

2009

MBoC

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Several well-studied promoters in yeast lose nucleosomes upon transcriptional activation and gain them upon repression, an observation that has prompted the model that transcriptional activation and repression requires nucleosome remodeling of regulated promoters. We have examined global nucleosome positioning before and after glucose-induced transcriptional reprogramming, a condition under which more than half of all yeast genes significantly change expression. The majority of induced and repressed genes exhibit no change in promoter nucleosome arrangement, although promoters that do undergo nucleosome remodeling tend to contain a TATA box. Rather, we found multiple examples where the pre-existing accessibility of putative transcription factor binding sites before glucose addition determined whether the corresponding gene would change expression in response to glucose addition. These results suggest that selection of appropriate transcription factor binding sites may be dictated to a large extent by nucleosome prepositioning but that regulation of expression through these sites is dictated not by nucleosome repositioning but by changes in transcription factor activity. INTRODUCTIONChromatin, whose basic unit is a nucleosome that consists of 147 base pairs of DNA wrapped twice around a histone octamer, plays a central role in the regulation of genes. Several experiments in yeast have shown that nucleosome depletion causes derepression of PHO5, GAL1, CUP1, SUC2, and HIS3 in the absence of their transcriptional activators Durrin et al., 1992;Hirschhorn et al., 1992). These observations suggested that nucleosomes in promoters can function as nonspecific repressors, consistent with the concept that DNA sequences incorporated into nucleosomes are less accessible to DNA binding proteins such as transcription factors (Morse, 2003(Morse, , 2007. Subsequent observations have demonstrated that chromatin structure can participate actively in gene regulation through repositioning of nucleosomes so as to block access of a transcription factor to its cognate binding sites or to remove a barrier to such access. Consistent with this notion, several examples have been reported in which gene induction involves recruitment to a promoter of chromatin remodeling factors and histone modifying activities designed to remove or reposition a nucleosome to allow access to an otherwise masked transcription factor binding site (Li et al., 2007;Williams and Tyler, 2007). For example, remodeling factors act at the above-mentioned promoters for PHO5, GAL1, CUP1, and SUC2 to facilitate nucleosome loss on transcriptional activation and conversely to assemble or stabilize nucleosomes on the gene promoter during transcriptional repression (Almer et al., 1986;Fedor and Kornberg, 1989;Shen et al., 2001;Kim et al., 2006).Chromatin can also play a more passive role in gene regulation by simply controlling which transcription factor binding sites are available for participation in gene regulation. Recent genome-wide studies of nucleosome positioning fo...

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Section: Preset Promotersmentioning

confidence: 67%

Section: Promoters Containing Tata Boxes Are More Likely To Undergo Nmentioning

confidence: 90%

Section: Remodeling Promotersmentioning

confidence: 90%

Section: Promoters Containing Tata Boxes Are More Likely To Undergo Nmentioning

confidence: 99%

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Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

Zawadzki

Morozov

Broach

2009

MBoC

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“…Another possibility for a characteristic of Tup1-controlled promoters that could influence which repression mechanisms are important at a particular gene is the composition of the general transcriptional machinery regulating expression at that promoter. For example, Basehoar et al (2004) and Huisinga and Pugh (2004) identified a set of genes (ϳ10% of the genome) whose regulation is dominated by the SAGA complex rather than the TFIID complex and showed that Tup1-controlled genes disproportionately fall into this category. However, all five subclasses of Tup1-repressed genes we describe in this article exhibit this same propensity for SAGA-dominated transcriptional regulation, so although inclusion in this group does seem to be a characteristic of Tup1-repressed genes, it does not seem to dictate the influence of a particular repression mechanism.…”

mentioning

confidence: 99%

Promoter-dependent Roles for the Srb10 Cyclin-dependent Kinase and the Hda1 Deacetylase in Tup1-mediated Repression inSaccharomyces cerevisiae

Green

Johnson

2004

MBoC

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The Tup1-Ssn6 complex has been well characterized as a Saccharomyces cerevisiae general transcriptional repressor with functionally conserved homologues in metazoans. These homologues are essential for cell differentiation and many other developmental processes. The mechanism of repression of all of these proteins remains poorly understood. Srb10 (a cyclin-dependent kinase associated with the Mediator complex) and Hda1 (a class I histone deacetylase) have each been implicated in Tup1-mediated repression. We present a statistically based genome-wide analysis that reveals that Hda1 partially represses roughly 30% of Tup1-repressed genes, whereas Srb10 kinase activity contributes to the repression of ϳ15% of Tup1-repressed genes. These effects only partially overlap, suggesting that different Tup1-repression mechanisms predominate at different promoters. We also demonstrate a distinction between histone deacetylation and transcriptional repression. In an HDA1 deletion, many Tup1-repressed genes are hyperacetylated at lysine 18 of histone H3, yet are not derepressed, indicating deacetylation alone is not sufficient to repress most Tup1-controlled genes. In a strain lacking both Srb10 and Hda1 functions, more than half of the Tup1-repressed genes are still repressed, suggesting that Tup1-mediated repression occurs by multiple, partially overlapping mechanisms, at least one of which is unknown. INTRODUCTIONThe Tup1-Ssn6 complex is a general transcriptional repressor in Saccharomyces cerevisisae that controls a diverse set of genes generally characterized as being important for adaptation to nonstandard growth. Homologues of Tup1 have been identified in several other organisms (for example, unc-37 in Caenorhabditis elegans, Groucho in Drosophila, and TLE proteins in humans), and their repression functions are essential for embryonic development, cell differentiation, neurogenesis, and other developmental processes (Pflugrad et al., 1997;Fisher and Caudy, 1998;Levanon et al., 1998;Grbavec et al., 1999). Consequently, a better understanding of the mechanism of Tup1-mediated repression in yeast should illuminate this same process and its wide-ranging downstream consequences in other organisms. The Tup1-Ssn6 complex does not itself bind DNA but is recruited to target promoters through an association with sequence-specific DNA binding proteins; however, the crucial question of how transcriptional repression is established once this event occurs has not been clearly answered.Two models for Tup1-mediated repression are supported by a number of earlier observations. One proposes that Tup1 produces a transcriptionally repressed chromatin state by recruiting histone deacetylases (HDACs). Hda1, a class I HDAC, has emerged as the most likely deacetylase to be acting with Tup1. Hda1 binds to Tup1 in vitro and an HDA1 deletion results in hyperacetylation of histones at several Tup1-controlled genes (Wu et al., 2001). Hyperacetylation of Tup1-repressed genes also is seen when Tup1 is deleted (Bone and Roth, 2001;Davie et al., 2002). ...

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DNA structural features of eukaryotic TATA‐containing and TATA‐less promoters

Yella

Bansal

2017

FEBS Open Bio

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Eukaryotic genes can be broadly classified as TATA‐containing and TATA‐less based on the presence of TATA box in their promoters. Experiments on both classes of genes have revealed a disparity in the regulation of gene expression and cellular functions between the two classes. In this study, we report characteristic differences in promoter sequences and associated structural properties of the two categories of genes in six different eukaryotes. We have analyzed three structural features, DNA duplex stability, bendability, and curvature along with the distribution of A‐tracts, G‐quadruplex motifs, and CpG islands. The structural feature analyses reveal that while the two classes of gene promoters are distinctly different from each other, the properties are also distinguishable across the six organisms.

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Identification and Distinct Regulation of Yeast TATA Box-Containing Genes

Cited by 601 publications

References 57 publications

Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

Promoter-dependent Roles for the Srb10 Cyclin-dependent Kinase and the Hda1 Deacetylase in Tup1-mediated Repression inSaccharomyces cerevisiae

DNA structural features of eukaryotic TATA‐containing and TATA‐less promoters

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