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Transcription of nearly all yeast RNA Polymerase II-transcribed genes is dependent on transcription factor TFIID

ABSTRACT: Previous studies suggested that expression of most yeast mRNAs is dominated by either transcription factor TFIID or SAGA. We reexamined this longstanding problem by rapid depletion of TFIID subunits and measurement of changes in nascent transcription. We find that transcription of nearly all mRNAs is strongly dependent on TFIID function. Degron-dependent depletion of Tafs 1,2,7,11, and 13 showed similar transcription decreases for genes in the Taf1-depleted, Taf1-enriched, TATA-containing and TATA-less gene classes. The magnitude of TFIID-dependence varies with growth conditions, although this variation is similar at all gene classes. Many studies have suggested differences in gene regulatory mechanisms between TATA and TATA-less genes and these differences have been attributed in part to differential dependence on SAGA or TFIID. Our work indicates that TFIID contributes significantly to expression of nearly all yeast mRNAs and that differences in regulation between these two gene classes is due to other properties.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE97081 | GEO | 2017/08/02

SECONDARY ACCESSION(S): PRJNA380638

REPOSITORIES: GEO

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A genome-wide housekeeping role for TFIID and a highly stress-related role for SAGA in Saccharomyces cerevisiae

Project description:TFIID and SAGA are the only two known yeast complexes that modify chromatin and deliver TBP to promoters. Previous genome wide expression studies indicated that TFIID and SAGA positively regulate most but not all yeast genes. Using a relatively low noise microarray approach, we have re-examined the genome-wide dependence on TFIID and SAGA. We find that TFIID and SAGA contribute to the expression of virtually the entire genome, with TFIID being preferred at ~90% of the genes, and SAGA being preferred at ~10%. SAGA-dominated genes were found to overlap substantially with a previously described set of highly active genes that are attenuated in part by the TBP regulator NC2, and an auto-inhibitory function of TFIID. These SAGA-dominated genes also encompass most of the previously reported âTAF-independentâ genes. These results build upon and refine the generally held view that activators recruit either TFIID or SAGA to promoters which then bind and acetylate nucleosomes locally, thereby enhancing TBP delivery to the TATA box. Promoter-specific differences in the ability to alleviate auto-inhibitory activities associated with TFIID and SAGA might contribute to the preferential use one complex versus the other. Keywords = Chromatin Immunoprecipitation Keywords = genome-wide binding

2010-06-09 | E-GEOD-1061 | biostudies-arrayexpress

A genome-wide housekeeping role for TFIID and a highly stress-related role for SAGA in Saccharomyces cerevisiae

Project description:TFIID and SAGA are the only two known yeast complexes that modify chromatin and deliver TBP to promoters. Previous genome wide expression studies indicated that TFIID and SAGA positively regulate most but not all yeast genes. Using a relatively low noise microarray approach, we have re-examined the genome-wide dependence on TFIID and SAGA. We find that TFIID and SAGA contribute to the expression of virtually the entire genome, with TFIID being preferred at ~90% of the genes, and SAGA being preferred at ~10%. SAGA-dominated genes were found to overlap substantially with a previously described set of highly active genes that are attenuated in part by the TBP regulator NC2, and an auto-inhibitory function of TFIID. These SAGA-dominated genes also encompass most of the previously reported “TAF-independent” genes. These results build upon and refine the generally held view that activators recruit either TFIID or SAGA to promoters which then bind and acetylate nucleosomes locally, thereby enhancing TBP delivery to the TATA box. Promoter-specific differences in the ability to alleviate auto-inhibitory activities associated with TFIID and SAGA might contribute to the preferential use one complex versus the other. Keywords = Chromatin Immunoprecipitation Keywords = genome-wide binding Keywords: other

2004-03-01 | GSE1061 | GEO

Genome-wide regulation by TFIID and SAGA

Project description:TFIID and SAGA share a common set of TAFs, regulate chromatin, and deliver TBP to promoters. Here we examine their relationship within the context of the Saccharomyces cerevisiae genome-wide regulatory network. We find that while TFIID and SAGA make overlapping contributions to the expression of all genes, TFIID function predominates at ~90% and SAGA at ~10% of the measurable genome. Strikingly, SAGA-dominated genes are largely stress-induced and TAF-independent, and are down-regulated by the coordinate action of a variety of chromatin, TBP, and RNA polymerase II regulators. In contrast, the TFIID-dominated class is less regulated, but is highly dependent upon TAFs including those shared between TFIID and SAGA. These two distinct modes of transcription regulation might reflect the need to balance inducible stress responses with the steady output of housekeeping genes. Keywords = Taf1 Keywords = Spt3 Keywords = Gcn5

2004-02-26 | E-GEOD-885 | biostudies-arrayexpress

MOT1-expression: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

Project description:An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA-dominated/TATA-box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA-like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA-box promoters are more dynamic because TBP recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA-box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class.

2016-11-11 | GSE81480 | GEO

HSF1-expression: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

2016-11-11 | GSE81479 | GEO

Hsf1-ChIP-on-chip: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

2016-11-11 | GSE81987 | GEO

HSF1 ChIP-seq: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

2016-11-11 | GSE81787 | GEO

Genome-wide transcriptional dependencies on TAF1 functional domains

Project description:TFIID plays a central role in regulating the expression of most eukaryotic genes. Of the 14 TAF subunits that compose TFIID, TAF1 is one of the largest and most functionally diverse. Yeast (Saccharomyces cerevisiae) TAF1 reportedly possesses at least four distinct activities including a histone acetyltransferase, and TBP, TAF, and promoter binding. Establishing the importance of each region in gene expression through deletion analysis has been hampered by the cellular requirement of TAF1 for viability. To circumvent this limitation we introduced galactose-inducible deletion derivatives of previously defined functional regions of TAF1 into a temperature sensitive taf1ts2 yeast strain. After galactose-induction and temperature inactivation of the temperature-sensitive allele, we examined the properties and phenotypes of the mutants, including their impact on genome-wide transcription. Virtually all TAF1-dependent genes, which comprise ~90% of the yeast genome, displayed a strong dependency upon all regions of TAF1 that were tested. This might reflect the need for each region of TAF1 to stabilize TAF1 against degradation or that all TAF1-dependent genes require the many activities of TAF1. Paradoxically, deletion of the region of TAF1 that is important for promoter binding interfered with the expression of many genes that are normally TFIID-independent/SAGA-dominated, suggesting that this region normally prevents TAF1 (TFIID) from interfering with the expression of SAGA-regulated genes. Keywords: genetic modification

2006-01-10 | GSE3006 | GEO

Large-scale reporter assay to assess expression and coactivator specificity of UAS-core promoter combinations (DNA)

Project description:Three general classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA and Mediator (MED) Tail, but little is known about whether this dependence is determined by the core promoter, Upstream activation sites (UAS), or other gene features. It is also unclear whether UASs can broadly activate transcription from the different promoter classes or whether efficient transcription requires matching UASs and promoters of similar gene class. Here we measure transcription and cofactor specificity for tens of thousands of UAS-core promoter combinations. We find that few UASs display strong core promoter specificity while most UASs can broadly activate promoters regardless of regulatory class. However, we find that matching UASs and promoters from the same gene class is generally important for optimal expression. We find that MED Tail and SAGA are dependent on the identity of both UAS and promoter while dependence on TFIID localizes to only the core promoter.

2023-03-17 | GSE217227 | GEO

Large-scale reporter assay to assess expression and coactivator specificity of UAS-core promoter combinations [III]

2023-03-17 | GSE227006 | GEO

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