Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA321756 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:HSF1-expression: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters
| PRJNA321757 | ENA
Project description:Hsf1-ChIP-on-chip: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters
| PRJNA323574 | ENA
Project description:HSF1 and MOT1-expression and binding: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters
| PRJNA321755 | ENA
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 | GSE81987 | GEO
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 | GSE81787 | GEO
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
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 | GSE81479 | GEO
Project description:Mot1 is an essential Snf2-family ATPase in budding yeast that regulates transcription by dissociating the general initiation factor TBP (TATA-binding protein) from DNA. Previous studies showed that in optimum growth conditions Mot1 preferentially removes TBP from stress-responsive promoters that utilize the coactivator SAGA to enhance TBP binding at TFIID-dependent promoters of “housekeeping” genes. In stress conditions of amino acid starvation, by contrast, we found that Mot1 promotes high-level TBP occupancy at genes activated by transcription factor Gcn4, enriched for SAGA-dependent promoters, and at highly-transcribed subsets of constitutively expressed SAGA- and TFIID-dependent genes, while suppressing TBP occupancies at lowly transcribed genes regardless of SAGA/TFIID dependence. Importantly, the response to Mot1 depletion for genes induced by starvation or oxidative stress switched from decreased to increased TBP occupancies when transcribed at low basal levels in non-stressed cells. Notably, reduced TBP binding on Mot1 depletion impairs transcription of highly expressed TFIID genes but not highly expressed SAGA/stress-activated genes, implying that promoter activation by SAGA produces a surfeit of incomplete preinitiation complexes dependent on Mot1 for their formation.
2025-09-25 | GSE299870 | GEO
Project description:Mot1 is an essential Snf2-family ATPase in budding yeast that regulates transcription by dissociating the general initiation factor TBP (TATA-binding protein) from DNA. Previous studies showed that in optimum growth conditions Mot1 preferentially removes TBP from stress-responsive promoters that utilize the coactivator SAGA to enhance TBP binding at TFIID-dependent promoters of “housekeeping” genes. In stress conditions of amino acid starvation, by contrast, we found that Mot1 promotes high-level TBP occupancy at genes activated by transcription factor Gcn4, enriched for SAGA-dependent promoters, and at highly-transcribed subsets of constitutively expressed SAGA- and TFIID-dependent genes, while suppressing TBP occupancies at lowly transcribed genes regardless of SAGA/TFIID dependence. Importantly, the response to Mot1 depletion for genes induced by starvation or oxidative stress switched from decreased to increased TBP occupancies when transcribed at low basal levels in non-stressed cells. Notably, reduced TBP binding on Mot1 depletion impairs transcription of highly expressed TFIID genes but not highly expressed SAGA/stress-activated genes, implying that promoter activation by SAGA produces a surfeit of incomplete preinitiation complexes dependent on Mot1 for their formation.
2025-09-25 | GSE299866 | GEO
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