Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA374588 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5251630.fastq.gz | Fastqsanger.gz | |||
| SRR5251631.fastq.gz | Fastqsanger.gz | |||
| SRR5251632.fastq.gz | Fastqsanger.gz | |||
| SRR5251629.fastq.gz | Fastqsanger.gz | |||
| SRR6354921.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:The goals of this study are to compare Next-Generation-Sequecing (NGS)-derived genome-wide occupancy of TAF (Taf1) comparing with other basal initiation components (TBP and TFIIB), histones (H3, H4, Htz1 and H4 acetylation) and histone regulator complexes (Swr1, Bdf1) in S. cerevisiae.
2017-02-14 | GSE94851 | GEO
Project description:The transcriptional mechanisms that allow neural stem cells (NSC) to balance self-renewal with differentiation are not well understood. We identify here a unique subset of TATA -binding protein associated factors (TAFs) as NSC identity genes in Drosophila. We found that depletion of any one of nine TAFs or the TBP-related factor 2 (TRF2), resulted in fewer NSCs exhibiting delayed cell cycle progression without impacting NSC survival. In contrast, depletion of TBP led to a delay in NSC cell cycle progression without loss of self-renewal. An integrated RNA-seq and DamID analysis revealed that TAFs function with both TBP and TRF2, and that TAF-TBP and TAF-TRF2 shared targets genes encode different subsets of transcription factors and RNA-binding proteins with established or emerging roles in NSC identity and brain development. Taken together, our results demonstrate that core promoter factors are selectively required for NSC identity in vivo by promoting cell cycle progression, NSC cell polarity and by preventing premature differentiation. Because pathogenic variants in TAF1, TAF2, TAF6, TAF8 and TAF13 have all been linked to human neurological disorders, this work may stimulate and inform future animal models of TAF-linked neurological disorders.
2019-04-01 | GSE120432 | GEO
Project description:The transcriptional mechanisms that allow neural stem cells (NSC) to balance self-renewal with differentiation are not well understood. We identify here a unique subset of TATA -binding protein associated factors (TAFs) as NSC identity genes in Drosophila. We found that depletion of any one of nine TAFs or the TBP-related factor 2 (TRF2), resulted in fewer NSCs exhibiting delayed cell cycle progression without impacting NSC survival. In contrast, depletion of TBP led to a delay in NSC cell cycle progression without loss of self-renewal. An integrated RNA-seq and DamID analysis revealed that TAFs function with both TBP and TRF2, and that TAF-TBP and TAF-TRF2 shared targets genes encode different subsets of transcription factors and RNA-binding proteins with established or emerging roles in NSC identity and brain development. Taken together, our results demonstrate that core promoter factors are selectively required for NSC identity in vivo by promoting cell cycle progression, NSC cell polarity and by preventing premature differentiation. Because pathogenic variants in TAF1, TAF2, TAF6, TAF8 and TAF13 have all been linked to human neurological disorders, this work may stimulate and inform future animal models of TAF-linked neurological disorders.
2019-04-01 | GSE120430 | GEO
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
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
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
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
Project description:Genome-wide transcriptional dependencies on TAF1 functional domains
| PRJNA93183 | ENA
Project description:We report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells. In addition to its role in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 localizes to chromosomal regions bound by CTCF and cohesin. Enrichment for TAF3/CTCF/cohesin bound regions distinguishes TAF3-activated from TAF3-repressed genes. Our findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions to safeguard the finely-balanced transcriptional programs that give rise to pluripotency. Genome-wide binding of TAF3, TAF1, TBP and PolII assayed by ChIP-Seq.
2011-09-02 | E-GEOD-31270 | biostudies-arrayexpress
Project description:This study investigates how the general transcription factor TFIID binds to different core promoter types in vivo. We performed high-resolution ChIP-nexus for all 14 subunits of the Drosophila TFIID complex (TBP and TAF1 to TAF13), as well as for NC2α, NC2β, and Mot1, under both DMSO (control) and Triptolide treatments to capture various transcriptional states.The goal of the study was to define TFIID's in vivo architecture and compare its function across promoters. We show that TBP binding is promoter-specific, enabling de novo classification of TATA, DPR, and housekeeping promoters. Crucially, we provide in vivo evidence for TAF-independent transcription initiation specifically at TATA promoters, which correlates with NC2 binding and offers a mechanistic explanation for their distinct transcriptional bursting properties.
2025-12-19 | GSE314459 | GEO