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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide association of Sus1 with RNAPII and tRNA genes depends on the distinctive SAGA subunits Spt8 and Spt7

ABSTRACT: We have analyzed the global effect of the conserved transcription-mRNA export factor Sus1 on transcription and its association with chromatin. We used genomic run-on experiments to show that Sus has a broad impact on the stability of most RNA polymerase II-transcribed genes. Genome association of Sus1 by the chromatin immunoprecipitation technique showed that Sus1 was widely distributed throughout coding regions, tending to accumulate towards the 3â ends of highly transcribed transcription factor IID (TFIID) and Spt-Ada-Gcn5 acetyltransferase (SAGA) dependent genes. This accumulation depends on growth conditions, the transcriptional rate and whether the genes are TFIID- or SAGA-regulated. Validation of Sus1 occupancy data also revealed that Sus1 appears at tRNAs. Concomitantly, deletion of SUS1 leads to tRNA overexpression. In addition, we discovered that distinctive SAGA subunits Spt8 and Spt7 play a key role in Sus1 enrichment at the 3â ends of SAGA-regulated genes upon temperature shift and at tRNAs. Thus, our study identifies the molecular mechanisms by which a SAGA factor is recruited genome-wide, and provides evidence of a more general role for this conserved coactivator in eukaryotic transcription. Genome wide analysis of Sus1 in wild type and Spt7 and Spt8 deletion mutants using ChIP-exo and genomic run-on experiments

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Susana RodrÃguez-Navarro

PROVIDER: E-GEOD-65902 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide association of Sus1 with RNAPII and tRNA genes depends on the distinctive SAGA subunits Spt8 and Spt7

Project description:We have analyzed the global effect of the conserved transcription-mRNA export factor Sus1 on transcription and its association with chromatin. We used genomic run-on experiments to show that Sus has a broad impact on the stability of most RNA polymerase II-transcribed genes. Genome association of Sus1 by the chromatin immunoprecipitation technique showed that Sus1 was widely distributed throughout coding regions, tending to accumulate towards the 3’ ends of highly transcribed transcription factor IID (TFIID) and Spt-Ada-Gcn5 acetyltransferase (SAGA) dependent genes. This accumulation depends on growth conditions, the transcriptional rate and whether the genes are TFIID- or SAGA-regulated. Validation of Sus1 occupancy data also revealed that Sus1 appears at tRNAs. Concomitantly, deletion of SUS1 leads to tRNA overexpression. In addition, we discovered that distinctive SAGA subunits Spt8 and Spt7 play a key role in Sus1 enrichment at the 3’ ends of SAGA-regulated genes upon temperature shift and at tRNAs. Thus, our study identifies the molecular mechanisms by which a SAGA factor is recruited genome-wide, and provides evidence of a more general role for this conserved coactivator in eukaryotic transcription.

2018-12-31 | GSE65883 | GEO

The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally

Project description:Eukaryotic transcription is regulated through two complexes, the general transcription factor IID (TFIID) and the coactivator Spt-Ada-Gcn5 acetyltransferase (SAGA). Recent findings confirm that both TFIID and SAGA contribute to the synthesis of nearly all transcripts and are recruited genome-wide in yeast. However, how this broad recruitment confers selectivity under specific conditions remains an open question. Here we find that the SAGA DUBm subunit Sus1 associates upstream regulatory regions of many yeast genes and that heat shock drastically changes Sus1 binding pattern. While Sus1 binding to TFIID-dominated genes is not affected by temperature, its recruitment to SAGA-dominated genes and RP genes is significantly disturbed under heat shock, being Sus1 relocated to environmental stress responsive genes in these conditions. Moreover, in contrast to recent results showing that SAGA deubiquitinating enzyme Ubp8 is dispensable for RNA synthesis, genomic run-on experiments demonstrate that Sus1 contributes to synthesis and stability for a wide range of transcripts. Our study provides support for a model in which SAGA acts as a global transcriptional regulator in yeast but acquires differential binding affinities under thermal stress conditions.

2016-05-15 | GSE65902 | GEO

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

The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription [Yeast cells]

Project description:The SAGA co-activator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Surprisingly, recent studies revealed little overlap between genome-wide SAGA-binding profiles and changes in gene expression upon depletion of subunits of the complex. As indicators of SAGA recruitment on chromatin, we monitored in yeast and human cells the genome-wide distribution of histone H3K9 acetylation and H2B ubiquitination, which are respectively deposited or removed by SAGA. Changes in these modifications after inactivation of the corresponding enzyme revealed that SAGA acetylates the promoters and deubiquitinates the transcribed region of all expressed genes. In agreement with this broad distribution, we show that SAGA plays a critical role for RNA polymerase II recruitment at all expressed genes. In addition, through quantification of newly synthesized RNA, we demonstrated that SAGA inactivation induced a strong decrease of mRNA synthesis at all tested genes. Analysis of the SAGA deubiquitination activity further revealed that SAGA acts on the whole transcribed genome in a very fast manner indicating a highly dynamic association of the complex with chromatin. Thus, our study uncovers a new function for SAGA as a bone fide co-factor for all RNA Polymerase II transcription. Comparison of H3K9ac, H2Bub and RNA Pol II distributions in WT yeast cells and upon the loss of SAGA activities.

2014-08-29 | E-GEOD-52997 | biostudies-arrayexpress

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

Gene deletion expression profiles of SAGA, TREX2 and Sem1

Project description:Evidence indicates that transcription and mRNA export are linked processes. The molecular mechanisms of this coordination are not clear however. Sus1 (hENY2) participates in this coordination as part of two protein complexes: SAGA, a transcriptional co-activator and TREX-2 that functions in mRNA biogenesis and export. Here we investigate the coordinated action of SAGA and TREX-2 that is required for gene expression. We demonstrate that the TREX-2/proteasomal subunit Sem1, influences Sus1 role in mRNA export and TREX-2 stability. Wide analyses of gene expression reveal that Sem1 and Sus1 have also overlapping functions in transcription. In the absence of Sem1, expression of some SAGA-dependent genes is compromised with a concomitant decrease of RNAP II recruitment to promoters. Notably, ChIP experiments revealed a distinct dependency for SAGA subunits recruitment on Sem1. While absence of Sem1 lowers Ada2 and Taf9 recruitment to GAL1 promoter upon activation, association of the deubiquitylation module remains intact. However, H2B deubiquitylation activity is dramatically decreased. These results unveil a new role for Sem1 in influencing activation of SAGA-dependent H2B deubiquitylation likely mediated by stabilization of TREX-2 complex and SAGA modular assembly. Our work gives insights in how modular architecture of SAGA is determinant for its function in gene expression.

2013-06-04 | GSE39861 | GEO

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

TAF10 interacts with GATA1 transcription factor and controls mouse erythropoiesis

Project description:The stoichiometries of TFIID and SAGA (TAF10-containing complexes) have been quantified in mouse and human erythroid cells. TAF10 immunoprecipitations (IPs) have been carried out in erythroid cells at different stages of differentiation and development followed by quantitative mass spectrometry (MS). Interactions of TFIID and SAGA with several transcription factors and specifically with GATA-1 have been identified. GATA-1 immunoprecipitation (IP) in MEL cells also identified the reverse interactions with subunits of the TFIID and SAGA after MS analysis.

2015-04-21 | PXD000729 | Pride

Changes in genome-wide occupancy of core transcriptional regulators during stress

Project description:Organisms respond to heat stress by reprogramming gene expression. Here we show that genome-wide reprogramming involves enhanced assembly of the TFIID and SAGA regulatory pathways at heat induced genes, and disassembly of the TFIID pathway at heat-repressed genes. While TFIID and SAGA are recruited to heat-induced genes, only SAGA appears to be associated with achieving maximal induction. Mot1, an ATP-dependent inhibitor of the TATA binding protein TBP, assembles at heat-induced SAGA-regulated genes, but functions to attenuate rather than promote activation. Changes in promoter occupancy of bromodomain factor Bdf1 are tightly linked to changes in TFIID occupancy, which further supports the notion that the two work together. Bdf1 is inhibitory to a number of SAGA-regulated genes and dissociates when these genes are activated, suggesting that Bdf1 normally blocks transcription complex assembly at these genes. These linkages in reprogramming of factor occupancy at promoters provide direct evidence for two functionally distinct transcription assembly pathways, and reveal unexpected cross-talk between the pathways. Keywords = Chromatin Immunoprecipitation Keywords = Microarray Keywords = TBP

2010-06-05 | E-GEOD-1373 | biostudies-arrayexpress

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [RNA-Seq]

Project description:Deletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that are generally more sensitive to rapid TFIID depletion. However, transcription of these “coactivator-redundant” genes is strongly affected by rapid depletion of both factors, showing the overlapping functions of TFIID and SAGA at this gene set. We suggest that this overlapping function is linked to TBP-DNA recruitment. The remaining 87% of expressed genes that we term “TFIID-dependent” are highly sensitive to rapid TFIID depletion and insensitive to rapid SAGA depletion. Genome-wide mapping of SAGA and TFIID found binding of both factors at many genes independent of gene class. DNA analysis suggests that the distinction between the gene classes is due to multiple components rather than any single regulatory factor or promoter sequence motif.

2020-01-09 | GSE142182 | GEO

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