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MRNA profiling of glucose-repressed 14-3-3 and hdac yeast mutants

ABSTRACT: Previous results suggest that Bmh might inhibit the activity of the transcription factor Adr1 after binding to Adr1-dependent promoters. In a strain lacking the two major histone deacetylases, Hda1 and Rpd3 (hdac∆), Adr1 is bound to its target promoters recruiting what appears to be an inactive RNA ploymerase II preinitiation complex (PIC). To determine whether Bmh activity inhibits this inactive PIC and the generality of this effect on glucose-repressed gene expression, the mRNA profiles of wild type, bmh mutant, hdac mutant, and bmh hdac mutant cells grown in high glucose medium were compared.

ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe

PROVIDER: GSE40116 | GEO | 2013/01/15

SECONDARY ACCESSION(S): PRJNA172859

REPOSITORIES: GEO

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mRNA profiling of glucose-repressed 14-3-3 and hdac yeast mutants

Project description:Previous results suggest that Bmh might inhibit the activity of the transcription factor Adr1 after binding to Adr1-dependent promoters. In a strain lacking the two major histone deacetylases, Hda1 and Rpd3 (hdac?), Adr1 is bound to its target promoters recruiting what appears to be an inactive RNA ploymerase II preinitiation complex (PIC). To determine whether Bmh activity inhibits this inactive PIC and the generality of this effect on glucose-repressed gene expression, the mRNA profiles of wild type, bmh mutant, hdac mutant, and bmh hdac mutant cells grown in high glucose medium were compared. Total RNAs were purified from triplicate cultures of W303-1A (wild type), YLL1087 (bmh1-ts bmh2?), CTY-TY44 (hda1? rpd3?) and KBY3 (bmh1-ts bmh2? hda1? rpd3?) cells exponentially growing in YP broth containing 5% glucose and then profiled using Affymetrix Yeast 2.0 arrays.

2013-01-15 | E-GEOD-40116 | biostudies-arrayexpress

Structure of transcription preinitiation complex engaged with the +1 nucleosome

Project description:The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles in chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is positioned downstream of the core promoter. Here we present the cryo-EM structure of the yeast PIC bound to promoter DNA and the +1 nucleosome at a resolution of 3.4–3.9 Å. The general transcription factor TFIIH forms four contacts with the nucleosome, indicating how PIC assembly can be assisted by the +1 nucleosome. The TFIIH subunit Ssl2 (XPB in human TFIIH) forms a wedge between promoter DNA and the nucleosome, stabilizing two turns of DNA that are detached from the nucleosome. During subsequent scanning for the transcription start site (TSS), three additional turns of DNA can be detached before the partially unraveled nucleosome may counteract further scanning, explaining why TSSs are located at a distance of ~60 bp from the dyad of the +1 nucleosome in yeast.

2023-03-11 | PXD029840 | Pride

Requirements for preinitiation complex formation in vivo

Project description:Transcription by RNA polymerase (Pol) II requires assembly of a preinitiation complex (PIC) composed of general transcription factors (GTFs) bound at the core promoter. In vitro, the TATA-binding protein (TBP), TFIIB, TFIIF, and Pol II are essential for PIC formation and transcriptional initiation, whereas TFIIA, TFIIE, and TFIIH are not required under certain conditions. In addition, the PIC is stable in the absence of nucleotide triphosphates, and sequential addition of GTFs results in a series of partial PICs. Here, we analyze the roles of all GTFs in yeast cells by measuring PIC formation and Pol II transcription upon depletion of individual GTFs. All GTFs are essential for TBP binding and Pol II transcription in vivo, suggesting that partial PICs composed of GTF subsets do not exist at appreciable levels. In contrast, TBP-associated factors (TAFs) contribute to Pol II transcriptional activity at most (and perhaps all) genes, but TAF-independent transcription occurs at a substantial level, particularly at promoters lacking canonical TATA elements. Lastly, unlike the case in vitro, PICs are not observed in cells deprived of uracil, and presumably UTP, suggesting a mechanism that removes transcriptionally inactive PICs from promoters.

2019-02-27 | GSE122734 | GEO

Features of cryptic promoters and their varied reliance on bromodomain-containing factors

Project description:The Set2-Rpd3S pathway is important for the control of transcription memory. Mutation of components of this pathway results in cryptic transcription initiation within the coding region of approximately 30% of yeast genes. Specifically, deletion of the Set2 histone methyltransferase or Rco1, a component of the Rpd3S histone deacetylase complex leads to hyperacetylation of certain open reading frames (ORFs). We used this mutant as a system to study the role of histone modifications and co-activator recruitment in preinitiation complex (PIC) formation. Specifically, we looked at the dependence of promoters on the bromodomain-containing RSC complex and the Bdf1 protein. We found that the dependence of cryptic promoters for these proteins varied. Overall, our data indicates that cryptic promoters are independently regulated, and their activation is dependent on factors that govern gene activation at canonical promoters. Two-sample experiment: chromatin immunoprecipitation (ChIP) sample vs. input. Biological replicates: 3 independent ChIP samples for each yeast strain.

2010-09-23 | E-GEOD-17521 | biostudies-arrayexpress

Interconversion between active and inactive TATA-binding protein transcription complexes in the mouse genome.

Project description:The conserved core domain of the TATA binding protein (TBP) interacts with multiple partners forming the complexes required for transcription by RNA Polymerases I, II and III. We use genetically modified mouse embryonic fibroblasts to show that many TBP core domain mutants complement loss of endogenous TBP, but this often results in a slow growth phenotype. Two TBP mutations, R188E and K243E, disrupt the TBP-BTAF1 interaction and B-TFIID complex formation. Transcriptome and ChIP-seq analyses show that loss of B-TFIID does not affect global genomic distribution of TBP, but positively or negatively affects TBP and/or RNA Polymerase II (Pol II) recruitment to a selected set of promoters. We identify a set of promoters where wild-type TBP assembles a partial inactive preinitiation complex lacking Pol II and TAF1. Our results suggest that an exchange of the B-TFIID complex in wild-type cells for TFIID in R188E and K243E mutant cells at these primed promoters recruits Pol II to activate their expression. We also observe that both Wt and mutant TBP can occupy promoters without concurrent Pol II recruitment and active transcription. Our data reveal a novel regulatory mechanism involving the formation of a partial preinitiation complex that primes the promoter for productive preinitiation complex formation in mammalian cells.

2012-03-01 | GSE27908 | GEO

Features of cryptic promoters and their varied reliance on bromodomain-containing factors

2010-09-23 | GSE17521 | GEO

Histone Exchange is Associated with Activator Function at Transcribed Promoters and with Repression at Histone Loci

Project description:Transcription in eukaryotes correlates with major chromatin changes, including the replacement of old nucleosomal histones by new histones at the promoters of genes. The role of these histone exchange events in transcription remains unclear. In particular, the causal relationship between histone exchange and activator binding, preinitiation complex (PIC) assembly, and/or subsequent transcription remains unclear. Here, we provide evidence that histone exchange at gene promoters is not simply a consequence of PIC assembly or transcription but instead is mediated by activators. We further show that not all activators up-regulate gene expression by inducing histone turnover. Thus, histone exchange does not simply correlate with transcriptional activity, but instead reflects the mode of action of the activator. Last, we show that histone turnover is not only associated with activator function but also plays a role in transcriptional repression at the histone loci.

2020-01-09 | GSE143305 | GEO

Structural basis of SNAPc-dependent snRNA transcription intiation by RNA polymerase II

Project description:RNA Polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at non-coding genes such as small nuclear RNA (snRNA) genes is not understood at the structural level. Here we study Pol II initiation at snRNA gene promoters and show that the snRNA-activating protein complex (SNAPc) enables DNA opening and transcription initiation independent of TFIIE and TFIIH in vitro. We then resolve cryo-EM structures of the SNAPc-containing Pol II preinitiation complex (PIC) assembled on U1 and U5 snRNA promoters. The core of SNAPc binds two turns of DNA and recognizes the snRNA promoter-specific proximal sequence element (PSE) located upstream of the TATA box-binding protein TBP. Two extensions of SNAPc called wing-1 and wing-2 bind TFIIA and TFIIB, respectively, explaining how SNAPc directs Pol II to snRNA promoters. Comparison of structures of closed and open promoter complexes elucidates TFIIH-independent DNA opening. These results provide the structural basis of Pol II initiation at non-coding RNA gene promoters.

2023-03-11 | PXD033638 | Pride

OFD1 interacts with the Preinitiation complex of translation and regulates translation of specific targets in the kidney

Project description:OFD1 is a centrosomal/basal body protein codified by a transcript that when mutated results in OFD type I (OFDI) syndrome, a pleiotropic disorders associated with ciliary dysfunction. We demonstrate that components of the Preinitiation complex of translation (PIC) colocalize to the centrosome and interact with OFD1. We showed that OFD1 functionally controls the protein synthesis machinery, modulating the translation of specific mRNAs in the kidney. Our results indicate a new role for a centrosomal/basal body protein. The dataset contains the microarray data on total and polysomal RNA from control and Ofd1-IND mutant kidneys at P8.

2017-03-15 | E-MTAB-2827 | biostudies-arrayexpress

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation [ChIP-Seq]

Project description:Histone modifications regulate chromatin-dependent processes, yet the mechanisms by which they contribute to specific outcomes remain unclear. H3K4me3 is a prominent histone mark that is associated with active genes and promotes transcription through interactions with effector proteins that include initiation factor TFIID. We demonstrate that H3K4me3-TAF3 interactions direct global TFIID recruitment to active genes, some of which are p53 targets. Further analyses show that (i) H3K4me3 enhances p53-dependent transcription by stimulating preinitiation complex (PIC) formation; (ii) H3K4me3, through TAF3 interactions, can act either independently or cooperatively with the TATA box to direct PIC formation and transcription; and (iii) H3K4me3-TAF3/TFIID interactions regulate gene-selective functions of p53 in response to genotoxic stress. Our findings indicate a mechanism by which H3K4me3 directs PIC assembly for the rapid induction of specific p53 target genes Examination of TAF3, RNAPII, and H3K4me3 distribution in HCT116 cells.

2013-03-02 | E-GEOD-43539 | biostudies-arrayexpress

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