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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: David Bentley

PROVIDER: E-GEOD-49928 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast (ChIP-Chip)

Project description:whole genome analysis of RNA pol II and histone H3 in WT and Spt6-depleted cells using a tetracycline regulated ts degron mutant, spt6-td. ChiP-ChIP using ligation-mediated PCR amplified material hybridized to Nimblegen 385K arrays 50mers median probe spacing 32 bp cat. No. C4214-00-01

2013-08-16 | E-GEOD-49927 | biostudies-arrayexpress

Budding yeast mRNA export and processing factor localization

Project description:The yeast mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A linking export to 3'-end formation. We found a surprising consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit, Clp1, for binding to Pcf11, and excess Yra1 inhibits 3' processing in vitro. Release of Yra1 at the 3' ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit, but instead Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A/B 3' processing factor. Key Words: Yra1, cleavage-polyadenylation, mRNA export, Pcf11, Clp1, Sub2, alternative polyadenylation Whole genome analysis of Yra1, Sub2, Pcf11, and Clp1 in WT and Yra1-depleted cells using a GAL1-YRA1 mutant. ChiP-ChIP using ligation-mediated PCR amplified material hybridized to Nimblegen 385K arrays 50mers median probe spacing 32 bp cat. No. C4214-00-01.

2011-09-24 | E-GEOD-30705 | biostudies-arrayexpress

Budding yeast RNA polymerase II CTD phosphorylation and transcription termination factor localization

Project description:Whole genome analysis of total RNA pol II, Ser2-, Ser5- and Ser7-phosphorylated RNA pol II, in WT and mutants of the C-terminal domain (CTD) kinases Ctk1 and Kin28, and localization of the termination factors Pcf11, Nrd1 and Rat1. ChIP-chip using ligation-mediated PCR-amplified material hybridized to NimbleGen 385K arrays (50mers, median probe spacing 32 bp, cat. No. C4214-00-01).

2010-09-15 | E-GEOD-23960 | biostudies-arrayexpress

Genome-wide effects of Spt6 on RNA pol II and Histone H3 occupancy in budding yeast (ChIP-Seq)

Project description:whole genome analysis of RNA pol II and histone H3 in WT and Spt6-depleted cells using a tetracycline regulated ts degron mutant, spt6-td. ChIP-seq of histone H3and pol II in budding yeast (W303 background)

2013-08-16 | E-GEOD-49926 | biostudies-arrayexpress

Budding yeast mRNA export and processing factors

Project description:This SuperSeries is composed of the following subset Series: GSE30703: Budding yeast mRNA poly( A) site mapping GSE30705: Budding yeast mRNA export and processing factor localization Refer to individual Series

2011-09-24 | E-GEOD-30706 | biostudies-arrayexpress

Chd1 co-occupancy with early transcription elongation factors

Project description:We report the genome-wide Chd1 co-occupancy with early transcription elongation factors ChIP-seq for Chd1 and elongating RNA polymerase II

2014-10-23 | E-GEOD-56061 | biostudies-arrayexpress

Expression analysis of wild-type and transcription factor mutants in response to rapamycin

Project description:Transcript level changes in transcription factor mutants after rapamycin treatment, compared to the wild-type strain. This data set accompanies the study "Widespread Misinterpretable ChIP-seq Bias in Yeast" (GSE51251) Four separate wild-type cultures of yeast were grown, and each culture was split into two. Then, one was treated with DMSO and the other one was treated with rapamycin. For transcription factor mutants, two separate cultures were grown, and rapamycin was treated in the same way as treated to the wild type. Total RNA was recovered from each culture, then labeled oligo was prepared following NimbleGene standard protocol. Each chip measures the expression levels of 5,777 genes from yeast.

2013-11-15 | E-GEOD-51376 | biostudies-arrayexpress

The transcriptome of erythromycin-resistant Campylobacter jejuni strain selected from NCTC 11168

Project description:Campylobacter, a major foodborne pathogen, is increasingly resistant to macrolide antibibotics. Previous findings suggested that development of macrolide resistance in Campylobacter requires a multi-step process, but the molecular mechanisms involved in the process are not known. In our study, erythromycin-resistant C. jejuni mutant (R) was selected in vitro by stepwise exposure of C. jejuni NCTC11168(S) to increasing concentrations of erythromycin.The resistant were subjected to microarray and the the global transcriptional profile was analyzed. In this series, DNA microarray was used to compare the gene expression profiles of the macrolide-resistant strain with its parent wild-type strain NCTC11168. A large number of gene showed significant changes in R. The up-regulated genes in the resistant strains are involved in miscellaneous periplasmic proteins, efflux protein and putative aminotransferase, while the majority of the down-regulated genes are involved in electron transport, lipoprotein, heat shock protein and unknown function proteins. The over-expression of efflux pump and periplasmic protein was involved in the development of resistance to macrolide in C. jejuni. An eight chip study using total RNA recovered from four separate resistant-type cultures of Erythrocin-resistant Campylobacter jejuni NCTC111168 (R) and four separate cultures of Campylobacter jejuni NCTC111168 (S). Each chip measures the expression level of 1634 genes from Campylobacter jejuni NCTC11168.

2013-08-13 | E-GEOD-49257 | biostudies-arrayexpress

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 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

2016-05-15 | E-GEOD-65902 | biostudies-arrayexpress

Transcription profiling of yeast with a C-terminal deletion of the RNA polymerase II elongation factor Spt6 or overexpression of Spt6

Project description:Influence of a C-terminal deletion of the RNA polymerase II elongation factor Spt6 on the transcription of the yeast genome. In parallel the influence of a Spt6 overexpression on gene expression is analyzed.

2009-04-08 | E-MEXP-2123 | biostudies-arrayexpress

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