GEO DataSets

(Submitter supplied) The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL15263

14 Samples

Download data: TXT

(Submitter supplied) We have identified mRNAs whose abundance or translational efficiency is regulated in nutrient-rich medium by the Scd6 or Dhh1 protein in either wild-type cells or dcp2∆ cells lacking the decapping enzyme

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

28 Samples

Download data: CSV

(Submitter supplied) To assess the role of the decapping activator Scd6 in mRNA decay, we used RNA-Seq to analyze the expression profile of yeast cells harboring a deletion of the SCD6 gene. Consistent with our recent model for decapping regulation, we found that Scd6 targets a small number of specific mRNAs in yeast cells. Interestingly, degradation of Scd6-targeted transcripts also requires the functions of the decapping activators Pat1, Lsm1, and Dhh1, suggesting that Scd6 functions together with Pat1, Lsm1, and Dhh1 in promoting mRNA decapping.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

6 Samples

Download data: TXT

(Submitter supplied) To assess the roles of the Dcp2 C-terminal domain and the decapping activators Pat1, Lsm1, and Dhh1 in mRNA decapping, we used RNA-Seq to analyze the expression profiles of yeast cells harboring a truncation of the Dcp2 C-terminal domain, mutations that render Dcp2 catalytically inactive, or deletions of the PAT1, LSM1, and DHH1 genes. Consistent with our recent model for decapping regulation, we found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation and that loss of these control functions causes significant deregulation of mRNA decapping; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap and, as expected, are targeted to decapping-dependent decay.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

24 Samples

Download data: TXT

(Submitter supplied) In budding yeast, the nuclear RNA surveillance system is active on all pre-mRNA transcripts and modulated by nutrient availability. To test the role of nuclear surveillance in reprograming gene expression, we identified transcriptome-wide binding sites for RNA polymerase II (Pol II) and the exosome cofactors Mtr4 (TRAMP complex) and Nab3 (NNS complex) by UV-crosslinking immediately following glucose withdrawal (0, 4, and 8 minutes). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

24 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) In this work, we determine total mRNA decay rates in rpb1-1 and rpb1-1/caf1∆ cells, calculate half-lives in rpb1-1/caf1∆ cells relative to rpb1-1 cells and correlate them with codon optimality.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

10 Samples

Download data: TXT

(Submitter supplied) Yeast mRNA decapping-activators Pat1 and Dhh1 have been implicated in repressing translation and mRNA degardation in glucose-deprived cells, but the specific mRNAs targeted by each factor and their functions in nutrient replete cells are poorly understood. To test this, we performed ribosome profiling and RNA-Seq in WT, pat1D and pat1Ddhh1D. Further, CAGE-Seq and Rpb1-ChIP Seq were employed to determine their role in decapping mediated degradation of mRNAs

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL17342 GPL19756 GPL27812

26 Samples

Download data: CSV

(Submitter supplied) Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, and as a translational repressor, but their functions in cells are incompletely understood. We have analyzed these questions by a combination of ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL27812 GPL17342

14 Samples

Download data: CSV

(Submitter supplied) Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, and as a translational repressor, but their functions in cells are incompletely understood. We have analyzed these questions by a combination of ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19756 GPL17342

24 Samples

Download data: CSV

(Submitter supplied) The Ydr374c is the only protein that has the YTH domain in Saccharomyces cerevisiae. The YTH domain was identified by comparing all known protein sequences with the YT521-B splicing factor, and it is found only in eukaryotes. Recently, it has been reported that the YTH domain conveys RNA-binding ability to a new class of proteins. However, the roles of most YTH family members lacking common sequence motifs outside the YTH domain are unknown. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7293

2 Samples

Download data: TXT

(Submitter supplied) The Poly(A)-Tail focused RNA-seq, or PAT-seq approach, is an affordable and efficient tool for the measure of 3’UTR dynamics. We show here that PAT-seq returns (i) digital gene expression, (ii) polyadenylation site usage within and between samples, including alternative adenylation, and (iii) the polyadenylation-state the transcriptome. PAT-seq differs from previous 3’ focused RNA-seq methods in that it strictly depends on native 3’ adenylation within total RNA samples and thus removes the need for ribosome depletion and, that the full native poly(A)-tail is included in the sequencing libraries. more...

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18085

13 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL13821 GPL19756

20 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, a crosstalk where mRNA decay machinery impacts transcription and transcription machinery influences mRNA stability. Rpb4, and likely the dimer Rpb4/7 seem to be the central components of the RNA pol II governing these processes. In this work we unravel more precisely the molecular mechanisms participated by Rpb4 that mediates the posttranscriptional events regulating mRNA imprinting and stability. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Gene expression involving RNA polymerase II is regulated by the concerted interplay between mRNA synthesis and degradation, a crosstalk where mRNA decay machinery impacts transcription and transcription machinery influences mRNA stability. Rpb4, and likely the dimer Rpb4/7 seem to be the central components of the RNA pol II governing these processes. Here we investigate the effect of ∆rrp4 on the potential chromatin association of the RNA binding protein Puf3 to chromatin in S. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

16 Samples

Download data: BW

(Submitter supplied) Proteins regulate gene expression by controlling mRNA biogenesis, localization, translation and decay. Identifying the composition, diversity and function of mRNPs (mRNA protein complexes) is essential to understanding these processes. In a global survey of S. cerevisiae mRNA binding proteins we identified 120 proteins that cross-link to mRNA, including 66 new mRNA binding proteins. These include kinases, RNA modification enzymes, metabolic enzymes, and tRNA and rRNA metabolism factors. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

9 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of yeast strains (WT, rim15Δ, and igo1Δigo2Δ) treated with 100nM rapamycin at 20, 60, 120, 180min post treatment with respect to immediately before treatment as reference. Goal of the experiment was to test whether Rim15 and Igo1/2 are implicated in proper regulating of gene expression during nutrient limitation and TORC1 inhibition by rapamycin. At 180 minutes after rapamycin treatment, 478 genes were upregulated more than 2.8 fold in the wild-types cells; whereas the upregulation of 54 were diminished in rim15 mutant and upregulation of 103 genes diminished in cells lacking Igo1 and Igo2. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7293

14 Samples

Download data: TXT

(Submitter supplied) Antisense long non-coding (aslnc)RNAs represent a substantial part of eukaryotic transcriptomes that are, in yeast, controlled by the Xrn1 exonuclease. Nonsense-Mediated Decay (NMD) destabilizes the Xrn1-sensitive aslncRNAs (XUT), but what determines their sensitivity remains unclear. We report that 3’ single-stranded (3’-ss) extension mediates XUTs degradation by NMD, assisted by the Mtr4 and Dbp2 helicases. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17342 GPL13272

36 Samples

Download data: GFF, TXT

(Submitter supplied) Small RNA produced by Dicer (Dcr1) are used to map dsRNA in wild-type strain and a xrn1-delta mutant of S. cerevisiae, inactivated for the cytoplasmic 5'-3' RNA decay pathway.

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13272

4 Samples

Download data: TXT

(Submitter supplied) This study involves the role of yeast mRNA decay factors in transcription. The experiment included here are the ChIP-exo results of three decay factors: Xrn1, Dcp2 & Lsm1.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

4 Samples

Download data: BEDGRAPH, TAB, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome binding/occupancy profiling by array

Platform:

GPL16503

22 Samples

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