Browse
Submit Data
Databases
API
Help

Dataset Information

495 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Yeast not5 mutant protein translation analysis

ABSTRACT: Analysis of translation rate and turnover differences between wild type and not5 mutant yeast using pulse-chase mass spectrometry.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Christopher Hughes

LAB HEAD: Gregg Morin

PROVIDER: PXD003871 | Pride | 2016-06-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MaxQuant_Output_wReQ.zip	Other
	MaxQuant_Output_woReQ.zip	Other
	ch_10Aug2014_Ish-Snyth_Cont_A_1.raw	Raw
	ch_10Aug2014_Ish-Snyth_Cont_A_10.raw	Raw
	ch_10Aug2014_Ish-Snyth_Cont_A_11.raw	Raw

Items per page:

1 - 5 of 50

Publications

Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex.

Gupta Ishaan I Villanyi Zoltan Z Kassem Sari S Hughes Christopher C Panasenko Olesya O OO Steinmetz Lars M LM Collart Martine A MA

Cell reports 20160512 8

The current understanding of gene expression considers transcription and translation to be independent processes. Challenging this notion, we found that translation efficiency is determined during transcription elongation through the imprinting of mRNAs with Not1, the central scaffold of the Ccr4-Not complex. We determined that another subunit of the complex, Not5, defines Not1 binding to specific mRNAs, particularly those produced from ribosomal protein genes. This imprinting mechanism specific ...[more]

PMID: 27184853

Similar Datasets

Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data

Project description:Pulse chase measurements using thiouracil (DTU) labeling via UPRT and chasing with uracil Data from tachyzoites is labeled "DTU Pulse Chase". Two independent pulse chase experiments were performed in tachyzoites, pulse chase 1 and 2. Duplicate arrays at each timepoint were performed for pulse chase 2 (2 a and b). Data from bradyzoites are labeled "DTU Bradyzoite Pulse Chase". Two independent pulse chase experiments were performed in bradyzoites and a single set of arrays were performed for each experiment. Just one chase timepoint was used in the bradyzoite experiments, the 2 hour chase. An RNA stablity experiment design type examines stability and/or decay of RNA transcripts. Keywords: RNA_stability_design

2005-07-16 | GSE2947 | GEO

Transcription profiling of Toxoplasma gondii thiouracil pulse-chase, tachyzoites and bradyzoites mRNA stability data

2005-07-07 | E-SMDB-2949 | biostudies-arrayexpress

Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data

2005-07-16 | E-GEOD-2947 | biostudies-arrayexpress

Genomewide measurements of whole embryo mRNA decay in Drosophila

Project description:whole embryo (all tissues) measurement of mRNA decay by 4-thiouridine pulse-chase These TU-Decay microarrays analyze mRNA levels at three timepoints: a one hour pulse, one hour chase, and three hour chase. Measurements with or without transcription inhibition by actinomycin D (ActD) were compared.

2015-03-31 | E-GEOD-67435 | biostudies-arrayexpress

Pulse-chase SILAC of Mycobacterium tuberculosis infected THP-1 macrophages

Project description:Pulse chase SILAC was used to identify protein turnover within human macrophages infected with mycobacterium tuberculosis CDC1551, a ppe38-71 mutant strain, a complemented strain and an uninfected control.

2021-06-15 | PXD021166 | Pride

3T3-L1 adipocyte protein turnover

Project description:Insulin is a potent regulator of protein metabolism. Here we describe a time-resolved map of insulin-regulated protein turnover in 3T3-L1 adipocytes using metabolic pulse-chase labelling and high-resolution mass spectrometry.

2016-10-07 | PXD003696 | Pride

Genomewide measurements of whole embryo mRNA decay in Drosophila

Project description:whole embryo (all tissues) measurement of mRNA decay by 4-thiouridine pulse-chase

2015-03-31 | GSE67435 | GEO

Genome-scale CRISPR-Cas9 screen of OVCAR3 and CCL218 cancer cells with or without hydroxychloroquine

Project description:A Brunello CRISPR-Cas9 library screen was performed with OVCAR3 and CCL218 cells in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After each pulse-chase, a pool of cells were collected for sgRNA quantitation. Three pulse chases were performed. Cell pellets were processed for genomic DNA and sgRNA sequences amplified by PCR for NGS-based quantitation. Once quantified by NGS analysis, MAGeCK MLE analysis was performed to determine which sgRNAs were most associated with resistance or sensitization to hydroxychloroquine.

2024-03-18 | GSE245215 | GEO

Protein turnover dynamics of IAV-infected HeLa cells

Project description:The abundance of a protein is defined by its continuous synthesis and degradation, a process known as protein turnover. Here, we systematically profiled the turnover of proteins in influenza A virus (IAV) infected cells using a pulse-chase SILAC-based approach combined with downstream statistical modeling. We identified 1414 virus-affected proteins with turnover changes (tVAPs) out of 7739 detected proteins. In particular, the affected proteins were involved in RNA transcription, splicing and nuclear transport, protein translation and stability, and energy metabolism. Many tVAPs are known IAV-interacting proteins that regulate virus propagation, such as KPNA6, PPP6C and POLR2A. Notably, our analysis identified novel IAV host and restriction factors, such as the splicing factor GPKOW, that exhibit significant turnover rate changes, while their total abundance is not affected. Overall, we show that protein turnover is a critical factor both for virus replication and antiviral defense.

2025-04-09 | PXD047063 | Pride

Expression profiles of the NuB4/HAT-B complex and histone knockouts

Project description:Dynamic modification of histone proteins plays a key role in regulating gene expression. However, histones themselves can also be dynamic, which potentially affects the stability of histone modifications. To determine the molecular mechanisms of histone turnover we developed a parallel screening method for epigenetic regulators by analyzing chromatin states on DNA barcodes. Histone turnover was quantified by employing a genetic pulse-chase technique called RITE, which was combined with chromatin immunoprecipitation and high-throughput sequencing. In this screen, the NuB4/HAT-B complex, containing the conserved type B histone acetyltransferase Hat1, was found to promote histone turnover. Unexpectedly, the three members of this complex could be functionally separated from each other as well as from the known interacting factor and histone chaperone Asf1. Thus, systematic and direct interrogation of chromatin structure on DNA barcodes can lead to the discovery of genes and pathways involved in chromatin modification and dynamics. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used for each separate hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Up to five deletion strains were grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.

2012-05-14 | E-GEOD-30168 | biostudies-arrayexpress