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Ribosome profiling in RPEI cells upon CDK1-inhibition

ABSTRACT: Ribosome profiling in RPEI cells upon CDK1-inhibition

PROVIDER: PRJNA528026 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8752380.fastq.gz	Fastqsanger.gz
	SRR8752381.fastq.gz	Fastqsanger.gz
	SRR8752382.fastq.gz	Fastqsanger.gz
	SRR8752383.fastq.gz	Fastqsanger.gz
	SRR8752384.fastq.gz	Fastqsanger.gz

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Ribosome profiling in RPEI cells upon CDK1-inhibition

Project description:Protein synthesis is the second most energy-intensive process in the cell. Therefore, cells tightly control mRNA translation rates in response to external stimuli (growth factors, differentiation signals) and the internal resources available (nutrients, energy). We set out to unravel new molecular mechanisms of global translation control required for cellular homeostasis. Using a siRNA screening approach to knock-down all human kinases and phosphatases, we analyzed the impact of protein phosphorylation on translation regulation in unstressed, proliferating cells. A visual screen was conducted to assess stress granule formation (as a consequence of translational shutdown) in the absence of 711 kinases and 256 phosphatases. Several candidates identified in the screen are linked, either directly or indirectly, to cell cycle regulation. We further identified a cyclin-dependent kinase (CDK), whose genetic downregulation or chemical inhibition results in global translation suppression. In order to assess CDK downstream signaling, we performed phosphoproteomics analysis and found the phosphorylation status of many ribosomal proteins to be altered upon CDK inhibition. Indeed, we could show that S6-kinase 1 partially contributes to CDK-dependent translational control. Ribosome profiling further revealed that the translation of 5’TOP mRNAs, including many mRNAs encoding for ribosomal proteins, is especially sensitive to CDK inhibition. While the translation regulatory function of this kinase is independent of the cell cycle phase, its activity is ideally suited to couple the overall proliferation rate of cells to the global rate of protein synthesis. Our results identify a pathway that enables cells to directly adapt protein homeostasis to proliferation and growth signals.

2020-02-06 | GSE128538 | GEO

Ribosome profiling upon inhibition of eIF4A

Project description:Ribosome profiling of MDA-MB-231 cells treated with Silvestrol to monitor transcriptome wide, eIF4A-dependent changes in translation efficiency Translation efficiency (TE) of mRNAs dervied from ribosome footprints was monitored in the presence or absence of 25 nM Silvestrol, an inhibitor of eukaryotic translation initiation factor 4A (eIF4A). Transcripts with reduced TE in the presence of Silvestrol were compare to transcripts with reduced TE in the presence of INK128, a catalytic mTOR inhbitor.

2014-09-13 | E-GEOD-61375 | biostudies-arrayexpress

Ribosome profiling upon inhibition of eIF4A

Project description:Ribosome profiling of MDA-MB-231 cells treated with Silvestrol to monitor transcriptome wide, eIF4A-dependent changes in translation efficiency

2014-09-13 | GSE61375 | GEO

Tight CDK1 inhibition elicits domain-specific pre-RC setting in S-phase, suppressing CFS instability

Project description:Genome integrity requires replication to be completed before chromosome segregation. This coordination essentially relies on replication-dependent activation of a dedicated checkpoint that inhibits CDK1, delaying mitotic onset. Under-replication of Common Fragile Sites (CFSs), however, escapes surveillance, which generates mitotic chromosome breaks. Using human cells, we asked whether this leakage results from insufficient CDK1 inhibition under modest stresses used to destabilize CFSs. We found that tight CDK1 inhibition does suppress CFS instability in so-stressed cells. Molecular combing and Repli-Seq analyses consistently showed a burst of replication initiations in mid S-phase across large origin-poor domains shaped by transcription, including CFSs. CFS rescue and extra-initiations strikingly require availability of essential pre-Replication Complex (pre-RC) proteins during the S-phase, showing that CDK1 inhibition promotes targeted and mistimed pre-RC reloading. In addition to delay mitotic onset, tight checkpoint activation therefore advances replication completion of origin-poor domains at risk of under-replication, two complementary roles preserving genome stability.

2022-12-31 | GSE185282 | GEO

Ribosome profiling upon overexpression of the RNA-binding protein Unkempt

Project description:Ribosome profiling to assess changes in ribosome occpancy upon overexpression of the RNA-binding protein Unkempt (most likely acts as a translational regulator) in human HeLa cell lines.

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Profiling of bulk and ribosome associated mRNA of Arabidopsis roots upon lateral root induction upon TOR activity inhibition with AZD8055 [dataset2]

Project description:Profiling of bulk and ribosome associated mRNA of Arabidopsis roots upon lateral root induction upon TOR activity inhibition with AZD8055 [dataset2]

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Ribosome profiling upon overexpression of the RNA-binding protein Unkempt

Project description:Ribosome profiling upon overexpression of the RNA-binding protein Unkempt

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Cdk1 controls global epigenetic landscape in embryonic stem cells

Project description:In this study, we found that in ES cells the majority of Cdk1 substrates are localized on chromatin. Cdk1 phosphorylates a large number of proteins involved in epigenetic regulation, including writers and erasers of all major histone marks. High levels of Cdk1 in ES cells phosphorylate and partially inactivate Dot1l, the histone H3 lysine 79 methyltransferase responsible for placing activating H3K79 marks on gene bodies. Decrease of Cdk1 activity during ES cell differentiation de-represses Dot1l, thereby allowing coordinated expression of differentiation genes. These analyses indicate that Cdk1 functions to maintain the epigenetic identity of ES cells.

2020-04-04 | GSE134645 | GEO

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2024-09-30 | GSE241588 | GEO

The role of Cdk1-cyclin B in G1/S transition revealed by chemical genetic inhibition of Cdc7

Project description:Entry of mammalian cells into DNA synthesis (S-phase) represents a key event in cell division. According to the current cell cycle models, the Cdc7 kinase represents the essential and rate-limiting trigger of DNA replication, acting together with the cyclin-dependent kinase Cdk2. Using chemical genetic systems which allow an acute shutdown of Cdc7 in in vitro cultured cells as well as in vivo in a living mouse, that Cdc7 is dispensable for cell division of many different cell types. Proteomic and phosphoproteomic analysis were performed to elucidate the compensating mechanism. We demonstrate that Cdk1-cyclin B, a kinase currently thought to act exclusively during mitosis, is also active during G1/S transition both in cycling cells and in cells exiting quiescence. We show that Cdc7 and Cdk1-cyclin B play redundant roles during G1/S transition, and at least one of these kinases is needed to allow S-phase entry. These observations revise our fundamental understanding of cell cycle progression by demonstrating that Cdk1-cyclin B physiologically regulates two distinct transitions during cell division cycle, while Cdc7 plays a redundant function in DNA replication. In TMT1, to analyze the expression of Cdc7 and its partners upon auxin-mediated induction of Cdc7 degradation, we performed a TMT analysis of ES cells treated with IAA for 24 hours. In TMT2, to analyze the phosphorylation of Cdc7 targets as a function of time upon degradation of the kinase we performed the time-resolved TMT analysis of ES cells subjected to Cdc7 degradation for three different amounts of time. In TMT3, to determine the ability of Cdk1 to phosphorylate Mcm2, we analyzed the phosphoproteome of mES cells and focused on the phosphorylation of Mcm2 upon Cdk1 inhibition.

2022-03-11 | PXD025625 | Pride

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