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Differential expression analysis connects knock-downs of eIF3e and eIF3d with the MAP kinase signaling pathway

ABSTRACT: Differential expression analysis connects knock-downs of eIF3e and eIF3d with the MAP kinase signaling pathway

PROVIDER: PRJNA896488 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22122961.fastq.gz	Fastqsanger.gz
	SRR22122962.fastq.gz	Fastqsanger.gz
	SRR22122963.fastq.gz	Fastqsanger.gz
	SRR22122964.fastq.gz	Fastqsanger.gz
	SRR22122965.fastq.gz	Fastqsanger.gz

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Similar Datasets

Differential expression analysis connects knock-downs of eIF3e and eIF3d with the MAP kinase signaling pathway

Project description:A prominent hallmark of cancer is deregulated protein synthesis. It is well established that various translation initiation factors (eIFs) are either overexpressed or under-expressed in numerous types of cancer. Recent studies suggest that rather than representing an indirect consequence of neoplasia, imbalanced expression of eIFs significantly contributes to cellular transformation, tumor development, cancer cell survival, metastasis and tumor angiogenesis. Among them, eIF3 stands out as the largest complex composed of 12 subunits with a modular assembly, where aberrant expression of one subunit leads to partially functional subcomplexes. Here we took advantage of well-established knockdowns of subunits d, e and h of human eIF3, all implicated in cancer, and investigated their impact on differential gene expression translatome-wide by Ribo-Seq. We demonstrate that eIF3e and eIF3d knock-downs result in reduced translation efficiency of numerous components of the MAPK signaling pathway, a pathway often upregulated in cancer, and pathways preventing genotoxic stress. Concurrently, depletion of eIF3d increased translation of proteins associated with membrane organelles, whereas eIF3e depletion increased expression of numerous ribosomal proteins, implicating eIF3e in controlling the balanced production of mature ribosomes. Overall, our data illustrate that individual eIF3 subunits exert specific translational control over a broad range of cellular transcripts.

2024-04-25 | GSE216967 | GEO

eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by small molecules

Project description:Exposure to hypoxia is linked to increased cellular plasticity and enhanced metastasis; effects which are primarily attributed to the transcriptional activation of large gene programs downstream of hypoxia inducible factors (HIFs). However, translational effects in hypoxia, that likely precede transcriptional effects, have remained largely unexplored. Using ribosome-profiling, we uncovered a selective translational response in acute hypoxia that is eIF3d/eIF3e-dependent and controls downstream hypoxic responses including HIF1a accumulation and cellular invasion. We further demonstrated that eIF3e copy number and eIF3e- and eIF3d-expression signatures are associated with worsened outcomes for breast cancer patients. Finally, we identified a class of novel small molecules that target eIF3e specifically, reducing the translational response to hypoxia and to ER stress, another stressor that is dependent on eIF3d/eIF3e-mediated translation. Our data uncover critical functions for eIF3d/eIF3e in the hypoxic response and identify a potential means to inhibit stress-induced translation, and potentially plasticity and metastasis, mediated by eIF3e.

2025-11-06 | GSE307666 | GEO

eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by small molecules

Project description:eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by small molecules

| PRJNA1322474 | ENA

Quantitative mRNA profile of eif3e (yin6, int6) deleted S. pombe cells

Project description:Int6/yin6 encodes the eIF3e subunits of the eukaryotic translation initiation factor 3 complex (eIF3). To assess the impact of eIF3e on the global transcriptome, RNA seq of total mRNA was performed. Total RNA was prepared from wildtype S. pombe (h- ura4-D18 leu1-32) and cells deleted for eif3e (int6, yin6, SPBC646.09c; h- int6::kanMX6 ura4-D18 leu1-32). Following rRNA depletion and library construction, samples were sequenced on the SOLID4 platform. Two replicates were analyzed and statistical analysis was performed to identify significant differences in mRNA levels.

2016-07-29 | E-GEOD-80349 | biostudies-arrayexpress

Domains architecture and phospho-switches of eIF3e translation subunit control pollen tube growth and morphology

Project description:The eIF3e subunit form an octameric ribonucleoprotein complex to initiate translation, and its PCI domain engage in the assembly of the proteolytic 26S proteosome supercomplex. These two complexes are central in translation initiation and protein quality surveillance and turnover. However, how eIF3e is structurally regulated remain unknown. Here, using RIPseq approach we revealed that eIF3e co-immunoprecipitate with mRNAs involved in RNA biosynthesis (U3 snRNA12a and ncRNA processing) and cell morphology, and its PCI domain is crucial for regulation of pollen tube pulse growth and eIF3e dissociation post initiation. We show that motifs within eIF3e associated target RNAs can repress or activate translation. Since the PCI domain associate with the proteosome machinery, we show that pharmacological inhibition of the proteosome complex accumulate eIF3e, eIF3eΔPCI and the proteosome lid subunits RPN7/RPN12a to the nucleus and generate nuclear condensates. Importantly, constitutive dephosphorylation of eIF3e revealed antagonistic phosphosites at the PCI domain that balance pollen tube growth and cellular membrane morphology. These findings inform structural features that control eIF3e activities and that antagonistic de-phosphorylation of eIF3e maintain equilibrium of pollen tube growth rate dynamics and membrane structural morphology.

2026-04-06 | PXD048337 | Pride

Quantitative mRNA profile of eif3e (yin6, int6) deleted S. pombe cells

2016-07-29 | GSE80349 | GEO

eIF3d controls the persistent integrated stress response

Project description:All cells respond to intrinsic and extrinsic stresses by reducing global protein synthesis and activating select gene programs necessary for survival. Here, we show the fundamental integrated stress response (ISR) is driven by the non-canonical cap-binding protein eIF3d which acts as a master effector to control core stress response orchestrators, the translation factor eIF2ɑ and the transcription factor ATF4. We find that during persistent stress, eIF3d activates translation of the protein kinase GCN2, inducing eIF2ɑ phosphorylation and inhibiting global protein synthesis. In parallel, eIF3d upregulates the m6A demethylase enzyme ALKBH5 to drive 5′ UTR-specific demethylation of stress response genes, including ATF4. Ultimately, this cascade converges on ATF4 expression by increasing mRNA engagement of translation machinery and enhancing ribosome bypass of upstream open reading frames. Our results reveal that eIF3d acts as a critical life-or-death decision point during adaptation to chronic stress and uncover a synergistic signaling mechanism in which translational cascades dynamically complement transcriptional amplification to control essential cellular processes.

2023-09-11 | GSE236188 | GEO

eIF4E-independent translation is largely eIF3d-dependent

Project description:We study here how mRNAs are translated in an eIF4E1-independent manner by blocking eIF4E1 using a constitutively active version of eIF4E-binding protein (4E-BP). Via ribosome profiling we identify a subset of mRNAs that are still efficiently translated when eIF4E1 is inactive. We find that these mRNAs preferentially release eIF4E1 when eIF4E1 is inactive and bind instead to eIF3D via its cap-binding pocket. eIF3D then enables these mRNAs to be efficiently translated due to its cap-binding activity.

2024-08-07 | GSE243708 | GEO

Cytoplasmic mRNA and Heavy polysome-associated mRNAs from U251 Cells treated with Control or eIF3e siRNAs

Project description:Transcriptional profiling of Cytoplasmic mRNA and Heavy polysome-associated mRNAs extracted from U251 Cells treated with control siRNA or siRNA targeting eIF3e . Goal was to determine the effect of eIF3e knockdown on translation of specific mRNAs.

2020-09-09 | GSE157608 | GEO

A phosphorylation-regulated eIF3d translation switch mediates cellular adaptation to metabolic stress

Project description:Shutoff of global protein synthesis is a conserved response to cellular stresses. This general phenomenon is accompanied by induction of distinct gene programs tailored to each stress condition. Although the mechanisms that lead to general repression of protein synthesis are well characterized, how cells reprogram the translation machinery for selective gene expression remains poorly understood. Here we show that the noncanonical 5′ cap-binding protein eIF3d is specifically activated in response to metabolic stress, due to loss of CK2-mediated phosphorylation near the eIF3d cap-binding pocket. Activated eIF3d controls a gene program enriched in factors important for glucose homeostasis, including members of the mTOR pathway, and eIF3d-mediated translation adaptation is essential for cell survival during chronic glucose deprivation. Our findings reveal a new mechanism of translation reprogramming engaged in response to metabolic stress.

2020-11-16 | GSE158249 | GEO

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