Transcriptional buffering compensates for eIF4E deficiency 2 in mRNA translation in transformed but not normal cells
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ABSTRACT:
PROVIDER: PRJNA636348 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11893000_1.fastq.gz | Fastqsanger.gz | |||
| SRR11893000_2.fastq.gz | Fastqsanger.gz | |||
| SRR11893001_1.fastq.gz | Fastqsanger.gz | |||
| SRR11893001_2.fastq.gz | Fastqsanger.gz | |||
| SRR11893002_1.fastq.gz | Fastqsanger.gz |
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Project description:Translation initiation is a rate-limiting step in protein synthesis. The eukaryotic translation initiation factor 4E (eIF4E) plays an essential role in the translation initiation process. However, how eIF4E-dependent translation initiation regulates plant growth and development remains not fully understood. In this study, we have found that Arabidopsis eIF4E proteins distribute both in the nucleus and cytoplasm, and only cytoplasmic eIF4E is implicated in the control of flowering time. Results of profiling the genome-wide translation by Ribo-tag sequencing further reveal that eIF4E may regulate plant flowering by affecting homeostatic translation of flowering-time genes, including the Central Oscillator Genes (COGs). Consistent with the hypothesis that transcription-translation feedback loop is the core mechanism to drive the oscillation of circadian clock, we show that the eIF4E-dependent translation modulates the rhythmic oscillation of protein abundance of the clock-related genes (CCGs). Together, our study provides mechanistic insights into how the protein translation regulates multiple developmental processed in Arabidopsis including circadian clock and photoperiodic flowering.
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Project description:eIF4E-independent translation is largely eIF3d-dependent
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Project description:Eukaryotic translation initiation factor 4E (eIF4E)–binding protein 1 (4E-BP1) inhibits cap-dependent translation in eukaryotes by competing with eIF4G for an interaction with eIF4E. Phos-phorylation at Ser-83 of 4E-BP1 occurs during mitosis through the activity of cyclin-dependent kinase 1 (CDK1)/cyclin B rather than through canonical mTOR kinase activity. Here, we investi-gated the interaction of eIF4E with 4E-BP1 or eIF4G during interphase and mitosis. We observed that 4E-BP1 and eIF4G bind eIF4E at similar levels during interphase and mitosis. The most highly phosphorylated mitotic 4E-BP1 isoform (δ) did not interact with eIF4E, whereas a distinct 4E-BP1 phospho-isoform, EB-γ—phosphorylated at Thr-70, Ser-83, and Ser-101—bound to eIF4E during mitosis. Two-dimensional gel electropho-retic analysis corroborated the identity of the phosphorylation marks on the eIF4E-bound 4E-BP1 isoforms and uncovered a population of phosphorylated 4E-BP1 molecules lacking Thr-37/Thr-46–priming phosphorylation. Moreover, proximity ligation assays for phospho–4E-BP1 and eIF4E revealed different in situ interactions during interphase and mitosis. The eIF4E:eIF4G interaction was not inhibited, but rather increased in mitotic cells, consistent with active translation initiation during mitosis. Phospho-defective substitution of 4E-BP1 at Ser-83 did not change global translation or individual mRNA translation profiles as measured by single-cell nascent protein synthesis and eIF4G RNA-immunoprecipitation sequencing. Mitotic 5’-terminal oligopyrimidine RNA translation was active and, unlike interphase translation, resistant to mTOR inhibition. Our findings reveal the phosphorylation profiles of 4E-BP1 isoforms and their interactions with eIF4E throughout the cell cycle and indicate that 4E-BP1 does not specifically inhibit translation initiation during mitosis.
2019-06-14 | GSE131668 | GEO
Project description:Translation is a fundamental step in gene expression that regulates multiple developmental and stress responses. One key step of translation is the association between eIF4E and eIF4G. This process is regulated in different eukaryotes by proteins which bind to eIF4E and block the formation of the eIF4E/eIF4G complex. Here, we report the discovery of CERES, the first functional eIF4E regulator described in plants. CERES is a modular protein that contains a LRR domain and a canonical eIF4E binding site (4E-BS), critical for CERES interaction with eIF4E in planta. CERES/eIF4E interaction excludes eIF4G from the complex. Despite this observation, CERES promotes translation in vivo interacts with eIF4A and with eIF3 in vivo and cosediments with translation initiation complexes in sucrose gradients. Moreover, ceres mutants display a sharp increase of the 80S peak and a reduction of polysome content at specific periods of the diel cycle. Super-resolution ribosome profiling demonstrates that these mutants show a change of translation efficiency of mRNAs related to light response and glucose management. Consistently, these mutants show a hypersensitive response to glucose. These data show that CERES is a “non canonical” translation initiation factor that, through the formation of alternative translation initiation complexes, modulates translation during the light cycle in plants.
2019-12-04 | GSE124290 | GEO
Project description:Combining a genetic and pharmacological approach, we modulated eIF4E activity across its physiological activity range and identified subsets of genes whose translation was either hypo- or hyper- sensitive to eIF4E activity changes. eIF4E hypersensitive genes had longer 5'UTRs with higher GC content; and longer 3'UTRs with lower GC content and a higher density of unique microRNA target sites. Proliferation related genes were enriched among eIF4E hypersensitive genes; and consistent with this, decreasing eIF4E activity inhibited cell cycle transit. Our findings provide genome wide insights into the properties of mRNAs under translational control across the physiological range of eIF4E activity.
2015-12-31 | GSE56072 | GEO
Project description:Combining a genetic and pharmacological approach, we modulated eIF4E activity across its physiological activity range and identified subsets of genes whose translation was either hypo- or hyper- sensitive to eIF4E activity changes. eIF4E hypersensitive genes had longer 5'UTRs with higher GC content; and longer 3'UTRs with lower GC content and a higher density of unique microRNA target sites. Proliferation related genes were enriched among eIF4E hypersensitive genes; and consistent with this, decreasing eIF4E activity inhibited cell cycle transit. Our findings provide genome wide insights into the properties of mRNAs under translational control across the physiological range of eIF4E activity. NIH 3T3 derivatives genetically altered to induce eIF4E when treated with mifepristone and a non-inducible control NIH 3T3 derivative were cultured with or without treatment with mifepristone and varying doses of a pharmacological eIF4E inhibiting agent, 4Ei-1 (0 μM, 10 μM, 50 μM, 100 μM, 200 μM). Total RNA and polyribosome RNA were isolated after 4h of treatment. Three replicates of each experimental group were completed. In addition, three replicates of the inducible cell line treated with less potent analog to the inhibiting agent, 4Ei-4, were completed to probe for non-specific drug effects.
2015-12-31 | E-GEOD-56072 | biostudies-arrayexpress
Project description:This work explores the therapeutic potential for the translation initiation factor eIF4E in multiple myeloma (MM). We show that targeting eIF4E is deleterious to MM cells and causes reduction of targets with established importance to the disease progression. We demonstrate that eIF4E inhibition may be achieved by treating the MM cells with the already clinically employed anti-viral drug Ribavirin. Results indicate that tetraspanin overexpression in MM cell lines increased global protein synthesis; CD81N1/CD82N1 also caused a decrease in peIF4E, its regulators and targets; direct inhibition of eIF4E (siRNA, Ribavirin) deleteriously affected MM cell lines; and Ribavirin attenuated viability and induced death of primary BM MM cells. Multiple Myeloma cell lines RPMI 8226 and CAG were each transiently transfected with purified plasmids of tetraspanins: pEGFP-N1 (N1, control), CD81N1-eGFP (81N1) or CD82N1-eGFP (82N1) (Clontech). Transfected cells were separated by Sorter Flow Cytometer 24 hours after transfection. Total RNA was extracted from sorted transfected cells with the Qiagen kit. Three separate experiments were analyzed by Whole Genome Affymetrix microarray chips (N1, 81N1, 82N1 in each cell line).
2011-03-11 | E-GEOD-27897 | biostudies-arrayexpress
Project description:This work explores the therapeutic potential for the translation initiation factor eIF4E in multiple myeloma (MM). We show that targeting eIF4E is deleterious to MM cells and causes reduction of targets with established importance to the disease progression. We demonstrate that eIF4E inhibition may be achieved by treating the MM cells with the already clinically employed anti-viral drug Ribavirin. Results indicate that tetraspanin overexpression in MM cell lines increased global protein synthesis; CD81N1/CD82N1 also caused a decrease in peIF4E, its regulators and targets; direct inhibition of eIF4E (siRNA, Ribavirin) deleteriously affected MM cell lines; and Ribavirin attenuated viability and induced death of primary BM MM cells.
2011-03-11 | GSE27897 | GEO
Project description:Translation initiation factor eIF4E is overexpressed early in breast cancers in association with disease progression and reduced survival. Much remains to be understood regarding the role of eIF4E in human cancer. Using immortalized human breast epithelial cells, we report that elevated expression of elF4E translationally activates the TGFβ pathway, promoting cell invasion, loss of cell polarity, increased cell survival and other hallmarks of early neoplasia. Overexpression of eIF4E is shown to facilitate selective translation of integrin β1 mRNA, which drives the translationally controlled assembly of a TGFβ receptor signaling complex containing α3β1 integrins, β-catenin, TGFβ receptor I, E-cadherin and phosphorylated Smads2/3. This receptor complex acutely sensitizes non-malignant breast epithelial cells to activation by typically sub-stimulatory levels of activated TGFβ. TGFβ can promote cellular differentiation or invasion and transformation. As a translational coactivator of TGFβ, eIF4E confers selective mRNA translation, reprogramming non-malignant cells to an invasive phenotype by reducing the set-point for stimulation by activated TGFβ. Overexpression of eIF4E may be a pro-invasive facilitator of TGFβ activity.
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