Quantitative mRNA profile of eif3e (yin6, int6) deleted S. pombe cells
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ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
PROVIDER: GSE80349 | GEO | 2016/07/29
SECONDARY ACCESSION(S): PRJNA318639
REPOSITORIES: GEO
Similar Datasets
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
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
Project description:Translation initiation in eukaryotes is multi-step pathway and the most regulated phase of translation. Eukaryotic initiation factor 3 is the largest and most complex of the translation initiation factors, and it contributes to events throughout the initiation pathway. In particular, eIF3 appears to play critical roles in mRNA recruitment. More recently, eIF3 has been implicated in driving the selective translation of specific classes of mRNAs. However, unraveling the mechanism of these diverse contributions — and disentangling the roles of the individual subunits of the eIF3 complex — remains challenging. We employed ribosome profiling of budding yeast cells expressing two distinct mutations targeting the eIF3 complex. These mutations either disrupt the entire complex or subunits positioned near the mRNA-entry channel of the ribosome which appear to relocate during or in response to mRNA binding and start-codon recognition. Disruption of either the entire eIF3 complex or specific targeting of these subunits affects mRNAs with long 5’-untranslated regions and whose translation is more dependent on eIF4A, eIF4B, and Ded1 but less dependent on eIF4G, eIF4E, and PABP. Disruption of the entire eIF3 complex further affects mRNAs involved in mitochondrial processes and with structured 5’-untranslated regions. Comparison of the suite of mRNAs most sensitive to both mutations with those uniquely sensitive to disruption of the entire complex sheds new light on the specific roles of individual subunits of the eIF3 complex.
2022-01-11 | GSE190601 | GEO
Project description:Improper regulation of translation initiation, a vital check-point of protein synthesis in the cell, has been linked to a number of cancers. Overexpression of protein subunits of eukaryotic translation initiation factor 3 (eIF3) has been associated with increased translation of mRNAs involved in cell proliferation. In addition to playing a major role in general translation initiation by serving as a scaffold for the assembly of translation initiation complexes, eIF3 regulates translation of specific cellular mRNAs and viral RNAs. Mutations in the N-terminal Helix-Loop-Helix (HLH) RNA-binding motif of the EIF3A subunit in eIF3 interfere with Hepatitis C Virus Internal Ribosome Entry Site (IRES) mediated translation initiation in vitro. Here we use RNA-seq and ribosome profiling of engineered lentiviral HEK293T cells to show that the EIF3A HLH motif controls translation of a small set of cellular transcripts enriched in oncogenic mRNAs, including MYC.
2018-08-08 | GSE118239 | GEO
Project description:eIF3 is a multi-subunit complex thought to execute numerous functions in canonical translation initiation, including mRNA recruitment to the 40S ribosome, scanning for the start codon, and inhibition of 60S subunit joining 1–3. eIF3 was also found to interact with 40S and 60S ribosomal proteins and translation elongation factors 4, but a direct involvement in translation elongation has never been demonstrated. Using selective ribosome profiling, we made the unexpected observation that eIF3 remains bound to post-initiation 80S ribosomes, followed by release after translation of ~50 codons. Furthermore, eIF3 deficiency reduces early ribosomal elongation speed, particularly on mRNAs encoding proteins associated with membrane-associated functions, resulting in defective synthesis of their encoded proteins and abnormal mitochondrial and lysosomal physiology. Accordingly, heterozygous eIF3e+/- knockout mice accumulate giant mitochondria in skeletal muscle and show a progressive decline in muscle strength with age. Hence, in addition to its canonical role in translation initiation, eIF3 interacts with 80S ribosomes to enhance, at the level of early elongation, the synthesis of proteins with membrane-associated functions, an activity that is critical for normal muscle health.
2020-06-01 | GSE131074 | GEO
Project description:eIF3 is a multi-subunit complex thought to execute numerous functions in canonical translation initiation, including mRNA recruitment to the 40S ribosome, scanning for the start codon, and inhibition of 60S subunit joining 1–3. eIF3 was also found to interact with 40S and 60S ribosomal proteins and translation elongation factors 4, but a direct involvement in translation elongation has never been demonstrated. Using selective ribosome profiling, we made the unexpected observation that eIF3 remains bound to post-initiation 80S ribosomes, followed by release after translation of ~50 codons. Furthermore, eIF3 deficiency reduces early ribosomal elongation speed, particularly on mRNAs encoding proteins associated with membrane-associated functions, resulting in defective synthesis of their encoded proteins and abnormal mitochondrial and lysosomal physiology. Accordingly, heterozygous eIF3e+/- knockout mice accumulate giant mitochondria in skeletal muscle and show a progressive decline in muscle strength with age. Hence, in addition to its canonical role in translation initiation, eIF3 interacts with 80S ribosomes to enhance, at the level of early elongation, the synthesis of proteins with membrane-associated functions, an activity that is critical for normal muscle health.
2020-06-15 | GSE149697 | GEO
Project description:Microarray comparisons of transcript level in wild-type Arabidopsis and eif3h mutant plants. Goal:; To detect any change in transcript level between WT and eif3h mutant. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of; eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5â leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Microarray comparisons of polysome loading in wild-type and eif3h mutant plants revealed that eIF3h generally helps to maintain efficient polysome loading of mRNAs harboring multiple uORFs. Independently, eIF3h also boosted polysome loading of mRNAs with long coding sequences. Moreover, the lesion in eIF3h revealed a concerted upregulation of translation for specific functional subgroups of mRNAs, including ribosomal proteins and proteins involved in photosynthesis. CONCLUSIONS: The intact eIF3h protein contributes to efficient translation initiation on 5â leader sequences harboring multiple uORFs, although mRNA features independent of uORFs were also implicated. Moreover, our data suggest that regulons of translational control can be revealed by mutations in generic translation initiation factors. Experiment Overall Design: Total RNA samples were isolated from 10-day-old wild-type and eif3h mutant plants
2008-06-14 | E-GEOD-6025 | biostudies-arrayexpress
Project description:Microarray comparisons of polysome loading in wild-type Arabidopsis and eif3h mutant; Goal: ; To find the target mRNAs that are translationally regulated by eIF3h. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of; eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5â leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Microarray comparisons of polysome loading in wild-type and eif3h mutant plants revealed that eIF3h generally helps to maintain efficient polysome loading of mRNAs harboring multiple uORFs. Independently, eIF3h also boosted polysome loading of mRNAs with long coding sequences. Moreover, the lesion in eIF3h revealed a concerted upregulation of translation for specific functional subgroups of mRNAs, including ribosomal proteins and proteins involved in photosynthesis. CONCLUSIONS: The intact eIF3h protein contributes to efficient translation initiation on 5â leader sequences harboring multiple uORFs, although mRNA features independent of uORFs were also implicated. Moreover, our data suggest that regulons of translational control can be revealed by mutations in generic translation initiation factors. Experiment Overall Design: Polysomal and non-polysomal RNA samples were isolated from 10-day-old wild-type and eif3h mutant plants. The translation state (ratio between the polysome and non-polysome, PL/NP) for each gene in the WT and in the mutant was separately established, and then the translation states between the genotype were compared.
2008-06-14 | E-GEOD-6024 | biostudies-arrayexpress
Project description:Many viruses potently inhibit host protein synthesis while employing unconventional strategies to sustain their own translation, but how and why certain cellular mRNAs continue to be translated remains unclear. Here, we show that during shutoff by Vaccinia Virus (VacV) several host mRNAs increase in polysome occupancy but few, topped by JUN, result in increased protein abundance. Translation of viral mRNAs depended on the small ribosomal protein, Receptor for Activated C Kinase 1 (RACK1) and the eukaryotic Initiation Factor, eIF3. Cryo-electron microscopy (cryo-EM) further showed that eIF3 bound to virus-modified RACK1-containing 40S subunits that exhibit altered head rotation during infection. By contrast, RACK1 and eIF3 were dispensable for JUN translation. Moreover, structurally distinct 5’ untranslated regions (5’UTRs) in viral versus JUN mRNAs conferred differential eIF3 dependencies. Altogether, we reveal how distinct modes of non-canonical initiation support the production of both host and viral proteins that facilitate poxvirus replication despite infection-induced shutoff.
2024-10-30 | GSE278320 | GEO
Project description:Eukaryotic initiation factor 3c,one of the important subunits of eIF3 that is the largest mammalian scaffolding initiation factor. We used microarray analysis to identify the genes that are regulated by EIF3C in TE-1 cells.
2022-04-01 | GSE167263 | GEO