Polysome profiling of Huh7.5 cells expressing HCV NS5A
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE46273 | GEO | 2014/05/01
SECONDARY ACCESSION(S): PRJNA198502
REPOSITORIES: GEO
Similar Datasets
Project description:Hepatitis C Virus protein NS5A was found to upregulate assembly of cap binding initiation complex eIF4F in Huh7.5 cells. NS5A also was found to associate with translation machinery. To understand consequences of NS5A mediation in host translation, we analyzed mRNA associated with polysome fractions of NS5A expressing Huh7.5 cells and compared them with the corresponding fractions from control cells. Agilent-027114 Genotypic Technology designed Custom Human Whole Genome 8x60k Microarray
2014-05-01 | E-GEOD-46273 | biostudies-arrayexpress
Project description:Transcriptional profiling of human hepatoma cell lines comparing control uninfected Huh7.5 cells with Huh7.5 cells persistently infected with HCV (HPI cell). The latter maintains and produces HCV.
2014-12-01 | GSE52321 | GEO
Project description:Polysome Profiling was used to evaluated whether changes in abundance of tRNAIleUAU and tRNAIleGAU would affect codon dependent translation and quantify the abundance of these tRNAs in highly translated fractions.
2023-04-01 | GSE172349 | GEO
Project description:In eukaryotic cells, protein synthesis typically begins with the binding of eIF4F to the 7-methylguanylate (m7G)cap found on the 5’ end of the majority of mRNAs. Surprisingly, overall translational output remains robust under eIF4F inhibition. The sustained protein synthesis has been largely attributed to cap-independent translation mediated by internal ribosome entry sites (IRES). However, the IRES-driven translation is substrate-specific and largely incompatible with the broad spectrum of eIF4F-resistant translatomes.Here, we report that N6-methyladenosine (m6A)-mediated translation prevails on capped mRNAs and is resistant to eIF4F inactivation.Depletion of the methyltransferase METTL3 selectively inhibits translation of mRNAs bearing 5’UTR methylation, but not mRNAs with 5’ terminal oligopyrimidine (TOP) elements. Mechanistically, we identify ABCF1 as a critical mediator of m6A-promoted translation under both stress and physiological conditions. Supporting the role of ABCF1 in m6A-mediated cap-independent translation, ABCF1-sensitive transcripts largely overlap with METTL3-responsible mRNA targets. By illustrating the scope and the mechanism of translation initiation that is neither cap- nor IRES-dependent, these findingsreshape our current perceptions of cellular translational pathways
2017-07-26 | GSE101865 | GEO
Project description:Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Although most eukaryotic mRNAs need a functional cap binding complex eIF4F for efficient 5' end-dependent scanning to initiate translation, picornaviral, hepatitis C viral, and a few cellular RNAs have been shown to be translated by internal ribosome entry, a mechanism that can operate in the presence of low levels of functional eIF4F. To identify cellular mRNAs that can be translated when eIF4F is depleted or in low abundance and that, therefore, may contain internal ribosome entry sites, mRNAs that remained associated with polysomes were isolated from human cells after infection with poliovirus and were identified by using a cDNA microarray. Approximately 200 of the 7000 mRNAs analyzed remained associated with polysomes under these conditions. Among the gene products encoded by these polysome-associated mRNAs were immediate-early transcription factors, kinases, and phosphatases of the mitogen-activated protein kinase pathways and several protooncogenes, including c-myc and Pim-1. In addition, the mRNA encoding Cyr61, a secreted factor that can promote angiogenesis and tumor growth, was selectively mobilized into polysomes when eIF4F concentrations were reduced, although its overall abundance changed only slightly. Subsequent tests confirmed the presence of internal ribosome entry sites in the 5' noncoding regions of both Cyr61 and Pim-1 mRNAs. Overall, this study suggests that diverse mRNAs whose gene products have been implicated in a variety of stress responses, including inflammation, angiogenesis, and the response to serum, can use translational initiation mechanisms that require little or no intact cap binding protein complex eIF4F. This study is described more fully in Johannes G et al.(1999) Proc Natl Acad Sci U S A 96:13118-23.
2002-06-27 | E-GEOD-62 | biostudies-arrayexpress
Project description:Gene expression in the total RNA and heavy polysome fractions of Eif4g3 siRNA treated lymph node stromal cells (LNSCs) compared to control-sIRNA treated samples The objective of this study was to identify genes whose translation are reduced after silencing Eif4g3 (the gene which encodes the translation initiation factor eIF4GII). Genes with reduced translation are expected to have lower expression in RNA samples isolated from heavy polysomes but not in RNA samples isolated from whole cell lysates. LNSCs were grown in 10 cm plates, allowed to reach M-bM-^IM-% 80% confluency and then transfected with 400 pmol of control or Eif4g3 siRNA using Lipofectamine 2000. 7 plates were transfected with control or Eif4g3 siRNA. Total RNA was extracted from cells 48h after transfection. To isolate RNA from the heavy polysome fractions, cells were pooled, lysed and fractionated on a 10% to 60% continuous sucrose gradient. Fractions containing the heavy polysome fractions were pooled. RNA was extracted from these samples and used for microarrays on the Agilent Whole Mouse Genome Microarray Kit, 4M-CM-^W44K 2-color arrays.
2012-07-19 | E-GEOD-39408 | biostudies-arrayexpress
Project description:Although most eukaryotic mRNAs need a functional cap binding complex eIF4F for efficient 5' end- dependent scanning to initiate translation, picornaviral, hepatitis C viral, and a few cellular RNAs have been shown to be translated by internal ribosome entry, a mechanism that can operate in the presence of low levels of functional eIF4F. To identify cellular mRNAs that can be translated when eIF4F is depleted or in low abundance and that, therefore, may contain internal ribosome entry sites, mRNAs that remained associated with polysomes were isolated from human cells after infection with poliovirus and were identified by using a cDNA microarray. Approximately 200 of the 7000 mRNAs analyzed remained associated with polysomes under these conditions. Among the gene products encoded by these polysome-associated mRNAs were immediate-early transcription factors, kinases, and phosphatases of the mitogen-activated protein kinase pathways and several protooncogenes, including c-myc and Pim-1. In addition, the mRNA encoding Cyr61, a secreted factor that can promote angiogenesis and tumor growth, was selectively mobilized into polysomes when eIF4F concentrations were reduced, although its overall abundance changed only slightly. Subsequent tests confirmed the presence of internal ribosome entry sites in the 5' noncoding regions of both Cyr61 and Pim-1 mRNAs. Overall, this study suggests that diverse mRNAs whose gene products have been implicated in a variety of stress responses, including inflammation, angiogenesis, and the response to serum, can use translational initiation mechanisms that require little or no intact cap binding protein complex eIF4F.
2005-06-24 | E-SMDB-59 | biostudies-arrayexpress
Project description:It has been shown that in mammalian cells alternative transcription initiation is extensively regulated during development and across cell-types, which confers dynamic transcript 5âUTR repertoire. However it is underexplored how the heterogeneity of 5âUTR isoforms would affect the downstream steps for protein expression, such as translation. To this end, we globally compared the translational profile of distinct mRNA TSS isoforms in mouse fibroblast cells, by combining deep-sequencing based mRNA 5âends profiling and polysome fractionation. We demonstrated the extensive translation regulation conferred by TSS heterogeneity. 5'end sequencing in seven polysome fractions, in two replicates, using Illumina Hiseq2000
2016-07-20 | E-GEOD-78241 | biostudies-arrayexpress
Project description:Differential expression study of lncRNAs (long non-coding RNAs) and mRNAs in HCV infection. For this we infected Huh7.5 cells with HCV (JFH-1) virus and control cells were mock infected. 48h post infection we isolated total RNA using qiagen RNeasy kit as per manufacturer's protocol. The total RNA was then subjected to microarray for both lncRNAs and mRNAs. The resultant profile can be used to compare gene expression in HCV infection versus mock infected cells.
2016-05-01 | GSE76333 | GEO
Project description:Polysome profiling experiments were carried out to identify the mRNAs that have altered the translation efficiency (counts in polysomal fraction/counts in monosomal fractions) in the presence of an oligonucleotide targeting a specific region of the ribosomal RNA, to study the implication of this region in the translation of specific mRNAs
2019-12-10 | GSE129651 | GEO