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IRES containing mRNAs and mitotic cell cycle

ABSTRACT: A cell synchronization protocol was established in which global and individual mRNA translational efficiencies could be examined. While global translational efficiency was reduced in mitotic cells, approximately 3% of mRNAs remained predominantly associated with large polysomes during mitosis, as determined by cDNA microarray analyses. The 5 noncoding regions of six mRNAs were shown to contain internal ribosome entry sites (IRES). However, not all known mRNAs that contain IRES elements were actively translated during mitosis, arguing that specific IRES sequences are differentially regulated during mitosis. A cell cycle design experiment design type is one that assays events that occurs in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. Keywords: cell_cycle_design

ORGANISM(S): Homo sapiens

PROVIDER: GSE3957 | GEO | 2005/12/31

SECONDARY ACCESSION(S): PRJNA94211

REPOSITORIES: GEO

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IRES containing mRNAs and mitotic cell cycle

Project description:A cell synchronization protocol was established in which global and individual mRNA translational efficiencies could be examined. While global translational efficiency was reduced in mitotic cells, approximately 3% of mRNAs remained predominantly associated with large polysomes during mitosis, as determined by cDNA microarray analyses. The 5 noncoding regions of six mRNAs were shown to contain internal ribosome entry sites (IRES). However, not all known mRNAs that contain IRES elements were actively translated during mitosis, arguing that specific IRES sequences are differentially regulated during mitosis. A cell cycle design experiment design type is one that assays events that occurs in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. User Defined

2005-12-30 | E-GEOD-3957 | biostudies-arrayexpress

Transcription profiling analysis of human global and individual mRNA translational efficiencies

2005-10-31 | E-SMDB-2546 | biostudies-arrayexpress

Identification of the TXNIP IRES and characterization of the impact of regulatory IRES trans-acting factors

Project description:Translation is a tightly regulated and is predominantly controlled at the level of its initiation. Initiation occurs in a cap-dependent manner. Under stress conditions when cap-dependent translation is hampered, internal ribosome entry sites (IRESes) allow for cap-independent translation of certain mRNAs. IRES-dependent translation is commonly regulated by RNA-interacting proteins, known as IRES trans-acting factors (ITAFs). In the present study, we searched for new IRESes by identifying 5’ untranslated regions (UTRs) bound by the ITAF hnRNPA1. Using a PAR-iCLIP approach, we found the mRNA of thioredoxin interacting protein (TXNIP) bound by hnRNPA1. Upon verification of an IRES element within the 5’UTR of TXNIP, we determined additional interacting proteins, which predominantly appeared to interact with the IRES-regulatory second half of the 5’UTR. Amongst these PTB, FBP3, and GEMIN5 emerged as functional ITAFs. Finally, we found that the TXNIP IRES-inhibitory effect of PTB was dominant over the activating effect of FBP3, while it succumbed to the stimulatory function of GEMIN5. In summary, we identified and characterized a novel IRES within the 5’UTR of TXNIP, which is regulated by the ITAFs PTB, FBP3, and GEMIN5.

2018-01-23 | GSE97159 | GEO

A versatile IRES toolbox to determine IRES-like activity exemplified by Hoxa mRNA expression and translation in mouse embryonic tissues

Project description:Widespread control of gene expression at the level of translation has emerged as a key point of protein expression regulation in space and time. Internal ribosomal entry sites (IRESes) are a prominent mechanism by which ribosomes can confer greater gene regulation. However, their rigorous functional characterization remains difficult. Here we present a versatile toolbox of technologies in embryos and cells including single-molecule mRNA isoform imaging, Pacbio long read sequencing, isoform-sensitive mRNA quantification along polysome profiles, and IRES-like translation of circular RNA (circRNA) reporters as a new guide to understanding IRES-mediated regulation. We investigate the disputed IRES-like RNA elements in embryonic Hoxa mRNAs. We show the relative expression, localization and translation of the IRES-like containing Hoxa9 mRNA isoform in specific embryonic tissues, and Hoxa IRES-like dependent translation in circRNAs. We thereby provide a new resource of technologies to elucidate the roles of IRES-like elements in gene regulation and embryonic development.

2025-03-06 | GSE250214 | GEO

Identification of ribosome proteins bound to IRES in hypoxia

Project description:Hypoxic conditions prompt internal ribosome entry site (IRES)-mediated translation of some of the hallmark cancer genes, such as VEGF. This translational switch is extremely vital for cell survival and tumor progression. Heterogeneity in ribosomes due to the diversity of ribosomal RNA (rRNA) and protein composition has been postulated to generate ‘specialized ribosomes’ that differentially regulate translation. A VEGF IRES sequence was used as bait to identify unique proteins bound at the IRES in breast cancer cells grown in hypoxia.

2021-01-06 | PXD019238 | Pride

Regulation of protein translation during mitosis

Project description:Entry into and exit from mitosis is driven by precisely-timed changes in protein abundance, and involves transcriptional regulation and protein degradation. However, the role of translational regulation in modulating cellular protein content during mitosis remains poorly understood. Here, using ribosome profiling, we show that translational, rather than transcriptional regulation is the dominant mechanism for modulating protein synthesis at mitotic entry. The vast majority of regulated mRNAs are translationally repressed, which contrasts previous findings of selective mRNA translational activation at mitotic entry. One of the most pronounced translationally repressed genes in mitosis is Emi1, an inhibitor of the anaphase promoting complex (APC), which is degraded during mitosis. We show that Emi1 degradation is insufficient for full APC activation and that simultaneous translational repression is required. These results provide a genome-wide view of protein translation during mitosis and suggest that translational repression may be used to ensure complete protein inactivation Ribosome profiling and mRNA-seq from 3 time points in the cell cycle

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IRES-dependent ribosome repositioning directs translation of a +1 overlapping ORF that enhances viral infection

Project description:Elucidation of a novel +1 frame translational mechanism from the CrPV intergenic region IRES.

2018-11-22 | PXD011388 | Pride

Regulation of protein translation during mitosis

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Identification of human FGF9 IRES interacting proteins

Project description:We have previously shown that FGF9 is overexpressed in hypoxia through the IRES located in the 5’UTR. To identify the protein that binds to FGF9 IRES and controls FGF9 protein synthesis in hypoxia, FGF9 IRES RNA was in vitro synthesized and used to pulled-down interacting proteins. The RNA-protein complexes were first visualized by sliver staining, followed by cutting specific bands for protein identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS).

2019-11-13 | PXD012892 | Pride

Pervasive translation of circular RNAs driven by short IRES-like elements

Project description:Circular RNAs (circRNAs) are a class of abundant RNAs with ambiguous function. Although some circRNAs can be translated through IRES driven mechanisms, the scope and functions of circRNA translation are unclear because endogenous IRESs are rare. To determine the prevalence and mechanism of circRNA translation, we developed a cell-based system to screen random sequences and identified 97 overrepresented AU-rich hexamers (>2% of all hexamers) that drive cap-independent translation of circRNAs. These IRES-like short elements are significantly enriched in circRNAs and sufficient to drive circRNA translation. We further identified multiple trans-acting factors that bind these IRES-like short elements to initiate translation. Using mass-spectrometry data, hundreds of circRNA-coded peptides were identified, most of which have low abundance due to rapid degradation. As judged by mass-spectrometry, 50% of translatable endogenous circRNAs undergo rolling circle translation, several of which were experimentally validated by western blotting. Consistently, the mutation of the IRES-like short element in one circRNA reduced its translation. Collectively, our findings suggest a pervasive translation of circRNAs, providing profound implications in circRNA function.

2022-06-03 | GSE152560 | GEO

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