RIP-Seq of Eif4a2 in mouse embryonic stem cell
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE153456 | GEO | 2022/02/02
REPOSITORIES: GEO
Similar Datasets
Project description:Stemness is a defining feature in embryonic and cancer stem cells. How stemness is regulated at the mRNA translational initiation remains undefined. We carried out an RNAi screen for key translation initiation factors that maintain the stemness in mouse embryonic stem cells (ESCs). We identified eIF4A2 and defined its mechanistic action through Rps26-depleted and -containing ribosomes in translational initiation activation of mRNAs encoding pluripotency factors and H3.3 for embryonic and extraembryonic lineage repression, respectively. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent 2-cell (2C) transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Knockdown of eIF4A2 disrupts ESC proteome causing the loss of stemness in ESCs as well as in human glioblastomas where eIF4A2 is highly enriched. Collectively, our study establishes an eIF4A2-mediated translation initiation control of stemness and provides insight into cancer therapeutics targeting the translation initiation machinery.
2022-04-20 | GSE150680 | GEO
Project description:Stemness is a defining feature in embryonic and cancer stem cells. How stemness is regulated at the mRNA translational initiation remains undefined. We carried out an RNAi screen for key translation initiation factors that maintain the stemness in mouse embryonic stem cells (ESCs). We identified eIF4A2 and defined its mechanistic action through Rps26-depleted and -containing ribosomes in translational initiation activation of mRNAs encoding pluripotency factors and H3.3 for embryonic and extraembryonic lineage repression, respectively. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent 2-cell (2C) transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Knockdown of eIF4A2 disrupts ESC proteome causing the loss of stemness in ESCs as well as in human glioblastomas where eIF4A2 is highly enriched. Collectively, our study establishes an eIF4A2-mediated translation initiation control of stemness and provides insight into cancer therapeutics targeting the translation initiation machinery.
2022-04-20 | GSE150676 | GEO
Project description:Stemness is a defining feature in embryonic and cancer stem cells. How stemness is regulated at the mRNA translational initiation remains undefined. We carried out an RNAi screen for key translation initiation factors that maintain the stemness in mouse embryonic stem cells (ESCs). We identified eIF4A2 and defined its mechanistic action through Rps26-depleted and -containing ribosomes in translational initiation activation of mRNAs encoding pluripotency factors and H3.3 for embryonic and extraembryonic lineage repression, respectively. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent 2-cell (2C) transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Knockdown of eIF4A2 disrupts ESC proteome causing the loss of stemness in ESCs as well as in human glioblastomas where eIF4A2 is highly enriched. Collectively, our study establishes an eIF4A2-mediated translation initiation control of stemness and provides insight into cancer therapeutics targeting the translation initiation machinery.
2022-04-20 | GSE150673 | GEO
Project description:Translational control has emerged as a fundamental regulatory layer of proteome complexity that governs cellular identity and functions. As initiation is the rate-limiting step of translation, we carried out an RNAi screen for key translation initiation factors required to maintain embryonic stem cell (ESC) identity. We identified eIF4A2 and defined its mechanistic action through Rps26-independent and -dependent ribosomes in translation initiation activation of mRNAs encoding pluripotency factors and the histone variant H3.3 with demonstrated roles in maintaining stem cell pluripotency. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent 2-cell transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Accordingly, knockdown of eIF4A2 disrupts ESC proteome causing the loss of ESC identity. Collectively, we establish a translational paradigm of the protein synthesis of pluripotency transcription factors and epigenetic regulators imposed on their established roles in controlling pluripotency.
2024-12-20 | GSE192843 | GEO
Project description:Cell fate transitions depend on balanced rewiring of transcription and translation programmes to enable ordered developmental progression. We identified a feedback loop between nonsense-mediated mRNA decay (NMD) and translation initiation, in which NMD controls the translation initiation factor Eif4a2 and its premature termination codon encoding isoform (Eif4a2-PTC). This leads to translation of a specific truncated protein, which elicits increased translation rates and is causative for significant delays in mouse embryonic stem cell differentiation. Using immunoprecipitation coupled with mass spectrometry, we identified the interactome of full length Eif4a2 (Eif4a2-iso1) and Eif4a2-PTC. We find that Eif4a2-iso1 is mainly involved in translation initiation, while unstable Eif4a2-PTC shows little interaction with translation initiation factors. Both isoforms can bind to mRNA, as indicated by the interaction with mRNA binding protein, such as NMD factors and Ago2. Finally, Eif4a2-iso1 and Eif4a2-PTC interact with key pluripotency factors, providing a potential explanation for how Eif4a2 controls ESC differentiation.
2022-03-09 | PXD019588 | Pride
Project description:Background: Regulation of the mRNA life cycle is central to gene expression control and determination of cell fate. miRNAs represent a critical mRNA regulatory mechanism, but despite decades of research, their mode of action is still not fully understood. Results: Here, we show that eIF4A2 is a major effector of the repressive miRNA pathway functioning via the Ccr4-Not complex. We demonstrate that while DDX6 interacts with Ccr4-Not, its effects in the mechanism are not as pronounced. Through its interaction with the Ccr4- Not complex, eIF4A2 represses mRNAs at translation initiation. We show evidence that native eIF4A2 has similar RNA-selectivity to chemically inhibited eIF4A1. eIF4A2 exerts its repressive effect by binding purine-rich motifs which are enriched in the 5’UTR of target mRNAs directly upstream of the AUG start codon. Conclusions: Our data support a model whereby purine motifs towards the 3’ end of the 5’UTR are associated with increased ribosome occupancy and possible uORF activation upon eIF4A2 binding.
2019-10-09 | GSE94690 | GEO
Project description:RIP-Seq of Eif4a2 in mouse embryonic stem cell
| PRJNA642755 | ENA
Project description:Here we show eIF4A2 is a major effector of the represive miRNA pathway functioning via the Ccr4_Not complex; through its interaction with the Ccr4-Not complex eIF4A2 represses mRNAs at translation initiation. We show evidence that native eIF4A2 has similar properties to chemically inhibited eIF4A1. eIF4A2 exerts its repressive effect by binding purine-rich motifs which are enriched in the 5'UTR directly upstream of the AUG codon.
2019-10-10 | PXD015772 | Pride
Project description:While cell-type-restricted enhancers are initially detected following cooperative binding of positionally-determined DNA binding transcription factors during determination/differentiation, it remains unknown whether there are preceding events in embryonic stem cells (ESCs) that are functionally important to activate cell-type-restricted enhancer networks. Here, using murine macrophages as a model, we report that, while largely devoid of characteristic enhancer marks (H3K4me1, H3K4me2, H3K27Ac, H3K27me3 and p300) in ESCs, macrophage enhancers are activated as transcription units mainly by the binding of a single, at most two, ESC transcription factors. This provides “premarking” of these enhancers, as is also observed for other cell types. In contrast, ESC-active enhancers are cooperatively bound by multiple ESC transcription factors, including Esrrb, Nanog, Oct4 and Sox2 (ENOS). Interestingly, the strength of this signature in ESCs is functionally important for subsequent robust cell-restricted enhancer activation during macrophage differentiation events, as independently demonstrated by analysis of multiple ENOS motif–deleted macrophage-restricted enhancers. The ENOS-determined location of hydroxymethylation of the enhancers in ESCs could serve as a potential molecular memory for subsequent enhancer activation in the mature macrophage. These findings suggest that the massive repertoire of cell-type-restricted enhancers are essentially hierarchically and obligatorily “barcoded” by binding of a single ESC transcription factor in ESCs, with the strength of their binding dictating enhancer activation in mature cells.
2018-04-21 | GSE81680 | GEO
Project description:While cell-type-restricted enhancers are initially detected following cooperative binding of positionally-determined DNA binding transcription factors during determination/differentiation, it remains unknown whether there are preceding events in embryonic stem cells (ESCs) that are functionally important to activate cell-type-restricted enhancer networks. Here, using murine macrophages as a model, we report that, while largely devoid of characteristic enhancer marks (H3K4me1, H3K4me2, H3K27Ac, H3K27me3 and p300) in ESCs, macrophage enhancers are activated as transcription units mainly by the binding of a single, at most two, ESC transcription factors. This provides “premarking” of these enhancers, as is also observed for other cell types. In contrast, ESC-active enhancers are cooperatively bound by multiple ESC transcription factors, including Esrrb, Nanog, Oct4 and Sox2 (ENOS). Interestingly, the strength of this signature in ESCs is functionally important for subsequent robust cell-restricted enhancer activation during macrophage differentiation events, as independently demonstrated by analysis of multiple ENOS motif–deleted macrophage-restricted enhancers. The ENOS-determined location of hydroxymethylation of the enhancers in ESCs could serve as a potential molecular memory for subsequent enhancer activation in the mature macrophage. These findings suggest that the massive repertoire of cell-type-restricted enhancers are essentially hierarchically and obligatorily “barcoded” by binding of a single ESC transcription factor in ESCs, with the strength of their binding dictating enhancer activation in mature cells.
2018-04-21 | GSE81679 | GEO