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Mus musculus

ABSTRACT: Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells [ribosome profiling]

PROVIDER: PRJNA349752 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4436400.fastq.gz	Fastqsanger.gz
	SRR4436410.fastq.gz	Fastqsanger.gz
	SRR4436401.fastq.gz	Fastqsanger.gz
	SRR4436411.fastq.gz	Fastqsanger.gz
	SRR4436402.fastq.gz	Fastqsanger.gz

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Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells

Project description:Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells

| PRJNA349751 | ENA

Mus musculus

Project description:Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells [expression]

| PRJNA349775 | ENA

Mus musculus

Project description:Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells [expression 2]

| PRJNA352687 | ENA

Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells [expression 2]

Project description:Nat1 (also known as p97/Dap5/Eif4g2) is a ubiquitously expressed cytoplasmic protein that is homologous to the c-terminal two thirds of eukaryotic translation initiation factor 4G (also known as Eif4g1). We previously showed that Nat1-null mouse embryonic stem cells (mESCs) were resistant to differentiation. In the current study, we found that NAT1 and eIF4G1 share many binding proteins, such as eIF3, eIF4A and ribosomal proteins. However, NAT1did not bind to eIF4E or poly A binding proteins, which are critical for cap-dependent translation initiation. In contrast, compared to eIF4G1, NAT1 preferentially interacts with eIF2, FMR and related proteins, and especially PRRC2 family members. We also found that Nat1-null mESCs possess a transcriptional profile similar, though not identical, to ground state, which is established in wild-type mES cells when treated with inhibitors of the ERK and GSK3 signaling pathways. In Nat1-null mESCs, the ERK pathway is suppressed even without inhibitors. Ribosome profiling revealed that translation of Map3k3 and Sos1 is suppressed in the absence of Nat1. Forced expression of Map3k3 induced differentiation of Nat1-null mESCs. These data collectively showed that Nat1 is involved in translation of proteins that are required for cell differentiation.

2017-01-06 | GSE89600 | GEO

Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells [expression]

Project description:Nat1 (also known as p97/Dap5/Eif4g2) is a ubiquitously expressed cytoplasmic protein that is homologous to the C-terminal two thirds of eukaryotic translation initiation factor 4G (also known as Eif4g1). We previously showed that Nat1-null mouse embryonic stem cells (mESCs) were resistant to differentiation. In the current study, we found that Nat1 and Eif4g1 share many binding proteins, such as Eif3s, Eif4s and ribosomal proteins. However, Nat1 did not bind to Eif4e or poly A binding proteins, which are critical for cap-dependent translation initiation. In contrast, Nat1 binds to Eif2s, Fmr and related proteins, and Prrc2 proteins more preferentially than does Eif4g1. We also found that Nat1-null mESCs possess a status partially similar to ground state, which is established in wild-type mES cells when treated with inhibitors of the ERK and GSK3 signaling pathways. In Nat1-null mESCs, the ERK pathway is suppressed even without inhibitors. Ribosomal profiling revealed that translation of Map3k3 and Sos1 is suppressed in the absence of Nat1. Forced expression of Map3k3 induced differentiation of Nat1-null mESCs. These data collectively showed that Nat1 is involved in translation of proteins that are required for cell differentiation.

2017-01-06 | GSE89007 | GEO

Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells [ribosome profiling]

2017-01-06 | GSE89011 | GEO

Critical roles of translation initiation and RNA uridylation in endogenous retroviral expression and neural differentiation in pluripotent stem cells

Project description:Previous studies have suggested that the loss of the translation initiation factor eIF4G1 homolog NAT1 induces excessive self-renewability of naïve pluripotent stem cells (PSCs). Yet the role of NAT1 in the self-renewal and differentiation of primed PSCs, is still unclear. Here we generated conditional knockout of NAT1 in primed PSCs and used the cells for the functional analyses of NAT1. Our results showed that NAT1 is required for the self-renewal and neural differentiation of primed PSCs. In contrast, NAT1 deficiency in naïve pluripotency attenuated the differentiation to all cell types. We also found that NAT1 is involved in efficient protein expression of an RNA uridyltransferase TUT7. TUT7 is involved in the neural differentiation of primed PSCs via the regulation of human endogenous retrovirus accumulation. These data demonstrated the essential roles of NAT1 and TUT7 in the precise transition of stem cell fate.

2020-06-02 | GSE129429 | GEO

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes

Project description:The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep-sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and novel translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a new class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes. Examination of translation in mouse embryonic stem cells and during differentiation into embryoid bodies

2011-11-03 | E-GEOD-30839 | biostudies-arrayexpress

Pseudouridine-dependent ribosome biogenesis selectively regulates translation of polyglutamine proteins during Drosophila oogenesis [pulldown]

Project description:Stem cells in many systems, including Drosophila germline stem cells (GSCs), have increased ribosome biogenesis and translation during terminal differentiation. Here, we show that pseudouridylation of ribosomal RNA (rRNA) mediated by the H/ACA box is required for ribosome biogenesis and oocyte specification. Reducing ribosome levels during differentiation decreased the translation of a subset of mRNAs that are enriched for CAG repeats and encodes polyglutamine-containing proteins, including differentiation factors such as RNA-binding Fox protein 1. Moreover, ribosomes were enriched at CAG repeats within transcripts during oogenesis. Increasing TOR activity to elevate ribosome levels in H/ACA box-depleted germlines suppressed the GSC differentiation defects, whereas germlines treated with the TOR inhibitor rapamycin had reduced levels of polyglutamine-containing proteins. Thus, ribosome biogenesis and ribosome levels can control stem cell differentiation via selective translation of CAG repeat-containing transcripts.

2023-11-22 | GSE206691 | GEO

Pseudouridine-dependent ribosome biogenesis selectively regulates translation of polyglutamine proteins during Drosophila oogenesis [polysome-seq]

2023-11-22 | GSE206690 | GEO