GEO DataSets

(Submitter supplied) We study here how mRNAs are translated in an eIF4E1-independent manner by blocking eIF4E1 using a constitutively active version of eIF4E-binding protein (4E-BP). Via ribosome profiling we identify a subset of mRNAs that are still efficiently translated when eIF4E1 is inactive. We find that these mRNAs preferentially release eIF4E1 when eIF4E1 is inactive and bind instead to eIF3D via its cap-binding pocket. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21697

19 Samples

Download data: TXT

(Submitter supplied) We report the application of polysome profiling sequencing technology for high-throughput transcriptomics and translatomics in mammalian cells. We compare reduction of Dap5 to control in metastatic breast cancer cells in transcription and polysome enriched translation using RNA sequencing. Genome-wide transcriptomic and translatomic analyses indicate that DAP5 is required for translation of many transcription factor and receptor capped mRNAs and their mRNA targets involved in cell survival, motility, DNA repair and translation initiation, among other mRNAs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

14 Samples

Download data: TXT

(Submitter supplied) Ribsome profiling analysis of mRNA translation in mouse cells under conditions of mTOR activiation or inhibition.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

12 Samples

Download data: TXT

(Submitter supplied) N6-methyladenosine (m6A) is a widespread internal RNA modification whose function is poorly understood. Here we report that m6A residues within the 5'UTR promote a novel form of cap-independent translation which is mediated through an interaction between m6A residues and the translation initiation factor, eIF3. We performed m6A profiling in cells subjected to heat shock stress and observed increased 5'UTR methylation after heat shock. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL16791 GPL11154

7 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Here we develop a novel methodology, capCLIP, to capture and identify mRNA interactions with the major cellular cap-binding protein eIF4E.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: BED, NARROWPEAK, TSV

(Submitter supplied) Regulatory T cells (Tregs) inhibit effector T cells and maintain immune system homeostasis. Treg maturation in peripheral sites (pTregs) is poorly understood but is known to require inhibition of protein kinase mTORC1 (e.g.RAD001) and exposure to TGFb. Paradoxically, Treg maturation requires protein synthesis yet mTORC1 inhibition downregulates it, leaving unanswered how Tregs carry-out essential mRNA translation for development and immune suppression activity. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

16 Samples

Download data: CEL

(Submitter supplied) The protozoan parasite Toxoplasma gondii causes serious opportunistic disease due to its ability to persist in patients as latent tissue cysts. The molecular mechanisms coordinating conversion between proliferative parasites (tachyzoites) and latent cysts (bradyzoites) are not fully understood. We previously showed that phosphorylation of eIF2α accompanies bradyzoite formation, suggesting that this clinically relevant process involves regulation of mRNA translation. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26742

18 Samples

Download data: TABULAR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Toxoplasma gondii

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL23466

24 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Ingestion of Toxoplasma gondii results in life-long infection due to its ability to convert from the rapidly disseminating tachyzoite stage to the chronic, encysted bradyzoite stage. The control of mRNA translation has been suggested to play a key role in the signaling required to trigger bradyzoite formation. In eukaryotes, translational control primarily operates at two key points during the assembly of translation initiation factors. more...

Organism:

Toxoplasma gondii

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL23466

12 Samples

Download data: TXT

(Submitter supplied) Ingestion of Toxoplasma gondii results in life-long infection due to its ability to convert from the rapidly disseminating tachyzoite stage to the chronic, encysted bradyzoite stage. The control of mRNA translation has been suggested to play a key role in the signaling required to trigger bradyzoite formation. In eukaryotes, translational control primarily operates at two key points during the assembly of translation initiation factors. more...

Organism:

Toxoplasma gondii

Type:

Other

Platform:

GPL23466

12 Samples

Download data: BED, BIGWIG

(Submitter supplied) To identify which mRNAs bind to RBM4/HIF-2a

Organism:

Homo sapiens

Type:

Other

Platform:

GPL9115

2 Samples

Download data: TXT

(Submitter supplied) Translation regulation occurs largely during initiation. Currently, translation initiation can be studied in vitro, but these systems lack features present in vivo and on endogenous mRNAs. Here we develop selective 40S footprinting for visualizing initiating 40S ribosomes on endogenous mRNAs in vivo. It pinpoints where on an mRNA initiation factors join the ribosome to act, and where they leave. We discover that in human cells most scanning ribosomes remain attached to the 5’ cap. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21626 GPL21697

60 Samples

Download data: XLSX

(Submitter supplied) Eukaryotic translation initiation factor 4E (eIF4E)–binding protein 1 (4E-BP1) inhibits cap-dependent translation in eukaryotes by competing with eIF4G for an interaction with eIF4E. Phos-phorylation at Ser-83 of 4E-BP1 occurs during mitosis through the activity of cyclin-dependent kinase 1 (CDK1)/cyclin B rather than through canonical mTOR kinase activity. Here, we investi-gated the interaction of eIF4E with 4E-BP1 or eIF4G during interphase and mitosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: TXT

(Submitter supplied) The phosphorylation of eIF4E1 at serine 209 by MNK1 or MNK2 has been shown to initiate oncogenic mRNA translation, a process that favours cancer development and maintenance. Here, we interrogate the MNK-eIF4E axis in diffuse large B-cell lymphoma (DLBCL) and show a distinct distribution of MNK1 and MNK2 in germinal centre B-cell (GCB) and activated B-cell (ABC) DLBCL. Despite displaying a differential distribution in GCB and ABC, both MNKs functionally complement each other to sustain cell survival. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

18 Samples

Download data: TXT

(Submitter supplied) 4E-BP (eIF4E-BP) represses translation initiation by binding to the 5’cap-binding protein eIF4E and inhibiting its activity. Although 4E-BP has been shown to be important in growth control, stress response, cancer, neuronal activity and mammalian circadian rhythms, it is not understood how it preferentially represses a subset of mRNAs. We successfully used hyperTRIBE (Targets of RNA-binding proteins identified by editing) to identify in vivo 4E-BP mRNA targets in both Drosophila and mammals under conditions known to activate 4E-BP. more...

Organism:

Homo sapiens; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19132

35 Samples

Download data: BW, TXT

(Submitter supplied) The mRNA 5′ cap is normally essential for eukaryotic mRNA translation, stabilization and transport and both the cap and eIF4E are important elements of post-transcriptional gene regulation. To further our understanding of mRNA translation in the human malaria parasite Plasmodium falciparum, we have investigated the parasite translation initiation factor eIF4E and its interaction with 5′ capped mRNA. more...

Organism:

Plasmodium falciparum

Type:

Other

Platform:

GPL4583

4 Samples

Download data: DAT, XLS

(Submitter supplied) Translation is a fundamental step in gene expression that regulates multiple developmental and stress responses. One key step of translation is the association between eIF4E and eIF4G. This process is regulated in different eukaryotes by proteins which bind to eIF4E and block the formation of the eIF4E/eIF4G complex. Here, we report the discovery of CERES, the first functional eIF4E regulator described in plants. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

18 Samples

Download data: XLS

(Submitter supplied) The eIF4E are a family of initiation factors that bind the mRNA 5’ cap, regulating the proteome and the cellular phenotype. eIF4E1 mediates global translation and its activity is controlled via the PI3K/AKT/mTOR pathway. mTOR down-regulation results in eIF4E1 sequestration into an inactive complex with the 4E binding proteins (4EBPs). The second member, eIF4E2, regulates the translatome during hypoxia. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21103

24 Samples

Download data: TXT