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Eukaryotic Initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs

ABSTRACT: Eukaryotic Initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs

PROVIDER: PRJNA979168 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24819249.fastq.gz	Fastqsanger.gz
	SRR24819250.fastq.gz	Fastqsanger.gz
	SRR24819251.fastq.gz	Fastqsanger.gz
	SRR24819252.fastq.gz	Fastqsanger.gz
	SRR24819253.fastq.gz	Fastqsanger.gz

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Eukaryotic Initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs

Project description:In diffuse large B-cell lymphoma (DLBCL) poor outcome is associated with EIF4B-dependent stimulation of the DEAD box helicase eIF4A that unwinds RNA structures in 5’ untranslated regions (UTRs) in mRNAs that encode proteins with a role in cell proliferation. We carried out iCLIP to examine differences in RNAs bound by eIF4B in DLBCL-derived- versus control B-cells and show that eIF4B bound ~10-fold more mRNAs in DLBCL-derived cells. In addition to interacting with 5' UTRs we unexpectedly find that eIF4B binds across the entire mRNA transcripts, with mutually exclusive, position-dependent binding related to different functional protein groups. Interestingly, there was an enrichment for binding within the 3’ UTR of mRNAs encoding replication-dependent histones, and consistent with this, we find that eIF4B interacts with UPF1, a helicase that plays a key role in the turnover of histone mRNAs at the end of S-phase. We identify a direct role for eIF4B in the turnover of histone mRNAs and demonstrate that eIF4B contributes to regulated cell cycle progression through controlling the translation and turnover of selected mRNAs.

2024-09-04 | PXD042538 | Pride

Eukaryotic Initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs

Project description:In diffuse large B-cell lymphoma (DLBCL) poor outcome is associated with eIF4B-dependent stimulation of the DEAD box helicase eIF4A that unwinds RNA structures in 5’ untranslated regions (UTRs) in mRNAs that encode proteins with a role in cell proliferation. We carried out iCLIP to examine differences in RNAs bound by eIF4B in DLBCL-derived versus -control B-cells.

2024-09-04 | GSE233998 | GEO

Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs.

Project description:RNA binding proteins drive proliferation and tumorigenesis by regulating the translation and stability of specific subsets of messenger RNAs (mRNAs). We have investigated the role of eukaryotic initiation factor 4B (eIF4B) in this process and identify 10-fold more RNA binding sites for eIF4B in tumour cells from patients with diffuse large B-cell lymphoma compared to control B cells and, using individual-nucleotide resolution UV cross-linking and immunoprecipitation, find that eIF4B binds the entire length of mRNA transcripts. eIF4B stimulates the helicase activity of eIF4A, thereby promoting the unwinding of RNA structure within the 5' untranslated regions of mRNAs. We have found that, in addition to its well-documented role in mRNA translation, eIF4B additionally interacts with proteins associated with RNA turnover, including UPF1 (up-frameshift protein 1), which plays a key role in histone mRNA degradation at the end of S phase. Consistent with these data, we locate an eIF4B binding site upstream of the stem-loop structure in histone mRNAs and show that decreased eIF4B expression alters histone mRNA turnover and delays cell cycle progression through S phase. Collectively, these data provide insight into how eIF4B promotes tumorigenesis.

| S-EPMC11514447 | biostudies-literature

Binding to the Ribosome by Eukaryotic Initiation Factor 4B Drives Yeast Translational Control in Response to Urea

Project description:The yeast eukaryotic initiation factor 4B binds the 40S subunit in translation preinitiation complexes (PICs) and promotes mRNA binding. Here we have compared the effects of disrupting eIF4B RNA- and ribosome-binding domains under ~1400 growth conditions. The RNA-binding RRM was dispensable for stress responses, but ribosome binding stimulated by the NTD promoted growth in response to a number of stressors through changes in translation. In particular, the NTD confers a strong growth advantage in the presence of the denaturing reagent, urea, and a number of osmolytes that require robust cellular integrity for survival. Ribosome profiling of cells with and without the NTD of eIF4B reveals changes in translation of mRNAs containing longer than average and highly structured 5-prime untranslated regions both normally, and in response to urea exposure. Because these changes require 40S binding, our results suggest eIF4B regulates mRNA recruitment as a part of the scanning PIC, rather than by activating isolated mRNPs prior to ribosome binding. This analysis indicates the cellular response to urea in yeast includes a translational component, driven by increased translation of mRNAs encoding proteins associated with the cellular periphery, and highlights the importance of the general translation factor eIF4B in adapting to external conditions.

2020-04-15 | GSE139097 | GEO

Cellular translational enhancer elements that recruit eukaryotic initiation factor 3

Project description:Translation initiation is a highly regulated process which broadly affects eukaryotic gene expression. Eukaryotic initiation factor 3 (eIF3) is a central player in canonical and alternative pathways for ribosome recruitment. Here we have investigated how direct binding of eIF3 contributes to the large and regulated differences in protein output conferred by different 5′-untranslated regions (5′-UTRs) of cellular mRNAs. Using an unbiased high-throughput approach to determine the affinity of budding yeast eIF3 for native 5′-UTRs from 4,252 genes, we demonstrate that eIF3 binds specifically to a subset of 5′-UTRs that contain a short unstructured binding motif, AMAYAA. eIF3 binding mRNAs have higher ribosome density in growing cells and are preferentially translated under certain stress conditions, supporting the functional relevance of this interaction. Our results reveal a new class of translational enhancer and suggest a mechanism by which changes in core initiation factor activity enact mRNA-specific translation programs.

2022-07-06 | GSE180046 | GEO

Cellular translational enhancer elements that recruit eukaryotic initiation factor 3

2025-02-12 | GSE264057 | GEO

Binding to the Ribosome by Eukaryotic Initiation Factor 4B Drives Yeast Translational Control in Response to Urea

Project description:Binding to the Ribosome by Eukaryotic Initiation Factor 4B Drives Yeast Translational Control in Response to Urea

| PRJNA578373 | ENA

Selective translation mechanism through two paralogs of eukaryotic initiation factor 4A

Project description:Eukaryotic initiation factor (eIF) 4A is a DEAD-box RNA-binding protein that plays a pivotal role in translation initiation. Although mammals have two eIF4A paralogs, eIF4A1 and eIF4A2, their redundancy has been long assumed because of high homology and their functional difference has been poorly understood. Here we show that eIF4A paralogs employ differential translation programs. Ribosome profiling of eIF4A1- and eIF4A2-knockout HEK293T cell lines revealed that translation efficiency changes were divergent across transcriptome and distinct group of mRNAs were regulated by each paralog. Our analysis indicates that eIF4A1 and eIF4A2 facilitate translation of specific mRNAs.

2019-10-26 | GSE126298 | GEO

Cobetia sp. 4B strain:4B

Project description:Cobetia sp. 4B strain:4B Genome sequencing

| PRJNA648281 | ENA

Pseudomonas sp. 4B strain:4B

Project description:Pseudomonas sp. 4B strain:4B Genome sequencing and assembly

| PRJNA511953 | ENA