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EIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [Quick-irCLIP]

ABSTRACT: eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [Quick-irCLIP]

PROVIDER: PRJNA1034503 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26625353_1.fastq.gz	Fastqsanger.gz
	SRR26625353_2.fastq.gz	Fastqsanger.gz
	SRR26625354_1.fastq.gz	Fastqsanger.gz
	SRR26625354_2.fastq.gz	Fastqsanger.gz
	SRR26625355_1.fastq.gz	Fastqsanger.gz

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eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [Quick-irCLIP]

Project description:Stem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized cell types. However, the molecular mechanisms underlying this translational burst and the involvement of initiation factors remains largely unknown. Here, we investigate the roles of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs). Using Quick-irCLIP and alternative polyadenylation (APA)-Seq, we show eIF3 crosslinks to many neurologically relevant mRNAs in NPCs. Our data reveal eIF3 predominantly interacts with 3’ untranslated region (3’-UTR) termini of multiple mRNA isoforms, adjacent to the poly(A) tail. High eIF3 crosslinking at 3’-UTR termini of mRNAs correlates with high translational activity, as determined by ribosome profiling. We identify the transcriptional regulator inhibitor of DNA binding 2 (ID2) mRNA as a case in which active translation levels and eIF3 crosslinking are dramatically increased upon early NPC differentiation. Furthermore, we find that eIF3 engagement at 3’-UTR ends is dependent on polyadenylation. The results presented here show that eIF3 engages with 3’-UTR termini in highly translated mRNAs, supporting a role of mRNA circularization in the mechanisms governing mRNA translation in NPCs.

2023-12-08 | GSE246727 | GEO

eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [APA-Seq]

2023-12-08 | GSE246786 | GEO

eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells

Project description:eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells

| PRJNA1034610 | ENA

eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [APA-Seq]

Project description:eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells [APA-Seq]

| PRJNA1034614 | ENA

eIF3 Engages with 3’-UTR Termini of Highly Translated mRNAs in Neural Progenitor Cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-12-08 | GSE246787 | GEO

eIF3 PAR-CLIP in 293T cells

Project description:Regulation of protein synthesis is fundamental for all aspects of eukaryotic biology by controlling development, homeostasis, and stress responses. The 13-subunit, 800-kDa eukaryotic initiation factor 3 (eIF3) organizes initiation factor and ribosome interactions required for productive translation. However, current understanding of eIF3 function does not explain genetic evidence correlating eIF3 deregulation with tissue-specific cancers and developmental defects. Here we report the genome-wide discovery of human transcripts that interact with eIF3 using photo-activatable crosslinking and immunoprecipitation (PAR-CLIP). eIF3 binds to a highly specific programme of messenger RNAs (mRNAs) involved in cell growth control processes, including cell cycling, differentiation, and apoptosis, via the mRNA 5' untranslated region (5' UTR). Surprisingly, functional analysis of the interaction between eIF3 and two mRNAs encoding cell proliferation regulators, c-Jun and BTG1, reveals that eIF3 employs different modes of RNA stem loop binding to exert either translational activation or repression. Our findings illuminate a new role for eIF3 in governing a specialized repertoire of gene expression and suggest that binding of eIF3 to specific mRNAs could be targeted to control carcinogenesis. 293T cells were treated with 4-thiouridine and protein-RNA complexes were crosslinked, and eIF3-RNA complexes were immunoprecipitated.

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Project description:We performed irCLIP-seq to determine the mRNA targets of YTHDF2 in mouse hematopoietic progenitor cell line HPC-7

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Project description:YTHDF2 irCLIP-seq

| PRJNA422164 | ENA

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