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Determine the effects of QKI7 on translation efficiency via ribosome profiling (Ribo-seq)

ABSTRACT: Determine the effects of QKI7 on translation efficiency via ribosome profiling (Ribo-seq)

PROVIDER: PRJNA793438 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17395478.fastq.gz	Fastqsanger.gz
	SRR17395479.fastq.gz	Fastqsanger.gz
	SRR17395480.fastq.gz	Fastqsanger.gz
	SRR17395481.fastq.gz	Fastqsanger.gz
	SRR17395482.fastq.gz	Fastqsanger.gz

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Determine the effects of METTL16 on global translation efficiency via ribosome profiling (Ribo-seq)

Project description:METTL16 is a member of methyltransferase like (METTL) family. Unlike well-studied METTL3 and METTL14, we found a much higher percentage of METTL16 is localized in the cytosol. The subcellular distribution holds the ability to potentiate translation efficiency. Via Far-western blotting and Co-Immunoprecipitation (Co-IP) assays, we have identified the direct interactions between METTL16 and eukaryotic initiation factor 3 (eIF3) a and b. Via cross-linking immunoprecipitation and qPCR (CLIP-qPCR), we have discovered the direct associations between METTL16 and rRNAs. The METTL16-eIF3a/b and METTL16-rRNAs interactions induce the binding between eIF3 and 18S rRNA, promote the formation of 43S preinitiation complex, and eventually expedite translation initiation, the rate-limiting step of translation. To determine the exact effects of METTL16 on translation efficiency, we performed ribosome profiling (Ribo-seq) with HEK293T upon CRISPR-Cas9-induced METTL16 knockout. To guarantee the repeatability and avoid any potential off-target effects, we included 3 distint sgRNAs against METTL16.

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Determine the effects of METTL16 on global translation efficiency via ribosome profiling (Ribo-seq)

Project description:Determine the effects of METTL16 on global translation efficiency via ribosome profiling (Ribo-seq)

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Determine the effects of QKI7 on translation efficiency via ribosome profiling (Ribo-seq)

Project description:N7-methylguanosine (m7G) modification, routinely occurring at the 5’ cap of mRNA or within tRNA and rRNA, also exists internally in mRNA. Although essential for mRNA translation as well as stress response, the “reader” protein for mRNA internal m7G modification is still unrevealed. Here, we reported that Quaking protein (QKI), especially QKI7, can selectively recognize the internal mRNA m7G decoration in the cytosol of various cell types. We identified over 1000 confident m7G-modified and QKI binding RNA targets with a conserved motif, “GANGAN (N=A/U/G)”. More strikingly, internal m7G reader QKI7 directly interacts with the SG core protein G3BP1 and can shuttle a subset of m7G-modified transcripts into SG mRNA pool under oxidative stress condition. Additionally, by sequestering mRNA within SGs, QKI7 modulates the translation efficiency of selected transcripts. Moreover, in line with the observation that doxorubicin triggers the assembly of SGs, QKI7 mediates the sensitivity of cancer cells to chemotherapy drug treatment.

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Translation efficiency changes measured using ribosome footprinting (Ribo-seq) in poorly and highly metastatic cancer cells

Project description:Translation efficiency changes measured using ribosome footprinting (Ribo-seq) in poorly and highly metastatic cancer cells

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Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture

Project description:In the ribosome complex, tRNA is a critical element of mRNA translation. We reported a new technology for profiling ribosome-embedded tRNAs and their modifications. With the method, we generated a comprehensive survey of the quanity and quality of intra-ribosomal tRNAs (Ribo-tRNA-seq). Ribo-tRNA-seq can provide new insights on translation control mechanism in diverse biological contexts.

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N6-methyladenosine Modulates Messenger RNA Translation Efficiency

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Ribo-seq analysis of Saccharomyces cerevisiae with and without 10 minute glucose starvation

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