Global mRNA polarization regulates translation efficiency in the intestinal epithelium
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA377081 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5280300.fastq.gz | Fastqsanger.gz | |||
| SRR5280310.fastq.gz | Fastqsanger.gz | |||
| SRR5280291.fastq.gz | Fastqsanger.gz | |||
| SRR5280301.fastq.gz | Fastqsanger.gz | |||
| SRR5280292.fastq.gz | Fastqsanger.gz |
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Project description:Asymmetric mRNA localization facilitates efficient translation in cells such as neurons and fibroblasts. However, the extent and significance of mRNA polarization in epithelial tissues is unclear. Here, we used single molecule transcript imaging and subcellular transcriptomics to uncover global apical-basal intracellular polarization of mRNA in the mouse intestinal epithelium. The localization of mRNAs did not generally overlap protein localization. Instead, ribosomes were more abundant on the apical sides, and apical transcripts were consequently more efficiently translated. Refeeding of fasted mice elicited a basal to apical shift in polarization of mRNAs encoding ribosomal proteins, which was associated with a specific boost in their translation. This lead to increased protein production, required for efficient nutrient absorption. These findings reveal a post-transcriptional regulatory mechanism involving dynamic polarization of mRNA and polarized translation.
2017-08-10 | GSE95415 | GEO
Project description:Asymmetric mRNA localization facilitates efficient translation in cells such as neurons and fibroblasts. However, the extent and significance of mRNA polarization in epithelial tissues is unclear. Here, we used single molecule transcript imaging and subcellular transcriptomics to uncover global apical-basal intracellular polarization of mRNA in the mouse intestinal epithelium. The localization of mRNAs did not generally overlap protein localization. Instead, ribosomes were more abundant on the apical sides, and apical transcripts were consequently more efficiently translated. Refeeding of fasted mice elicited a basal to apical shift in polarization of mRNAs encoding ribosomal proteins, which was associated with a specific boost in their translation. This lead to increased protein production, required for efficient nutrient absorption. These findings reveal a post-transcriptional regulatory mechanism involving dynamic polarization of mRNA and polarized translation.
2017-08-10 | GSE95276 | GEO
Project description:Asymmetric messenger RNA (mRNA) localization facilitates efficient translation in cells such as neurons and fibroblasts. However, the extent and importance of mRNA polarization in epithelial tissues are unclear. Here, we used single-molecule transcript imaging and subcellular transcriptomics to uncover global apical-basal intracellular polarization of mRNA in the mouse intestinal epithelium. The localization of mRNAs did not generally overlap protein localization. Instead, ribosomes were more abundant on the apical sides, and apical transcripts were consequently more efficiently translated. Refeeding of fasted mice elicited a basal-to-apical shift in polarization of mRNAs encoding ribosomal proteins, which was associated with a specific boost in their translation. This led to increased protein production, required for efficient nutrient absorption. These findings reveal a posttranscriptional regulatory mechanism involving dynamic polarization of mRNA and polarized translation.
| S-EPMC5955215 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2017-08-10 | GSE95416 | GEO
Project description:PABPN1 effect on translation efficiency.
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Project description:N6-methyladenosine (m6A) is the most abundant internal messenger (mRNA) modification in mammalian mRNA. This modification is reversible and non-stoichiometric, which potentially adds an additional layer of variety and dynamic control of mRNA metabolism. The m6A-modified mRNA can be selectively recognized by the YTH family “reader” proteins. The preferential binding of m6A-containing mRNA by YTHDF2 is known to reduce the stability of the target transcripts; however, the exact effects of m6A on translation has yet to be elucidated. Here we show that another m6A reader protein, YTHDF1, promotes ribosome loading of its target transcripts. YTHDF1 forms a complex with translation initiation factors to elevate the translation efficiency of its bound mRNA. In a unified mechanism of translation control through m6A, the YTHDF2-mediated decay controls the lifetime of target transcripts; whereas, the YTHDF1-based translation promotion increases the translation efficiency to ensure effective protein production from relatively short-lived transcripts that are marked by m6A. PAR-CLIP and RIP was used to identify YTHDF1 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF1 siRNA knock-down
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Project description:Whether the emergence of a nascent protein from the ribosome and the formation of structural elements are synchronized has been a longstanding question. Paradoxically, kinetically efficient translation can induce mis-folding and aggregation despite the presence of molecular chaperones, which in Escherichia coli are induced by unfolded protein via σ32. The molecular mechanisms mediating translation efficiency and protein folding efficiency remain poorly understood. Using ribosome profiling and protein quantitation, we show that synonymous changes to Firefly Luciferase (Luc) mRNA have a direct effect on its translation efficiency. These changes alone cause up to a 70-fold difference in Luc protein levels. However, increased Luc protein is met with at most a ~2-fold increase in chaperone levels, revealing that the σ32 transcriptional response has saturable properties. This response is found to be poised near its midpoint (where it is most sensitive to perturbation) when Luc mRNA has an intermediate translation efficiency. These results suggest not only that chaperone saturation limits the ability of cells to maintain protein folding homeostasis when challenged with highly efficient translation, but that translation efficiency and protein folding efficiency evolved for mutual sensitivity.
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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.
2021-10-28 | GSE156796 | GEO
Project description:The effect of PABPN1 on translation efficiency was assessed using RNA sequencing of polysomal fractions from muscle cells: parental vs. cells with stable PABPN1 down-regulation (shPAB). The library was constructed after rRNA depletion, allowing to investigate the abundance of different RNA biotypes.
2022-05-17 | GSE165609 | GEO
Project description:N6-methyladenosine (m6A) is the most abundant internal messenger (mRNA) modification in mammalian mRNA. This modification is reversible and non-stoichiometric, which potentially adds an additional layer of variety and dynamic control of mRNA metabolism. The m6A-modified mRNA can be selectively recognized by the YTH family “reader” proteins. The preferential binding of m6A-containing mRNA by YTHDF2 is known to reduce the stability of the target transcripts; however, the exact effects of m6A on translation has yet to be elucidated. Here we show that another m6A reader protein, YTHDF1, promotes ribosome loading of its target transcripts. YTHDF1 forms a complex with translation initiation factors to elevate the translation efficiency of its bound mRNA. In a unified mechanism of translation control through m6A, the YTHDF2-mediated decay controls the lifetime of target transcripts; whereas, the YTHDF1-based translation promotion increases the translation efficiency to ensure effective protein production from relatively short-lived transcripts that are marked by m6A.
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