Spatial discordances between mRNAs and proteins in the intestinal epithelium
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PROVIDER: PRJNA691886 | ENA |
REPOSITORIES: ENA
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Project description:We obtained a spatial measurement of RNA and Proteins in the small intestinal epithelium along the crypt-villus axis. We found that both were spatially heterogeneous, yet often spatially anti-correlated. We developed a Bayesian approach to infer protein translation and degradation rates from the combined spatial profiles, and demonstrate that space-independent protein-synthesis delays can explain the mRNA-protein discordances. Our work provides a proteomic spatial blueprint of the Intestinal epithelium and highlights the importance of protein measurements for inferring states of tissue cells that operate outside of steady state
2021-11-02 | PXD024906 | Pride
Project description:A cell’s proteome is an important determinant of its functional state, however the use of transcriptomes as reliable proxies for cellular proteomes is debatable. In the small intestine, nutrient absorbing enterocytes operate for four days as they migrate along villi, highly graded microenvironments. Spatial transcriptomics demonstrated profound zonation in enterocyte gene expression, but how this variability translates to protein content is unclear. Here, we used spatial sorting to generate global spatial maps of enterocyte proteins and mRNAs along the villus axis. We found that both were zonated, yet often spatially anti-correlated. We developed a Bayesian approach to infer protein translation and degradation rates from the combined spatial profiles, and demonstrate that space-independent protein-synthesis delays can explain the mRNA-protein discordances. Our work provides a proteomic spatial blueprint of the intestinal epithelium and highlights the importance of protein measurements for inferring states of tissue cells that operate outside of steady state.
2021-10-09 | GSE164746 | GEO
Project description:Healthy human and mouse colon epithelium is a major source of active thrombin, released in lumen. Using germ-free animals, we demonstrated that mucosal thrombin was directly regulated by the presence of commensal microbiota. Specific inhibition of lumenal thrombin activity caused macro-, microscopic damage and transcriptomic alterations of genes involved in host-microbiota interactions. Further, lumenal thrombin inhibition impaired the spatial segregation of microbiota biofilms, allowing bacteria to invade the mucus layer and to translocate across the epithelium. Thrombin proteolyzed the biofilm matrix of reconstituted mucosa-associated human microbiota. We demonstrated a previously unknown physiological role for epithelial thrombin that constrains biofilms at mucosal surfaces. We report that lung, bladder and skin epithelia also expressed thrombin, suggesting that this role may be applicable to other host-microbiome surfaces. Our discovery points route to new therapies targeting biofilms, important for a broad range of disorders, in the gut, and beyond.
2019-06-24 | PXD014315 | Pride
Project description:Interleukin-17 governs hypoxic adaptation of injured epithelium [spatial transcriptomics]
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Project description:Spatial organization of the transcriptome has emerged as a powerful means for regulating the post-transcriptional fate of RNA in eukaryotes; however, whether prokaryotes use RNA spatial organization as a mechanism for post-transcriptional regulation remains unclear. Here we used super-resolution microscopy to image the E. coli transcriptome and observed a genome-wide spatial organization of RNA: mRNAs encoding inner-membrane proteins are enriched at the membrane, whereas mRNAs encoding outer-membrane, cytoplasmic and periplasmic proteins are distributed throughout the cytoplasm. Membrane enrichment is caused by co-translational insertion of signal peptides recognized by the signal-recognition particle. Our time-resolved RNA-sequencing and live-cell super-resolution imaging experiments revealed a physiological consequence of this spatial organization and the underlying mechanism: membrane localization enhances degradation rates of inner-membrane-protein mRNAs by placing them in proximity to membrane-bound RNA degradation enzymes. Together, these results demonstrate that the bacterial transcriptome is spatially organized and that this organization shapes the posttranscriptional Spatial organization of the transcriptome has emerged as a powerful means for regulating the post-transcriptional fate of RNA in eukaryotes; however, whether prokaryotes use RNA spatial organization as a mechanism for post-transcriptional regulation remains unclear. Here we used super-resolution microscopy to image the E. coli transcriptome and observed a genome-wide spatial organization of RNA: mRNAs encoding inner-membrane proteins are enriched at the membrane, whereas mRNAs encoding outer-membrane, cytoplasmic and periplasmic proteins are distributed throughout the cytoplasm. Membrane enrichment is caused by co-translational insertion of signal peptides recognized by the signal-recognition particle. Our time-resolved RNA-sequencing and live-cell super-resolution imaging experiments revealed a physiological consequence of this spatial organization and the underlying mechanism: membrane localization enhances degradation rates of inner-membrane-protein mRNAs by placing them in proximity to membrane-bound RNA degradation enzymes. Together, these results demonstrate that the bacterial transcriptome is spatially organized and that this organization shapes the post-transcriptional dynamics of mRNAs.
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2019-11-12 | PXD013306 | Pride
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.
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Project description:Eukaryotic cells have to prevent the export of unspliced pre-mRNAs until intron removal is completed to avoid the expression of aberrant and potentially harmful proteins. Only mature RNAs associate with the export receptor Mex67 (mammalian TAP) and enter the cytoplasm. The underlying nuclear quality control mechanisms are still unclear. Here we show that two shuttling SR-proteins Gbp2 and Hrb1 are key surveillance factors for the selective export of spliced mRNAs in yeast. Their absence leads to the significant leakage of unspliced pre-mRNAs into the cytoplasm. They bind to pre-mRNAs and the spliceosome during splicing, where they are necessary for the surveillance of splicing and the stable binding of the TRAMP-complex to the spliceosome-bound transcripts. Faulty transcripts are marked for their degradation at the nuclear exosome. On correct mRNAs the SR-proteins recruit Mex67 upon completion of splicing to allow a quality controlled nuclear export. Altogether, these data identify a role for shuttling SR-proteins in mRNA surveillance and nuclear mRNA quality control. 6 samples, i.e. 2 replicates per protein Gbp2, Hrb1 and Npl3
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Project description:Spatial gene expression maps of the intestinal lymphoid follicle and associated epithelium identify zonated expression programs
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