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Global mRNA polarization regulates translation efficiency in the intestinal epithelium [RNAseq of LCM subcellular tissue fragments]

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE95276 | GEO | 2017/08/10

SECONDARY ACCESSION(S): PRJNA376549

REPOSITORIES: GEO

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Global mRNA polarization regulates translation efficiency in the intestinal epithelium [Ribo-Seq]

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

Expression data from postnatal mouse apical and basal organ of Corti from Dicer1 conditional knockout and littermate control cochleae.

Project description:Cre recombinase-mediated conditional knockout of floxed Dicer1 alleles causes depletion of small RNAs including microRNAs, which function to repress target mRNA expression by inhibiting translation and/or stimulating mRNA degradation. We used microarrays to examine gene expression in apical versus basal organ of Corti from the cochleae of control and mutant mice in which Dicer1 was deleted and microRNAs were depleted specifically in sensory hair cells by Atoh1 promoter-driven Cre recombinase expression. Each biological replicate represents the combined apical or combined basal segments of organ of Corti from both cochleae of a single mouse. Two biological replicates for apical and basal organ of Corti from Dicer1 conditonal knockout and littermate controls were collected for RNA extraction and microarray analysis.

2012-01-01 | E-GEOD-26822 | biostudies-arrayexpress

Laser Capture Microdissection (LCM) followed by RNA-seq of apical and basal domains of follicle cells from stage 9-10B Drosophila egg chambers

Project description:Laser Capture Microdissection (LCM) followed by RNA-seq of apical and basal domains of follicle cells from stage 9-10B Drosophila egg chambers. The experiment is composed of 5 Apical and 5 Basal biological replicates. Each biological replicate consists of a pool of 10 LCM fragments. Each fragment consists of 5-10 adjacent cell domains microdissected from either the apical half or the basal half of the follicular epithelium.

2022-09-02 | E-MTAB-9127 | biostudies-arrayexpress

RNA localization is a key determinant of neurite-enriched proteome - RNAseq

Project description:RNA localization and local translation are important biological processes that underlie establishment of body axis, cell migration and synaptic plasticity. However, it is unclear to which extent mRNA localization contributes toward local proteome and how much of protein localization is achieved via protein transport or local translation of uniformly distributed mRNAs. To address this question, we performed genome-wide analysis of the local proteome, transcriptome, and translation rates in neurites and cell bodies of neurons differentiated from mouse embryonic stem cells.

2017-07-23 | E-MTAB-4978 | biostudies-arrayexpress

RNA localization is a key determinant of neurite-enriched proteome - Riboseq

2017-07-23 | E-MTAB-4979 | biostudies-arrayexpress

Ribosome footprinting in the cytosol and endoplasmic reticulum

Project description:In eukaryotic cells, the spatial regulation of protein expression is frequently conferred through the coupling of mRNA localization and the local control of translation. mRNA localization to the endoplasmic reticulum (ER) is a prominent example of such regulation and serves a ubiquitous role in segregating the synthesis of secretory and integral membrane proteins to the ER. Recent genomic and biochemical studies have now expanded this view to suggest a role for the ER in global protein synthesis. We have utilized cell fractionation and ribosome profiling to obtain a genomic survey of the subcellular organization of mRNA translation and report that ribosomal loading of mRNAs, a proxy for mRNA translation, is biased to the ER. Notably, ER-associated mRNAs encoding both cytosolic and topogenic signal-encoding proteins display similar ribosome loading densities, suggesting that ER-associated ribosomes serve a global role in mRNA translation. We propose that the partitioning of mRNAs and their translation between the cytosol and ER compartments may represent a novel mechanism for the post-transcriptional regulation of gene expression. HEK293 cells were fractionated between the cytosol and endoplasmic reticulum. Within each fraction, ribosome footprints were generated and sequenced. In parallel, total mRNA was sequenced.

2011-12-20 | E-GEOD-31539 | biostudies-arrayexpress

Ribosome profiling upon glucose starvation in S. cerevisiae

Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions. Examination of mRNA translation in S. cerevisiae upon glucose starvation.

2014-07-28 | E-GEOD-56622 | biostudies-arrayexpress

Genome-wide profiling of somato-dendritic mRNA distribution in the hippocampus in RNG105/caprin1 conditional knockout (cKO) mice

Project description:Background: mRNA localization and translation in neuronal dendrites are the basis for long-term synaptic plasticity and memory formation. RNA granules, membrane-less macromolecular assemblies in which dendritic mRNAs are recruited, are thought to contribute to these processes. RNG105/caprin1 is an RNA granule assembly factor involved in mRNA transport. Results: Genome-wide profiling of mRNA distribution in distinct hippocampal layers revealed dendritically and somatically enriched mRNAs, and demonstrated marked reduction in the differential somato-dendritic localization of the mRNAs in RNG105 cKO mice. Conclusion: RNG105 is an essential factor for the localization of many, but particularly for specific mRNAs localized to dendrites.

2017-11-24 | GSE96552 | GEO

Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience

Project description:The subcellular localization and translation of messenger RNA (mRNA) supports functional differentiation between cellular compartments. In neuronal dendrites, local translation of mRNA provides a rapid and specific mechanism for synaptic plasticity and memory formation, and might be involved in the pathophysiology of certain brain disorders. Despite the importance of dendritic mRNA translation, little is known about which mRNAs can be translated in dendrites in vivo and when their translation occurs. Here we collect ribosome-bound mRNA from the dendrites of CA1 pyramidal neurons in the adult mouse hippocampus. We find that dendritic mRNA rapidly associates with ribosomes following a novel experience consisting of a contextual fear conditioning trial. High throughput RNA sequencing followed by machine learning classification reveals an unexpected breadth of ribosome-bound dendritic mRNAs, including mRNAs expected to be entirely somatic. Our findings are in agreement with a mechanism of synaptic plasticity that engages the acute local translation of functionally diverse dendritic mRNAs. RNA-Seq of ribosome-bound mRNA immunoprecipitated from dendrites and soma of CA1 pyramidal neurons in the mouse hippocampus

2014-07-30 | E-GEOD-58343 | biostudies-arrayexpress

Transcription profiling of Arabidopsis eif3h mutants vs. wild type

Project description:Microarray comparisons of transcript level in wild-type Arabidopsis and eif3h mutant plants. Goal:; To detect any change in transcript level between WT and eif3h mutant. BACKGROUND: The eukaryotic translation initiation factor eIF3 has multiple roles during the initiation of translation of cytoplasmic mRNAs. However, the contributions of individual subunits of eIF3 to the translation of specific mRNAs remain poorly understood. RESULTS: Working with stable reporter transgenes in Arabidopsis thaliana it was demonstrated that the h subunit of; eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5â leader sequence. uORFs, which can function as devices for translational regulation, are present in over 30% of Arabidopsis mRNAs, and are enriched among mRNAs for transcriptional regulators and protein modifying enzymes. Microarray comparisons of polysome loading in wild-type and eif3h mutant plants revealed that eIF3h generally helps to maintain efficient polysome loading of mRNAs harboring multiple uORFs. Independently, eIF3h also boosted polysome loading of mRNAs with long coding sequences. Moreover, the lesion in eIF3h revealed a concerted upregulation of translation for specific functional subgroups of mRNAs, including ribosomal proteins and proteins involved in photosynthesis. CONCLUSIONS: The intact eIF3h protein contributes to efficient translation initiation on 5â leader sequences harboring multiple uORFs, although mRNA features independent of uORFs were also implicated. Moreover, our data suggest that regulons of translational control can be revealed by mutations in generic translation initiation factors. Experiment Overall Design: Total RNA samples were isolated from 10-day-old wild-type and eif3h mutant plants

2008-06-14 | E-GEOD-6025 | biostudies-arrayexpress

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