Translational profiling reveals that mRNAs encoding cuticle collagens are translationally repressed upon nsun-1 knockdown
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ABSTRACT:
PROVIDER: PRJNA601121 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10895122.fastq.gz | Fastqsanger.gz | |||
| SRR10895123.fastq.gz | Fastqsanger.gz | |||
| SRR10895124.fastq.gz | Fastqsanger.gz | |||
| SRR10895125.fastq.gz | Fastqsanger.gz | |||
| SRR10895126.fastq.gz | Fastqsanger.gz |
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Project description:By comparing mRNAs contained in the polysome fraction to total mRNAs in Caenorhabditis elegans exposed to either RNAi control or nsun-1 RNAi, we found that loss of NSUN-1 translationally represses genes associated with collagens, cuticle integrity and development. These changes explain phenotypes of nsun-1 depletion, which include impaired fecundity, gonad extrusion and reduced barrier function.
2020-12-09 | GSE143618 | GEO
Project description:The cuticles of arthropods, including aquatic crustaceans like Daphnia, provide an interface between the organism and its environment. Thus, the cuticle’s structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the molted cuticle of Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology, anddetected 278 high confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin modifying enzymes as most abundant protein groups in the cuticle proteome.Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle . Finally, cuticle protein genes were clustered as tandem gene arrays in the Daphnia genome, indicating their importance for adaptation to environmental change. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
2024-09-02 | PXD040228 | Pride
Project description:The cuticles of arthropods, including aquatic crustaceans like Daphnia, provide an interface between the organism and its environment. Thus, the cuticle’s structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the molted cuticle of Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology, anddetected 278 high confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin modifying enzymes as most abundant protein groups in the cuticle proteome.Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle . Finally, cuticle protein genes were clustered as tandem gene arrays in the Daphnia genome, indicating their importance for adaptation to environmental change. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
2024-09-02 | PXD040304 | Pride
Project description:Important remodeling of the extracellular matrix is a hallmark of corneal wound healing. Besides the massive secretion of fibronectin (FN) that characterizes the early step of that process, alterations in the secretion of collagens also occurs as part of this wound healingresponse. In this study, we examined whether expression of the gene encoding the M-NM-15 subunit from the FN binding integrin M-NM-15M-NM-21 changes as corneal epithelial cells (CECs) are cultured in the presence of collagens. Responsiveness of the M-NM-15 gene toward collagen was determined by transfection of recombinant plasmids bearing the CAT reporter gene under the control of various segments from the human M-NM-15 promoter into primary cultured rabbit (RCECs) and human (HCECs) CECs cultured on BSA or on collagens. Electrophoretic mobility shift assays (EMSAs) and Western blot analyses were used to monitor both the DNA binding and expression of the transcription factors required to ensure basal transcription of the M-NM-15 gene. The influence collagens on the patterns of genes expressed by HCECs was also studied be gene profiling on microarrays. All collagen types repressed the transcriptional activity directed by the full-length M-NM-15 promoter/CAT construct in confluent CECs. A moderate increase in M-NM-15 promoter activity was observed in subconfluent RCECs grown on CIV but not on CI. These collagen-dependent regulatory influences also correlated with alterations in either the expression or the DNA binding of the transcription factors Sp1/Sp3, NFI and AP-1 that ensure basal transcription of the M-NM-15 gene. Gene profiling on microarray revealed that CI more profoundly alter the pattern of genes expressed by HCECs than what is observed with CIV. Collagens considerably suppressed expression of the M-NM-15 gene in CECs at confluence suggesting that the sustained staining for CI and CIV after corneal injury may play a role in controlling adhesion to the temporary FN matrix and further differentiation of CECs into suprabasal epithelial cells through a mechanism involving the M-NM-15M-NM-21 integrin. Primary cultures of human corneal epithelial cells cultivated on BSA (number of replicates: 2), Collagen type I (number of replicates: 2) and Collagen type IV (number of replicates: 2) matrix.
2015-01-30 | E-GEOD-65421 | biostudies-arrayexpress
Project description:To investigate the function of small RNAs in cuticle biosynthesis in B. napus, we constructed four small RNA libraries from stem epidermis of wax-deficient and wild-type materials for sequencing. Subsequently, a total of 43,840,451 clean reads were generated and 24nt sequences represented the dominant percentage. Totally, 300 unique conserved miRNAs were identified and 8 of them showed differentially expressed. In addition, the expression of six novel miRNAs were also changed. After target prediction and function annotation, three miRNAs (aly-miR165a-5p, aly-miR408-5p, and novel-mir2) might influence cuticle morphogenesis not only by repressing the biosynthesis of cuticular substrates and components, but also blocking the transmembrane transport processes. The expression level of aly-miR408-5p and aly-miR165a-5p were increased in glossy materials examined by stem-loop qRT-PCR, while their predicted target genes (BnaC04g29170D, BnaA01g25630D, BnaA06g40560D) were down-regulated. These results suggested that miRNAs might influence cuticle biosynthesis by repressing cuticle-related genes expression in B. napus. Both the biosynthesis and secretion processes of cuticlular components might be influenced by miRNAs. These results will promote the study of post-transcriptional regulation mechanisms of cuticle biosynthesis in B. napus and provide new direction for further research.
2018-11-30 | GSE115073 | GEO
Project description:The regulation of translation is crucial for cells to rapidly adapt to changing conditions. Although the transcriptional changes under inflammatory conditions are intensely studied, not much is known about translational changes. Therefore, this study aimed at identifying translationally deregulated targets in inflammatory settings.
2012-08-01 | GSE35022 | GEO
Project description:Here, we propose that the cuticle of the nematode Caenorhabditis elegans (C. elegans) can be used as a model for human skin to test potentially toxic compounds, in particular, those commonly used in skincare and household products. We examined the effect of toxic chemicals on cuticle morphology and mechanical behavior using atomic force microscopy (AFM) and our findings revealed that two parameters, surface roughness and elastic modulus, are good markers for quantifying cuticle damage caused by chemicals. The damage caused by the chemicals correlated to their toxicity, as expressed in terms of maximum concentration allowed by EU regulations for use in skincare and household products. Transcriptomic analysis showed us that each chemical elicited a specific response in terms of differential gene expression, suggesting the lack of a general response to chemical exposure from the worms in this study. It also showed that a large number of genes involved in the synthesis of cuticle proteins, as well as in metabolism and enzyme activity, were affected by chemical exposure. The number of genes with altered expression levels correlated with chemical toxicity, as well as with level of morphological and mechanical changes in the cuticle. The analysis of affected genes provides a pathway to understand the molecular mechanisms of toxic chemical action. Overall, we show that the cuticle of C. elegans is a good model for human skin for toxicological screening, and this approach will be of particular interest to the cosmetics and household chemical industries.
2025-07-01 | GSE300950 | GEO
Project description:The brown planthopper (BPH, Nilaparvata lugens) is the most destructive pest of rice and causes serious economic damage in Asia. Understanding the composition of Nilaparvata lugens cuticle protein will help pest control. In this study, Nilaparvata lugens cuticle was disserted, and underwent shotgun MS/MS analysis.
2022-12-12 | PXD036431 | Pride
Project description:Important remodeling of the extracellular matrix is a hallmark of corneal wound healing. Besides the massive secretion of fibronectin (FN) that characterizes the early step of that process, alterations in the secretion of collagens also occurs as part of this wound healingresponse. In this study, we examined whether expression of the gene encoding the α5 subunit from the FN binding integrin α5β1 changes as corneal epithelial cells (CECs) are cultured in the presence of collagens. Responsiveness of the α5 gene toward collagen was determined by transfection of recombinant plasmids bearing the CAT reporter gene under the control of various segments from the human α5 promoter into primary cultured rabbit (RCECs) and human (HCECs) CECs cultured on BSA or on collagens. Electrophoretic mobility shift assays (EMSAs) and Western blot analyses were used to monitor both the DNA binding and expression of the transcription factors required to ensure basal transcription of the α5 gene. The influence collagens on the patterns of genes expressed by HCECs was also studied be gene profiling on microarrays. All collagen types repressed the transcriptional activity directed by the full-length α5 promoter/CAT construct in confluent CECs. A moderate increase in α5 promoter activity was observed in subconfluent RCECs grown on CIV but not on CI. These collagen-dependent regulatory influences also correlated with alterations in either the expression or the DNA binding of the transcription factors Sp1/Sp3, NFI and AP-1 that ensure basal transcription of the α5 gene. Gene profiling on microarray revealed that CI more profoundly alter the pattern of genes expressed by HCECs than what is observed with CIV. Collagens considerably suppressed expression of the α5 gene in CECs at confluence suggesting that the sustained staining for CI and CIV after corneal injury may play a role in controlling adhesion to the temporary FN matrix and further differentiation of CECs into suprabasal epithelial cells through a mechanism involving the α5β1 integrin.
2015-01-30 | GSE65421 | GEO
Project description:Cellular responsiveness to environment, including changes in extracellular matrix (ECM), is critical for normal processes such as development and wound healing, but can go awry, as in oncogenesis and fibrosis. One type of molecular pathway contributing to this responsiveness is the BMP signaling pathway. Owing to their broad and potent functions, BMPs and their pathways are regulated at multiple levels. In Caenorhabditis elegans, the BMP ligand DBL-1 is a regulator of body size. We previously showed that DBL-1/BMP signaling determines body size through transcriptional regulation of cuticle collagen genes. We now identify feedback regulation of DBL-1/BMP through analysis of four DBL-1-regulated collagen genes. Inactivation of any of these genes reduces DBL-1/BMP signaling, measured by a pathway activity reporter. Furthermore, depletion of these collagens reduces GFP::DBL-1 fluorescence and acts unexpectedly at the level of dbl-1 transcription. We conclude that cuticle, a specialized ECM, impinges on DBL-1/BMP expression and signaling. Interestingly, the feedback regulation of DBL-1/BMP signaling by collagens is likely to be contact independent due to physical separation of the cuticle from DBL-1-expressing cells in the ventral nerve cord. Our results provide an entry point into a novel regulatory mechanism for BMP signaling, with broader implications for mechanical regulation of gene expression.
| S-EPMC7185965 | biostudies-literature