Transcriptomic analysis of gene expression pathways influenced by toxic chemical exposure on the Caenorhabditis elegans cuticle.
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PROVIDER: PRJNA1282725 | ENA |
REPOSITORIES: ENA
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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.
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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.
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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.
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Project description:Effective toxicological testing of the vast number of new and existing chemicals currently in use will require efficient and cost effective methods. We evaluated the utility of a simple, low cost toxicity testing system employing the nematode Caenorhabditis elegans to identify toxicologically relevant changes in gene expression. The objective of this research is to determine genomic and proteomic responses in the model nematode C. elegans to exposures to representatives of several classes of toxic industrial chemicals/materials (TICs/TIMs). A total of 3 chemicals (acrylamide, cadmium chloride, and mercuric chloride) were used in these experiments. Affymetrix GeneChip for C. elegans was used to examine genome-wide responses in the 19,000+ genes of this model organism.
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