Caenorhabditis elegans
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ABSTRACT:
PROVIDER: PRJNA95079 | ENA |
REPOSITORIES: ENA
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Project description:Under adverse environmental conditions, nematodes arrest into dauer, an alternative developmental stage for diapause. Dauers endure unfavorable environment and interact with host animals to access favorable environments, thus playing a critical role in the survival of both free-living and parasitic nematodes. Here, we discovered that in Caenorhabditis elegans, daf-42 is essential for development into dauer stage, as the null mutant shows lethal phenotype during dauer entry. To examine the transcriptional changes accompanied by the absence of DAF-42 during dauer entry, we performed RNA-sequencing on daf-2 and daf-2; daf-42 worms at 52 hours after egg laying (HAE) and 60 HAE, the time at which 0% and about 40% of daf-2; daf-42 mutants form dead dauer at 25 degrees Celcius, respectively. daf-2 control worms develop into dauer stage after 60 HAE, and half of its population develop into dauer by 72 HAE, when raised at 25 degrees Celcius.
2023-04-23 | GSE230353 | GEO
Project description:BACKGROUND: When resources are scant, C. elegans larvae arrest as long-lived dauers under the control of insulin/IGF- and TGFbeta-related signaling pathways. : We have identified genes that show different levels of expression in a comparison of wild-type L2 or L3 larvae (non-dauer) to TGFbeta mutants at similar developmental stages undergoing dauer formation. Many insulin/IGF pathway and other known dauer regulatory genes have changes in expression that suggest strong positive feedback by the TGFbeta pathway. In addition, many insulin-like ligand and novel genes with similarity to the extracellular domain of insulin/IGF receptors have altered expression. We have identified a large group of regulated genes with putative binding sites for the FOXO transcription factor, DAF-16. Genes with DAF-16 sites upstream of the transcription start site tend to be upregulated, whereas genes with DAF-16 sites downstream of the coding region tend to be downregulated. Finally, we also see strong regulation of many novel hedgehog- and patched-related genes, hormone biosynthetic genes, cell cycle genes, and other regulatory genes. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2006-02-02 | E-GEOD-4164 | biostudies-arrayexpress
Project description:BACKGROUND: When resources are scant, C. elegans larvae arrest as long-lived dauers under the control of insulin/IGF- and TGFbeta-related signaling pathways. RESULTS: We have identified genes that show different levels of expression in a comparison of wild-type L2 or L3 larvae (non-dauer) to TGFbeta mutants at similar developmental stages undergoing dauer formation. Many insulin/IGF pathway and other known dauer regulatory genes have changes in expression that suggest strong positive feedback by the TGFbeta pathway. In addition, many insulin-like ligand and novel genes with similarity to the extracellular domain of insulin/IGF receptors have altered expression. We have identified a large group of regulated genes with putative binding sites for the FOXO transcription factor, DAF-16. Genes with DAF-16 sites upstream of the transcription start site tend to be upregulated, whereas genes with DAF-16 sites downstream of the coding region tend to be downregulated. Finally, we also see strong regulation of many novel hedgehog- and patched-related genes, hormone biosynthetic genes, cell cycle genes, and other regulatory genes.
2006-01-06 | E-SMDB-3596 | biostudies-arrayexpress
Project description:Both plasticity and robustness are pervasive features of developmental programs. The dauer in Caenorhabditis elegans is an alternative to the third larval stage of the nematode and is an example of phenotypic plasticity. The dauer is an arrested, hypometabolic state that undergoes dramatic changes in gene expression compared to conspecifics that continue development, and can be induced by several adverse environments or genetic mutations that act as independent and parallel inputs into the larval developmental program. However, given the different genetic or environmental triggers that can induce dauer, gene expression in dauer larvae could be invariant or vary depending on the larvae’s route into dauer entry; this question has not been examined. Here we use RNA-sequencing to characterize gene expression in dauer larvae induced to arrest development in response to different stimuli. By assessing the variance in the expression levels of all genes and computing the Spearman's rank-order correlation of gene expression within several Gene Ontologies (GO) and gene networks, we find that the expression patterns of most genes, except for those that act in specific defense and metabolic pathways, are strongly correlated between the different dauer larvae, suggestive of transcriptional robustness. We speculate that the transcriptional robustness of core dauer pathways allows for the buffering of variation in the expression of genes involved in their response to the environment, allowing the different dauers to be better suited to survive in and exploit different niches.
2024-08-15 | GSE274872 | GEO
Project description:BACKGROUND: When resources are scant, C. elegans larvae arrest as long-lived dauers under the control of insulin/IGF- and TGFbeta-related signaling pathways. : We have identified genes that show different levels of expression in a comparison of wild-type L2 or L3 larvae (non-dauer) to TGFbeta mutants at similar developmental stages undergoing dauer formation. Many insulin/IGF pathway and other known dauer regulatory genes have changes in expression that suggest strong positive feedback by the TGFbeta pathway. In addition, many insulin-like ligand and novel genes with similarity to the extracellular domain of insulin/IGF receptors have altered expression. We have identified a large group of regulated genes with putative binding sites for the FOXO transcription factor, DAF-16. Genes with DAF-16 sites upstream of the transcription start site tend to be upregulated, whereas genes with DAF-16 sites downstream of the coding region tend to be downregulated. Finally, we also see strong regulation of many novel hedgehog- and patched-related genes, hormone biosynthetic genes, cell cycle genes, and other regulatory genes. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2006-02-03 | GSE4164 | GEO
Project description:There are two steps in the C. elegans decision to enter the dauer-diapause lifestage. The first is a choice between L2 and L2d and the second is between L3 and dauer. We studied the transcriptional changes when well-fed worms were given a cocktail of dauer-inducing ascarosides in the late L1 phase as opposed to worms that received no such treatment. This study was done in both N2 wild-type worms, and daf-22 worms, which lack an enzyme necessary to produce endogenous ascarosides.
2021-03-30 | GSE171089 | GEO
Project description:We applied a middle-down proteomics strategy for large scale protein analysis during in vivo development of Caenorhabditis elegans. We characterized post-translational modifications (PTMs) on histone H3 N-terminal tails at eight time points during the C. elegans lifecycle, including embryo, larval stages (L1 to L4), dauer and L1/L4 post dauer. Histones were analyzed by our optimized middle-down protein sequencing platform using high mass accuracy tandem mass spectrometry. This allows quantification of intact histone tails and detailed characterization of distinct histone tails carrying co-occurring PTMs. We measured temporally distinct combinatorial PTM profiles during C. elegans development. We show that the doubly modified form H3K23me3K27me3, which is rare or non-existent in mammals, is the most abundant PTM in all stages of C. elegans lifecycle. The abundance of H3K23me3 increased during development and it was mutually exclusive of the active marks H3K18ac, R26me1 and R40me1, suggesting a role for H3K23me3 in to silent chromatin. We observed distinct PTM profiles for normal L1 larvae and for L1-post dauer larvae, or L4 and L4 post-dauer, suggesting that histone PTMs mediate an epigenetic memory that is transmitted during dauer formation. Collectively, our data describe the dynamics of histone H3 combinatorial code during C. elegans lifecycle and demonstrate the feasibility of using middle-down proteomics to study in vivo development of multicellular organisms.
2015-11-02 | PXD002525 | Pride
Project description:Global analysis of dauer gene expression in Caenorhabditis elegans
| PRJNA92707 | ENA
Project description:C. elegans dauer recovery microbe interactions
| PRJNA622250 | ENA
Project description:Many organisms in the nature can drive themselves into an ametabolic state known as anhydrobiosis upon extreme desiccation. The nematode C. elegans is one of them. However, the anhydrobiotic ability of the worm is limited to a special developmental stage known as the dauer. Besides, the dauer larvae must be first treated by a mild desiccation stress (preconditioning) so that they gain desiccation tolerance. In this study, we investigated the differential gene expression during preconditioning in the C. elegans dauer.
2013-08-23 | E-MEXP-3899 | biostudies-arrayexpress