Pathway-Specific Canalization and Plasticity of Gene Expression during C. elegans Dauer Development
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ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE318477 | GEO | 2026/02/05
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE30977: C. elegans: Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms GSE31861: P. pacificus : Dauers and Dauer-Exit at 12 hour time-point vs. Mix-stage worms Refer to individual Series
2012-03-22 | E-GEOD-36644 | 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:Early environmental experiences and life histories profoundly influence adult phenotypes via as yet poorly understood mechanisms. We previously showed that wild-type adult C. elegans that transiently passed through the stress-induced dauer larval stage (post-dauers) exhibit different gene expression patterns, genome-wide chromatin structure, and life history traits when compared to adults that bypassed the dauer stage (controls). Here we show that endogenous small inhibitory RNAs (endo-siRNAs) and siRNA pathways may mediate developmental history-dependent phenotypic diversity. Deep sequencing of small RNA libraries show changes in endo-siRNA levels in post-dauer as compared to control animals, and meta analyses indicate that specific endo-siRNA pathways are targets of developmental history-dependent reprogramming. We demonstrate that mutations in specific endo-siRNA pathways affect the expected gene expression and chromatin state changes in post-dauer animals, and also disrupt their increased brood size phenotype. We find that the chromatin state and endo-siRNA distribution in dauers is also distinct and suggest that this remodeling in dauers provides a template for the subsequent establishment of adult post-dauer profiles. Together, our results imply a critical mechanistic role for endo-siRNA pathways in mediating early experience-dependent phenotypic divergence in adults, and suggest that regulation of these pathways contribute to increased fitness via non-genetic mechanisms.
2013-04-05 | GSE33313 | GEO
Project description:Early environmental experiences and life histories profoundly influence adult phenotypes via as yet poorly understood mechanisms. We previously showed that wild-type adult C. elegans that transiently passed through the stress-induced dauer larval stage (post-dauers) exhibit different gene expression patterns, genome-wide chromatin structure, and life history traits when compared to adults that bypassed the dauer stage (controls). Here we show that endogenous small inhibitory RNAs (endo-siRNAs) and siRNA pathways may mediate developmental history-dependent phenotypic diversity. Deep sequencing of small RNA libraries show changes in endo-siRNA levels in post-dauer as compared to control animals, and meta analyses indicate that specific endo-siRNA pathways are targets of developmental history-dependent reprogramming. We demonstrate that mutations in specific endo-siRNA pathways affect the expected gene expression and chromatin state changes in post-dauer animals, and also disrupt their increased brood size phenotype. We find that the chromatin state and endo-siRNA distribution in dauers is also distinct and suggest that this remodeling in dauers provides a template for the subsequent establishment of adult post-dauer profiles. Together, our results imply a critical mechanistic role for endo-siRNA pathways in mediating early experience-dependent phenotypic divergence in adults, and suggest that regulation of these pathways contribute to increased fitness via non-genetic mechanisms. We deep-sequenced small RNA libraries from 2 biological replicates each of control and postdauer adults, and one biological each of larval L3 and dauer stages.
2013-04-05 | E-GEOD-33313 | biostudies-arrayexpress
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:These are the 94 microarray experiments that are published in the paper: John Wang and Stuart K. Kim. Global analysis of dauer gene expression in Caenorhabditis elegans, Development 2003 130: 1621-1634. There are 94 individual microarray experiments divided into 3 broad experiments. The first experiment is a time course of dauer exit; each time course is labeled as "Dauer MTC#". The second experiment is a time course of L1 development after starvation arrest; each time couse is labeled "L1 MTC#". The final experiment is a comparison of pure dauers (0 hours) versus 12 hours after dauer exit and are labeled "Dauer Adjust". Every time course was repeated 4 times (#N)however for the dauer 4 and 7 hour time points there are only 3 replicates. For instance, all the time points labeled as "Dauer MTC#1" are from the same starting pool of dauer worms that were aliquoted into 10 fractions and analyzed at the time indicated. Every sample is compared to a common reference RNA that is used throughout all the hybridizations. In some cases there is a "-2" after the hour designation; this means the first hybridization failed for some technical reason and thus the second hybridization (same RNA) is reported. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-08-20 | GSE3169 | GEO
Project description:Transcriptional profiling of P. pacificus worms from (1) dauer stage, or (2) dauer-exit at 12 hours stage, compared to mix-stage worms as a common reference. The goal was to determine genes regulated during dauer development and recovery or exit from dauer stage. This data was then compared to data generated for corresponding developmental stages in the C. elegans (see NCBI GEO series GSE30977) , to study evolution of developmental pathways regulating dauer development. Two-condition experiments. Experiment 1 = Dauers vs. Mix-stage worms. 4 biological replicates for each condition, including 2 dye-swaps. Experiment 2 = Dauer-Exit at 12 hour time-point s vs. Mix-stage worms. 3 biological replicates for each condition, including 1 dye-swaps. Total samples from both experiments 1 and 2 = 7.
2011-09-02 | E-GEOD-31861 | biostudies-arrayexpress
Project description:These are the 94 microarray experiments that are published in the paper: John Wang and Stuart K. Kim. Global analysis of dauer gene expression in Caenorhabditis elegans, Development 2003 130: 1621-1634. There are 94 individual microarray experiments divided into 3 broad experiments. The first experiment is a time course of dauer exit; each time course is labeled as "Dauer MTC#". The second experiment is a time course of L1 development after starvation arrest; each time couse is labeled "L1 MTC#". The final experiment is a comparison of pure dauers (0 hours) versus 12 hours after dauer exit and are labeled "Dauer Adjust". Every time course was repeated 4 times (#N)however for the dauer 4 and 7 hour time points there are only 3 replicates. For instance, all the time points labeled as "Dauer MTC#1" are from the same starting pool of dauer worms that were aliquoted into 10 fractions and analyzed at the time indicated. Every sample is compared to a common reference RNA that is used throughout all the hybridizations. In some cases there is a "-2" after the hour designation; this means the first hybridization failed for some technical reason and thus the second hybridization (same RNA) is reported.
2005-07-13 | E-SMDB-1964 | biostudies-arrayexpress
Project description:Transcriptional profiling of C. elegans worms from (1) dauer stage, or (2) dauer-exit at 12 hours stage, compared to mix-stage worms as a common reference. The goal was to determine genes regulated during dauer development and recovery or exit from dauer stage. This data was then compared to data generated for corresponding developmental stages in the nematode Pristionchus pacificus (separate data-sets on a custom microarray platform designed by us and manufactured by Agilent) , to study evolution of developmental pathways regulating dauer development. Two-condition experiments. Experiment 1 = Dauers vs. Mix-stage worms. 4 biological replicates for each condition, including 2 dye-swaps. Experiment 2 = Dauer-Exit at 12 hour time-point s vs. Mix-stage worms. 4 biological replicates for each condition, including 2 dye-swaps. Total samples from both experiments 1 and 2 = 8.
2011-07-27 | E-GEOD-30977 | 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