Caenorhabditis elegans
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ABSTRACT:
PROVIDER: PRJNA149307 | ENA |
REPOSITORIES: ENA
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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: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:We show that C. elegans adults that passed through the stress-resistant dauer stage due to starvation exhibit opposite transcriptional profiles compared to adults that entered dauer due to crowding, and are distinct from animals that bypassed dauer. These “seesaw” trends in gene expression extend to a majority of genes in the genome and, based upon the direction of change, are enriched on different chromosomes.
2017-12-27 | GSE92954 | GEO
Project description:Expression data from C. elegans during L3 and L3-lethargus
| PRJNA198533 | ENA
Project description:Developmental experiences play critical roles in shaping adult physiology and behavior. We and others previously showed that adult C. elegans which transiently experienced dauer arrest during development (PD: post-dauer) exhibit distinct gene expression profiles as compared to control adults which bypassed the dauer stage. In particular, the expression patterns of subsets of chemoreceptor genes are markedly altered in PD adults. Whether altered chemoreceptor levels drive plasticity in chemosensory behaviors in PD adults is unknown. Via transcriptional profiling of sorted populations of AWA neurons from control and PD adults, we further show that the expression of a subset of chemoreceptor genes in AWA are differentially regulated in PD animals. Our results suggest that developmental experiences may be encoded at the level of olfactory receptor regulation, and provide an elegant mechanism by which C. elegans is able to precisely modulate its behavioral preferences as a function of its current and past experiences.
2022-09-07 | E-MTAB-11823 | biostudies-arrayexpress
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: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
Project description:Global analysis of dauer gene expression in Caenorhabditis elegans
| PRJNA92707 | ENA
Project description:we used short-reads to perform a comparative analysis S. carpocapsae ALL strain IJs and young adults and C.elegans dauer strain N2 and young adult strain him-8.
2020-08-18 | GSE156356 | GEO
Project description:C. elegans dauer recovery microbe interactions
| PRJNA622250 | ENA