Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1098345 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28604180_1.fastq.gz | Fastqsanger.gz | |||
| SRR28604180_2.fastq.gz | Fastqsanger.gz | |||
| SRR28604181_1.fastq.gz | Fastqsanger.gz | |||
| SRR28604181_2.fastq.gz | Fastqsanger.gz | |||
| SRR28604182_1.fastq.gz | Fastqsanger.gz |
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Project description:A long-lived species of zooplankton microcrustaceans, Daphnia magna, sometimes exhibits late-life rebound of reproduction, briefly reversing reproductive senescence. Such events are often interpreted as terminal investment in anticipation of imminent mortality. We demonstrate that such post-senescence reproductive events (PSREs) neither cause not anticipate increased mortality. We analyze an RNAseq experiment comparing young, old reproductively senescent, and old PSRE Daphnia females. We first show that overall age-related transcriptional changes are dominated by the increase transcription of guanidine monophosphate synthases and guanylate cyclases, as well as two groups of presumed transposon-encoded proteins and by a drop in transcription of protein synthesis-related genes. We then focus on gene families and functional groups in which full or partial reversal of age-related transcriptional changes occur. This analysis reveals reversal, in the PSRE individuals, of age-related up-regulation of apolipoproteins D, lysosomal lipases, and peptidases and of age-related down-regulation of E3 ubiquitin kinases, V-type proton ATPases, and numerous proteins related to mitochondrial and muscle functions. While it is certain which of these changes enable reproductive rejuvenation, and which are by-products of processes that lead to it, we present some evidence that post-senescence reproductive events are associated with the reversal of age-related protein and lipid aggregates removal, apoptosis, and with restoration of mitochondrial integrity.
2025-04-11 | GSE263788 | GEO
Project description:Age- and reproductive rejuvanation-related single-nuclei transcriptomics of Daphnia magna
| PRJNA1222346 | ENA
Project description:Reproductive aging in females is characterized by the irreversible depletion of ovarian follicles, yet the structure and function of the post-reproductive ovary remain poorly defined. Using paired histological and bulk transcriptomic analyses of ovaries from reproductively young (2 m), reproductively old (18 m), and post-reproductive (24 m) mice, we mapped how ovarian identity evolves beyond follicle exhaustion. As expected, follicle loss, stromal remodeling, and increased collagen deposition were observed in the reproductively old and post-reproductive cohorts. Transcriptomic analyses revealed a shift from reproductive functionality to an immune-dominant signature with age. Correspondingly, post-reproductive ovaries exhibited increased infiltration of T cells, macrophages, and multinucleated giant cells. Although old and post-reproductive ovaries diverged substantially from young ovaries, they also showed discrete transcriptomic differences, indicating that the ovary continues to undergo molecular changes after reproductive senescence. Lastly, age-dependent changes in ovarian factors that are predicted to be secreted suggest that the post-reproductive ovary may be a source of pro-inflammatory signaling mediators with the potential to modulate extra-ovarian tissues. These findings challenge the assumption that the post-reproductive ovary is inert, instead indicating that it acquires an immune identity with potential endocrine and paracrine influence on whole-body aging.
2026-03-17 | GSE310764 | GEO
Project description:Hormesis is a dose response phenomenon characterized by a stimulation of an organismal response at low doses of a chemical and inhibition of the response (toxicity) at a higher dose. In the present study, Daphnia magna were exposed to the energetic compound 2,4,6-trinitrotoluene (TNT) for 21 days, and the endpoints survival, growth (length and dry weight), and reproduction (number of neonates per survivor) were assesed, identifying hormetic responses at the lower treatment levels. In order to elucidate the mechanisms leading to hormesis, microarray analysis was performed at 0.004 (hormetic), 0.12 (sometimes hormetic), and 1.85 (toxic) mg/L TNT. Functional and transcriptional benchmark dose analyses performed on differentially expressed genes suggested the involvement of lipid metabolism in hormetic responses and subsequently lipidomic analysis was performed on the same treatments. Lipid analysis supported the hypothesis that TNT exposure affected lipid metabolism, and showed that hormetic effects could be related to increases in some polyunsaturated fatty acids and ecosanoids known to be involved in Daphnia growth and reproduction.
2013-02-01 | GSE43960 | GEO
Project description:Background: In the life history of Daphnia, the reproductive mode of parthenogenesis and sexual reproduction alternate in aquatic ecosystem, which are often affected by environmental and genetic factor. Although several functional genes on reproductive transition of Daphnia had been determined, molecular mechanism on the reproductive mode of Daphnia are still not known well, including differentially expressed genes in different developmental stages. Results: In this study, four developmental stages, juvenile female (JF), parthenogenetic female (PF), sexual female (SF) and male (M), of D. similoides sinensis were performed for transcriptome sequence, and candidate genes related to male sex determination were screened. A total of 110437 transcripts were obtained and assembled into 22996 unigenes. In the four developmental stages (JF, PF, SF and M), the number of unique unigenes is respectively 2863, 445, 437 and 586, and the number of common unigenes is 9708. The differentially expressed genes (DEGs) between male and other three female stages (M vs JF, M vs PF and M vs SF) were obtained. The GO gene enrichment analysis showed that the up-regulated genes in male were mainly enriched in hydrolase activity and peptidase activity. Thirty-six candidate genes related to male sex determination in male were significantly higher expression than those in the other three stages, including one Doublesex (Dsx) gene, one laminin gene, five trypsin genes and one serine protease genes, and one chitin synthase gene and two chitinase genes. In addition, in D. similoides sinensis male, the relative expression levels of two genes (Dsx1, antp) related to male sex determination observed in other Daphnia species were also significantly higher than those in other developmental stages. Conclusions: Our results showed that thirty-six candidate genes may involve in sex differetiation of D. similoides sinensis male, and it will provide a reference for further exploring the functional genes related to sex determination mechanism in Daphnia species. Moreover, according to previous investigations, we thought that the expression level of functional genes may be related to the development stage of organisms, and may be also affected by different Daphnia species.
2022-08-17 | GSE197943 | GEO
Project description:The self-renewal capacity of intestinal stem cells (ISCs) declines with aging, leading to a loss of homeostasis and an increased susceptibility to intestinal diseases. Despite the established significance of lipid metabolism and epigenetic regulation in ISC function, the molecular mechanisms that connect these processes to aging-related ISC dysfunction remain elusive. Here, we demonstrate that Histone 3 lysine 36 trimethylation (H3K36me3) caused by SETD2 is critical for ISC stemness. We found that H3K36me3 deficiency results in reduced ISC proliferation and differentiation, disrupts fatty acid oxidation (FAO) metabolism, and induces ISC senescence. Mechanistically, the loss of H3K36me3 triggers the activity of the SWI/SNF chromatin remodeling complex and leads to increased chromatin accessibility and enhancer activation, which alters FAO- and senescence-related gene expression. Importantly, we discover that metabolic intervention can prevent the senescence of ISC due to H3K36me3 deficiency. Our findings reveal a crucial role for H3K36me3 in maintaining the epigenetic landscape that orchestrates FAO metabolism and determines intestinal stem cell functions, emphasizing the role of FAO as a key modulator between H3K36me3 and ISC aging, suggesting that metabolic intervention may help mitigate age-related ISC dysfunction.
2026-03-25 | GSE292018 | GEO
Project description:The self-renewal capacity of intestinal stem cells (ISCs) declines with aging, leading to a loss of homeostasis and an increased susceptibility to intestinal diseases. Despite the established significance of lipid metabolism and epigenetic regulation in ISC function, the molecular mechanisms that connect these processes to aging-related ISC dysfunction remain elusive. Here, we demonstrate that Histone 3 lysine 36 trimethylation (H3K36me3) caused by SETD2 is critical for ISC stemness. We found that H3K36me3 deficiency results in reduced ISC proliferation and differentiation, disrupts fatty acid oxidation (FAO) metabolism, and induces ISC senescence. Mechanistically, the loss of H3K36me3 triggers the activity of the SWI/SNF chromatin remodeling complex and leads to increased chromatin accessibility and enhancer activation, which alters FAO- and senescence-related gene expression. Importantly, we discover that metabolic intervention can prevent the senescence of ISC due to H3K36me3 deficiency. Our findings reveal a crucial role for H3K36me3 in maintaining the epigenetic landscape that orchestrates FAO metabolism and determines intestinal stem cell functions, emphasizing the role of FAO as a key modulator between H3K36me3 and ISC aging, suggesting that metabolic intervention may help mitigate age-related ISC dysfunction.
2026-03-25 | GSE292016 | GEO
Project description:The self-renewal capacity of intestinal stem cells (ISCs) declines with aging, leading to a loss of homeostasis and an increased susceptibility to intestinal diseases. Despite the established significance of lipid metabolism and epigenetic regulation in ISC function, the molecular mechanisms that connect these processes to aging-related ISC dysfunction remain elusive. Here, we demonstrate that Histone 3 lysine 36 trimethylation (H3K36me3) caused by SETD2 is critical for ISC stemness. We found that H3K36me3 deficiency results in reduced ISC proliferation and differentiation, disrupts fatty acid oxidation (FAO) metabolism, and induces ISC senescence. Mechanistically, the loss of H3K36me3 triggers the activity of the SWI/SNF chromatin remodeling complex and leads to increased chromatin accessibility and enhancer activation, which alters FAO- and senescence-related gene expression. Importantly, we discover that metabolic intervention can prevent the senescence of ISC due to H3K36me3 deficiency. Our findings reveal a crucial role for H3K36me3 in maintaining the epigenetic landscape that orchestrates FAO metabolism and determines intestinal stem cell functions, emphasizing the role of FAO as a key modulator between H3K36me3 and ISC aging, suggesting that metabolic intervention may help mitigate age-related ISC dysfunction.
2026-03-25 | GSE292017 | GEO
Project description:The self-renewal capacity of intestinal stem cells (ISCs) declines with aging, leading to a loss of homeostasis and an increased susceptibility to intestinal diseases. Despite the established significance of lipid metabolism and epigenetic regulation in ISC function, the molecular mechanisms that connect these processes to aging-related ISC dysfunction remain elusive. Here, we demonstrate that Histone 3 lysine 36 trimethylation (H3K36me3) caused by SETD2 is critical for ISC stemness. We found that H3K36me3 deficiency results in reduced ISC proliferation and differentiation, disrupts fatty acid oxidation (FAO) metabolism, and induces ISC senescence. Mechanistically, the loss of H3K36me3 triggers the activity of the SWI/SNF chromatin remodeling complex and leads to increased chromatin accessibility and enhancer activation, which alters FAO- and senescence-related gene expression. Importantly, we discover that metabolic intervention can prevent the senescence of ISC due to H3K36me3 deficiency. Our findings reveal a crucial role for H3K36me3 in maintaining the epigenetic landscape that orchestrates FAO metabolism and determines intestinal stem cell functions, emphasizing the role of FAO as a key modulator between H3K36me3 and ISC aging, suggesting that metabolic intervention may help mitigate age-related ISC dysfunction.
2026-03-25 | GSE292892 | GEO
Project description:Current worldwide demographics came to the point of the prevalence of people of middle age when the majority of age-related disease start to occur. The existing strategies (dietary and pharmacological interventions) are mostly tested or include treatment starting from young age to promote healthy aging and do not consider altered metabolism, and mitochondrial malfunction at late life onset. With age, mitochondria are characterized by its compromised ability to maintain tubular integral mitochondrial network in cells and to provide essential level of metabolites, altogether leading to an emergence of age-associated diseases. Therefore finding the solution for improved plasticity of mitochondria during aging is fundament and of high importance. In this work, I searched for molecular adaptations that counteract mitochondrial defects systemically during aging using Caenorhabditis elegans as a genetic model system. With this purpose, I addressed paradox worms, clk-1(qm30) and isp-1(qm150), which were discovered by S. Hekimi group as the first long-lived organisms with hypomorphic mutations in electron transport chain of mitochondria. Using longitudinal and comparative whole proteome analysis, I observed age-associated decline of SAMS-1, an enzyme converting methionine into S-adenosyl methionine (SAM) within one-carbon metabolism pathway in the cell. Remarkably, both long-lived mitochondrial mutants express an elevated level of SAMS-1 compared to wild type during aging. Moreover, sams-1 RNAi-mediated knockdown (sams-1 KD) abrogated the extended longevity of mitochondrial mutants, but not wild type animals. I uncovered, that sams-1 KD promotes mitochondrial fragmentation and HSP-6 promoter expression, a marker of mitochondrial unfolded stress response, mtUPR, at young age. I showed that lifetime SAM supplementation restored a fraction of tubular mitochondria in sams-1 KD worms at post-reproductive age. I discovered, that SAM regulates mitochondrial morphology and mtUPR through the PMT-1-mediated pathway for synthesis of phosphatidylcholine, one of key lipid components of cellular membranes. Altogether, I deciphered, that SAMS-1 is a molecular switch controlling mitochondrial homeostasis during aging, and its enzymatic end-product SAM represents a promising natural intervention for a balanced mitochondrial plasticity at post-reproductive age. The future follow up study will show if SAM supplementation can improve mitochondrial function at old age and extend lifespan.
2026-02-23 | PXD024180 | Pride