Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1214429 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32095900.fastq.gz | Fastqsanger.gz | |||
| SRR32096000.fastq.gz | Fastqsanger.gz | |||
| SRR32096100.fastq.gz | Fastqsanger.gz | |||
| SRR32096200.fastq.gz | Fastqsanger.gz | |||
| SRR32095901.fastq.gz | Fastqsanger.gz |
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Project description:Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.
2021-09-07 | GSE153049 | GEO
Project description:Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.
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Project description:Stimulating brown adipose tissue (BAT) energy expenditure could be a therapy for obesity and related metabolic diseases. Achieving this requires a systems-level understanding of the biochemical underpinnings of thermogenesis. To identify novel metabolic features of active BAT, we measured protein abundance, protein acetylation, and metabolite levels in BAT isolated from mice living in their thermoneutral zone or in colder environments. We find that the enzymes which synthesize lipids from cytosolic acetyl-coA are among the most robustly increased proteins after cold acclimation, consistent with recent studies highlighting the importance of anabolic de novo lipogenesis in BAT. In addition, many mitochondrial proteins are hyperacetylated by cold acclimation, including several sites on UCP1, which may have functional relevance. Metabolomics analysis further reveals cold-dependent increases to acetylated carnitine and several amino acids. This BAT multi-omics resource highlights widespread proteomic and metabolic changes linked to acetyl-coA synthesis and utilization that may be useful in unraveling the remarkable metabolic properties of active BAT.
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Project description:Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. In parallel, we performed RNA Seq as a read out of gene expression. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.
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Project description:Many studies have shown that space environments can affect bacteria to varying degrees and cause a range of mutations. However, so far, there have been no relevant studies on the effects of long-term space flight (>1 month) on bacteria and the effects of different space residence time on bacteria. Therefore, we utilized the Staphylococcus warneri isolated from the Shenzhou-10 spacecraft that had experienced a space flight to carry into space again, in order to study the influence of the long flight formed by two space flights on the proteomic level.
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Project description:In this pioneering study, we present the first comprehensive catalog of 683 small non-coding miRNAs for Astyanax mexicanus. Focusing on an early developmental stage, miRNAs were extracted and sequenced from 24hpf embryos of surface fish and three distinct cavefish morphs (Pachón, Tinaja, and Molino). We utilized in silico analyses to predict putative 3’UTR targets of these miRNAs, revealing a unique and extensive miRNA landscape in cavefish. Small RNA sequencing identified over 100 differentially expressed miRNAs in each cave morph compared to surface fish at 24hpf, suggesting early activation of miRNA-mediated silencing pathways. Notably, a subset of miRNAs was common across all three cave morphs, constituting cave-specific miRNAs potentially instrumental in cave adaptation. To unravel the functional implications of these cave-specific miRNAs, we analyzed their predicted target genes. Gene Ontology (GO) term analysis unveiled pathways which align with known adaptations in cavefish, primarily affecting development and metabolism. Further, cross-validating with a sample mRNAseq data from Pachón and surface fish also strongly suggested impact of these miRNAs on cave adaptation associated pathways. This study establishes a foundation for exploring miRNA-mediated gene regulation in cavefish, shedding light on their potential role in regulating early developmental and metabolic adaptations crucial for troglomorphic features. The comprehensive miRNA catalog provided will also guide future investigations into the intricate world of miRNA-mediated evolution in cave-adapted species.
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