Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development of gene expression signatures during fasting and refeeding (compensatory growth) for zebrafish liver

ABSTRACT: Here, we certified zebrafish to be a suitable model for the compensatory growth study. After a 3-weeks fasting, recovered for 3 days, 10 days and 15 days were chose as the initial, middle and late sampling sites for compensatory growth analysis, and liver samples of each time point were chose for the microarray analysis.At the same time, zebrafish fed ad libitum, as well as fasting for 3 weeks were also added to the microarray research.

ORGANISM(S): Danio rerio

PROVIDER: GSE112272 | GEO | 2018/03/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Development of gene expression signatures during fasting and refeeding (compensatory growth) for zebrafish liver

Project description:Development of gene expression signatures during fasting and refeeding (compensatory growth) for zebrafish liver

| PRJNA445444 | ENA

Prolonged fasting/refeeding modifies proteome profile and parvalbumin expression in the fast-twitch muscle of pacu (Piaractus mesopotamicus)

Project description:Skeletal muscle in fish presents a high plasticity controlled by a dynamic balance between anabolic and catabolic signaling pathways. Decreased food availability can inhibit muscle growth and trigger muscle catabolism pathways, thu promoting muscle atrophy. In contrast, anabolism may be favored during restoration of food supply, promoting the muscle growth. Considering this, we analyzed fast-twitch muscle of juvenile Piaractus mesopotamicus (pacu) submitted to a prolonged fasting (30 days) and refeeding (up to 30 days) using shotgun proteomics and gene expression analysis. The relative rate of weight and length increase, as well as the expression of mafbx and igf -1 genes, suggest that prolonged fasting caused muscle atrophy and that 30 days of refeeding led to partial compensatory growth. Shotgun proteomics analysis identified 99 proteins after fasting and 71 proteins after refeeding periods, of which 23 and 17 were differentially expressed after fasting and after 30 days of refeeding, respectively. Most of these differentially expressed proteins were related to cytoskeleton, muscle contraction and muscle metabolism. Among these, parvalbumin (PVALB), a calcium-binding protein and food allergen, was selected for further RT-qPCR analysis, which showed that pvalb mRNA was not changed after 30 days of fasting and 30 days of refeeding, but it was downregulated after 6h and 24h of refeeding. This suggests a post-transcriptional regulation of PVALB in fish muscle. In conclusion, our results suggest that muscle atrophy and partial compensatory growth caused by prolonged fasting and refeeding affected the muscle proteome and PVALB expression. Our results can contribute to the understanding of muscle anabolic and catabolic pathways in response to changes in food availability.

2019-11-28 | PXD014232 | Pride

Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle.

Project description:Gene expression profile was investigated using zebrafish muscle unger fasting-refeeding conditions. This study revealed fasting-refeeding responsive genes in zebrafish muscle.

2022-05-27 | GSE201273 | GEO

Fasting/fed/refeeding RNAseq experiment conducted on mice with xenografted human livers.

Project description:Human hepatic gene regulations by fasting and refeeding in a mouse model with humanized liver generated from a single donor were reported.

2021-01-06 | GSE130525 | GEO

Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle.

Project description:Gene expression profile showing novel insight for fasting–refeeding response in zebrafish muscle.

| PRJNA830699 | ENA

Characterization of chromatin and gene expression changes during fasting and refeeding in mouse liver [RNA-Seq]

Project description:The discovery of FoxO1 as an effector of insulin action on gene expression filled a gap in our knowledge of insulin signaling. The metabolic impact of hepatic FoxO1 has been demonstrated in genetic mouse models showing that FoxO1 inhibition can reverse diabetes. However, the gamut of FoxO1 targets is unknown, due to the lack of robust genome-wide chromatin occupancy data. To elucidate the genomic architecture of the FoxO1 effect on liver metabolism, we integrated genome-wide ChIP-seq and RNA-seq. During the physiological transition from fasting to refeeding, hepatic FoxO1 translocated from the nucleus to the cytoplasm. At the same time points, cistrome analysis demonstrated that 60% of FoxO1 target sites were cleared by refeeding. RNA-seq from mice following acute liver-specific FoxO1 ablation allowed us to integrate the data in a comprehensive FoxO1 regulome. We identified four distinct classes of FoxO1 targets. Class I targets are enriched in genes regulating cell homeostasis, have FoxO1 sites clustered in promoters and do not show regulation with fasting/refeeding. Class II is comprised of canonical FoxO1 metabolic targets coordinately regulated with other fasting-inducible TFs, such as PPARA, CREB, and GR through promoters. Class III is enriched in glucose metabolic genes regulated through active enhancers, as detected by H3K4me1 and H3K27ac histone marks. Class IV is comprised of triglyceride (TG) and lipoprotein metabolism genes, regulated through intron sites, and characterized by an uneven response to fasting/refeeding regulation.

2022-05-24 | GSE151545 | GEO

Characterization of chromatin and gene expression changes during fasting and refeeding in mouse liver [ChIP-Seq]

2022-05-24 | GSE151544 | GEO

Profiling hepatic microRNAs in zebrafish: Fluoxetine exposure mimics a fasting response that targets AMP-activated protein kinase (AMPK)

Project description:Recent evidence has suggested that fluoxetine, a serotonin-reuptake inhibitor and emerging environmental contaminant, can have non-targeted effects on metabolism in fish exposed to this waterborne pollutant. Using the highest, environmentally relevant, detectable level of fluoxetine (540 ng/L) we examined the impact of fluoxetine on the miRNA profile in the liver of zebrafish that were both fed and fasted for a period of 7 days. These results were further compared to the miRNA profile of zebrafish fasted and fed for 7 days, which were not exposed to fluoxetine. Results indicated that several miRNA that were involved with downregulating genes/pathways in response to fasting were also upregulated in fish exposed to fluoxetine, irrespective to fasting or feeding. These results suggest fluoxetine can have non-targeted effects on metabolic pathways mediated through miRNA expression. Furthermore, specific miRNA (dre-let-7d & dre-miR-140-5p) were found to target the catalytic subunit (AMPKa1 & AMPKa2, respectively) of AMP-Kinase, a master regulator of metabolism. Using predictive software and qPCR validation, combined with the expression profile of these two miRNA, we were able to establish a significant relationship between the expression of these specific miRNA to the downregulation of AMPKa subunit under the influence of 540 ng/L fluoxetine. Adult, female zebrafish were either fed or fasted for 7 days with and without the presense of 540 ng/L fluoxetine, and livers extracted and miRNA purified for miRNA microaary experiment.

2014-02-21 | E-GEOD-55229 | biostudies-arrayexpress

Effects of extensive fasting on hepatic transcription

Project description:Temporally restricted feeding has a profound effect on the hepatic circadian clock. While the circadian clock is largely unaffected by by extensive fasting, many transcripts are known to be affected by a fasting paradigm. This dataset shows the effect of extensive fasting on dynamic gene expression in the liver C57/B6 mice were entrained to ad libitum feeding schedule for two weeks. They were then released into constant were food was withdrawn at CT16. On the second day in constant darkness tissue was collected at the indicated timepoints. Total RNA was extracted and 5ug of total RNA was used for the standard Affymetrix protocol of amplification, labeling and hybridization

2009-11-23 | E-GEOD-13064 | biostudies-arrayexpress

Prolonged fasting and refeeding modifies the proteome of slow-twitch skeletal muscle fibres in Piaractus mesopotamicus

Project description: In fish, the slow-twitch skeletal muscle fibres have an oxidative metabolism, present peripherical location in the red muscle, and are used for sustained movements. They may respond to alterations in food availability differently than the fast-twitch muscle. The aim of this manuscript was to study the slow-twitch muscle fibres of Piaractus Mesopotamicus, a neotropical fish, submitted to 30 days of fasting (D30) followed by one day (D31) or 30 days of refeeding (D60). The treated animals were compared with regularly fed fish. To verify the presence of atrophy and hypertrophy, we performed histological analysis of muscle fibre diameter in D30 and D60, and RT-qPCR gene expression analysis of catabolic (murfa, murfb, mafbx) and anabolic genes (igf-1, mTOR) in D30, D31 and D60. The gene expression of the allergen and Ca2+-carrier parvalbumin (pvalb) was also measured in D30, D31 and D60. The proteome of slow-twitch fibres at D30 and D60 was obtained by shotgun proteomics (digestion of proteins with trypsin followed by LC-MS/MS identification), and the proteins differentially expressed were used to construct protein interaction networks. The histological analysis showed no difference between treated fish in relation to the control. The expression of catabolic and anabolic genes was not changed, except for the negative regulation of igf-1 in D30 and of mtor in D31. The expression of pvalb was not changed in D30 and D60, but it was decreased in D31. The proteomic analysis identified 169 proteins in D30 (24 upregulated and 18 downregulated) and 170 proteins in D60 (17 upregulated and 21 downregulated). Many of them were related to energetic metabolism, including lipid metabolism, as shown by the protein network analysis. These results enlarge our understanding of the acclimation of slow-twitch fibres to changes in nutrient availability and set a path for future research.

2019-11-28 | PXD014320 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data