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

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

PROVIDER: PRJNA445444 | ENA |

REPOSITORIES: ENA

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

Project description: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.

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

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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.

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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.

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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.

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

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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.

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ATAC-sequencing to evaluate the global chromatin dynamics in the absence of hepatic-HMGB1 in livers from mice on fed with chow diet or after a metabolic stress induced by a fasting (6hours)-refeeding (8hours) challenge.

Project description:Hepatocyte nuclei were purified from liver samples harvested from HMGB1fl/fl (n=2) and HMGB1ΔHep (n=2) mice upon chow diet feeding or after fasting-refeeding.

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Recovery growth

Project description:We used cDNA microarrays to describe the changes in gene expression in muscle during recovery growth induced by a fasting-refeeding sequence. Keywords: muscle, fasting-refeeding, time-course

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