Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA324436 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The liver circadian clock is reprogrammed by nutritional challenge through the rewiring of specific transcriptional pathways. As the gut microbiota is tightly connected to host metabolism, whose coordination is governed by the circadian clock, we explored whether gut microbes influence circadian homeostasis and how they distally control the peripheral clock in the liver. Using fecal transplant procedures we reveal that, in response to high fat diet, the gut microbiota drives PPARγ-mediated activation of newly oscillatory transcriptional programs in the liver. Moreover, antibiotics treatment prevents PPARγ-driven transcription in the liver, underscoring the essential role of gut microbes in clock reprogramming and hepatic circadian homeostasis. Thus, a specific molecular signature characterizes the influence of the gut microbiome in the liver, leading to the transcriptional rewiring of hepatic metabolism. We used microarray to quantify the tissue specific expression level of circadian genes in terms of total RNA.
2016-06-04 | GSE82250 | GEO
Project description:Gut microbiota and the circadian clock are both key regulators of the metabolic processes. Although recent evidence points to the impact of the circadian clock on microbiota, gut microbiota effect on diurnal host gene expression remains elusive. A transcriptome analysis of germ-free mice reveals subtle changes in circadian clock gene expression. However, a lack of microbiome leads to liver feminization and alters the expression of male-specific genes involved in lipid metabolism and xenobiotic detoxification associated with sustained activation of the Growth Hormone pathway. These results emphasize the mutual interaction of gut microbiota and its host even on unexpected functions.
2018-09-01 | GSE114613 | GEO
Project description:Gut microbiota and the circadian clock are both key regulators of the metabolic processes. Although recent evidence points to the impact of the circadian clock on microbiota, gut microbiota effect on diurnal host gene expression remains elusive. A transcriptome analysis of germ-free mice reveals subtle changes in circadian clock gene expression. However, a lack of microbiome leads to liver feminization and alters the expression of male-specific genes involved in lipid metabolism and xenobiotic detoxification associated with sustained activation of the Growth Hormone pathway. These results emphasize the mutual interaction of gut microbiota and its host even on unexpected functions.
2018-09-01 | GSE114612 | GEO
Project description:Gut microbiota and the circadian clock are both key regulators of the metabolic processes. Although recent evidence points to the impact of the circadian clock on microbiota, gut microbiota effect on diurnal host gene expression remains elusive. A transcriptome analysis of germ-free mice reveals subtle changes in circadian clock gene expression. However, a lack of microbiome leads to liver feminization and alters the expression of male-specific genes involved in lipid metabolism and xenobiotic detoxification associated with sustained activation of the Growth Hormone pathway. These results emphasize the mutual interaction of gut microbiota and its host even on unexpected functions.
2018-09-01 | GSE114611 | GEO
Project description:Gut microbiota and the circadian clock are both key regulators of the metabolic processes. Although recent evidence points to the impact of the circadian clock on microbiota, gut microbiota effect on diurnal host gene expression remains elusive. A transcriptome analysis of germ-free mice reveals subtle changes in circadian clock gene expression. However, a lack of microbiome leads to liver feminization and alters the expression of male-specific genes involved in lipid metabolism and xenobiotic detoxification associated with sustained activation of the Growth Hormone pathway. These results emphasize the mutual interaction of gut microbiota and its host even on unexpected functions.
2018-09-01 | GSE114610 | GEO
Project description:The circadian clock orchestrates rhythms in physiology and behavior, allowing the organism to adapt to daily environmental changes. Recently, efforts have been made to unravel the connection between the circadian clock and metabolism and to understand how the peripheral clock in different organs coordinates circadian responses to maintain metabolic homeostasis. It is becoming clear that diet can influence diurnal rhythms, however, the molecular mechanisms responsible for alterations in daily oscillations and how tissue-specific clocks interpret a nutritional challenge are not well understood. Here, we reveal tissue-specific circadian plasticity in response to a ketogenic diet (KD) in both the liver and intestine and a remarkable deviation within these two tissues following subsequent carbohydrate supplementation. KD caused a dramatic change in the circadian transcriptome in both liver and intestine in a tissue-specific fashion. In particular, both the amplitude of clock genes as well as specific BMAL1 recruitment was profoundly altered by KD while the intestinal clock was devoid of such plasticity. While PPARG nuclear accumulation was circadian in both tissues, it showed substantial phase specificity as did downstream targets. Finally, the gut and liver clocks had distinct responses to carbohydrate supplementation to KD composition, suggesting a higher plasticity in the ileum whose gene expression was almost restored to control baseline. For the first time our results demonstrate how nutrients modulate clock function in a tissue-specific manner, suggesting that a food stress arouses unique circadian molecular signatures in distinct peripheral tissues.
2017-09-18 | GSE87425 | GEO
Project description:As a circadian organ, liver executes diverse functions in different phase of the circadian clock. This process is believed to be driven by a transcription program. Here, we present a TF DNA-binding activity centered multi-dimensional proteomics landscape, including DNA-binding activity of TFs, the phosphorylation pattern, ubiquitylation pattern, the nuclear sub-proteome, the whole proteome as well as the transcriptome, to portrait the hierarchical circadian clock network of mouse liver. The TF DNA-binding activity indicates diurnal oscillation in four major pathways, immune response, glucose metabolism, fatty acid metabolism, and the cell cycle. We also isolated the mouse liver Kupffer cells and measured their proteomes in the circadian clock to reveal cell type resolved circadian clock. These are the most comprehensive datasets for circadian clock in the mouse liver and provided the richest data resource for the understanding of mouse liver physiology around the circadian clock.
2018-06-25 | PXD008862 | iProX
Project description:As a circadian organ, liver executes diverse functions in different phase of the circadian clock. This process is believed to be driven by a transcription program. Here, we present a TF DNA-binding activity centered multi-dimensional proteomics landscape, including DNA-binding activity of TFs, the phosphorylation pattern, ubiquitylation pattern, the nuclear sub-proteome, the whole proteome as well as the transcriptome, to portrait the hierarchical circadian clock network of mouse liver. The TF DNA-binding activity indicates diurnal oscillation in four major pathways, immune response, glucose metabolism, fatty acid metabolism, and the cell cycle. We also isolated the mouse liver Kupffer cells and measured their proteomes in the circadian clock to reveal cell type resolved circadian clock. These are the most comprehensive datasets for circadian clock in the mouse liver and provided the richest data resource for the understanding of mouse liver physiology around the circadian clock.
2018-06-25 | PXD008771 | iProX
Project description:Ketone bodies, intermediates in energy metabolism and signaling, have attracted significant attention due to their role in health and disease. We performed around the clock study on ketone bodies and ketogenesis with mice on different diets. We found that caloric restriction, a dietary intervention that improves metabolism and longevity, induced high amplitude circadian rhythms in blood βOHB. The blood βOHB rhythms resulted from rhythmic ketogenesis in the liver controlled by the interaction between the circadian clock and PPAR transcriptional networks. This interaction results in transcriptional reprogramming of in beta-oxidation and ketogenesis enzymes. The reprogramming is impaired in circadian clock mutant mice. The circadian clock gated ketogenesis contributes to the diet impact on health and longevity.
2022-08-31 | GSE211975 | GEO
Project description:Gut microbiota and the circadian clock both regulate metabolism. The circadian clock and associated feeding rhythms were shown to impact on the microbial community. However, to what extent gut microbiota reciprocally affect daily rhythms of gene expression and physiology in the host remains elusive. Here, we analyzed the transcriptomes of male and female germ-free mice. While this revealed subtle changes in circadian clock gene expression in liver, intestine, and white adipose tissue, germ-free mice showed considerably altered expression of genes associated to rhythmic physiology. Strikingly, absence of microbiome severely compromised liver sex-dimorphism at the transcriptome and metabolome level. Their sex-specific rhythmicity was strongly attenuated. The resulting feminization of male and masculinization of female hepatic gene expression in germ-free animals is likely caused by altered sex-dimorphism in sex and growth hormone secretion, linked to differential activation of xenobiotic receptors. This defines a novel mechanism by which the gut microbiome regulates host metabolism.
2018-09-01 | GSE114402 | GEO