Circadian transcriptomic analysis of mouse liver
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ABSTRACT:
PROVIDER: PRJNA931272 | ENA |
REPOSITORIES: ENA
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Project description:Circadian transcriptomic analysis of mouse liver during a time restricted feeding
| PRJNA925874 | ENA
Project description:The circadian clock is an evolutionary system that allows organisms to anticipate and thus adapt to daily changes in the environment. In mammals, the circadian clock is found in virtually every tissue regulating rhythms of metabolism and physiology. While a lot of studies have focused in how circadian clocks regulate gene expression little is known about daily control of protein abundance. Here we applied state of the art mass spectrometry in combination with quantitative proteomics to investigate global circadian oscillations of the proteome in the mouse liver. We found that approximately 6% of the liver proteins are cycling daily and interestingly the majority of these oscillations diverge from the behavior of their transcripts. Our data indicates that post-transcriptional mechanisms play an essential role in shaping the phase of rhythmic proteins downstream of transcription regulation to ultimately drive rhythms of metabolism. Moreover, the contribution of post-transcriptional regulation seems to differ among distinct metabolic pathways. Overall we not only found circadian oscillations in the abundance of proteins involved in liver specific metabolic pathways but also in essential cellular processes. Data processing: Raw MS files were processed with MaxQuant (version. 1.1.1.9), a freely available software suite. Peak list files were searched by the ANDROMEDA a search engine, incorporated into the MaxQuant framework, against the IPI-mouse (version 3.68) containing both forward and reversed protein sequences. Initial maximum precursor and fragment mass deviations were set to 7 ppm and 0.5 Da, respectively, but MaxQuant achieved sub-ppm mass accuracy for the majority of peptide precursors. The search included variable modifications for oxidation of methionine, protein N-terminal acetylation and carbamidomethylation as fixed modification. Peptides with at least six amino acids were considered for identification specifying as enzyme LysC allowing N-terminal cleavage to proline. The false discovery rate, determined by searching a reverse database, was set at 0.01 for both peptides and proteins. Identification across different replicates and adjacent fractions was achieved by enabling matching between runs option in MaxQuant within a time window of 2 minutes. Quantification of SILAC pairs was performed by MaxQuant with standard settings using a minimum ratio count of 2.
2014-04-14 | PXD000601 | Pride
Project description:Exam change in the whole-cell and nuclear proteome circadian proteome in response to environmental circadian disruption (ECD) in mouse liver
2024-06-12 | PXD052085 | Pride
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 |
Project description:Determination, using microarrays, of the mouse hepatic global programme of gene expression variations around the clock when animals had ad libitum food access The unique functional versatility of the liver is paramount for the organism homeostasis. Both liver development and adult life are controlled by tightly regulated transcription factor networks, among which nuclear receptors (NRs) regulate essential functions of parenchymal and nonparenchymal cells. Acting as transcription factors sensitive to extracellular cues such as steroidal hormones, lipid metabolites, xenobiotics… and modulated by intracellular signaling pathways, NRs orchestrate many aspects of hepatic physiology. While liver functional zonation and adaptability to fluctuating conditions are known to rely on a sophisticated cellular architecture, the exact functions of NRs in liver cell types remain poorly characterized. As a first step toward the accurate mapping of NR functions in mouse liver, we characterized their levels of expression in whole liver as a function of time and diet, and explored NRs isoform expression in hepatocytes, cholangiocytes, Kupffer cells, hepatic stellate cells and liver sinusoidal cells. In addition, we leveraged liver single cell RNAseq studies to provide here an up-to-date compendium of NR expression in mouse liver in space and time.
2023-05-24 | GSE224446 | 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 |
Project description:Transcriptomic analysis of THRB-regulated genes in mouse liver
| PRJNA905356 | ENA
Project description:Genome-wide expression analysis of two circadian oscillatory mechanisms in the mouse liver To identify the genes of which the circadian expression is regulated by endogenous glucocorticoids, we performed DNA microarray analysis using hepatic RNA from adrenalectomized (ADX) and sham-operated mice. Mice were housed in a 12:12 h light-dark cycle (LD12:12; lights on at zeitgeber time (ZT) 0) for at least two weeks before the day of the experiment. Liver samples were dissected, quickly frozen, and stored in liquid nitrogen. Total RNA was purified from pools of 3 animal tissues collected at each time-point using ISOGEN (Nippon Gene Co., Ltd., Japan). Hybridization to Affymetrix GeneChip (MG-U74Av2) arrays proceeded as described (Oishi K et al., J Biol Chem, 278, 41519-41527, 2003). The average difference (AD) value for each gene was provided by GeneChip software. To identify putative glucocorticoid-regulated circadian genes, we compared AD values between two time points (ZT2 and ZT14) in sham operated and in ADX mice. We applied three criteria to the selection of putative glucocorticoid-regulated circadian genes: (i) the AD value is marked as “present” by the GeneChip software in at least one of two time points, (ii) the AD value exhibits a 2-fold or greater change in sham-operated mice and (iii) the fold change is below 2-fold in ADX mice. We identified 169 genes that fluctuated between day and night in the livers of sham-operated mice. Among these, 100 lost circadian rhythmicity in ADX mice. On the other hand, the circadian expression of clock or clock-related genes such as mPer2 and DBP remained almost totally intact in the liver of ADX mice. The present study showed that the circadian expression of one type of liver genes in the mouse is governed by core components of the circadian clock such as CLOCK and BMAL1, and the other depends on endogenous glucocorticoids. Keywords: parallel sample
2005-11-14 | GSE2162 | GEO
Project description:Genes encoding the circadian pacemaker in the hypothalamic suprachiasmatic nuclei (SCN) of mammals have recently been identified, but the molecubasis of circadian timing in peripheral tissue is not well understood. We used a bead-based microarray to identify mouse liver transcripts that show circadian cycles of abundance under constant conditions. Keywords: Time course microarray-based expression profiling of mRNA with triplicates in mouse liver for 48 hours at 4-hour intervals
2009-08-31 | E-GEOD-11516 | biostudies-arrayexpress
Project description:Gene regulatory circuit of circadian rhythm has been well studied at the transcriptional level. However, recent published Nascent-sequencing and proteomic data indicates that post-transcriptional mechanisms play essential roles in modulating temporal gene expression for proper circadian function. miRNAs are 19-25 nucleotides long small RNAs now well-known for their regulatory roles in the development and diseases through post-transcriptional and translational controls in a wide range of species. We systematically analyzed the miRNAs in mouse liver by Agilent microarray. Then by combining our results with the published high-through liver circadian microarray data, we identified nine mouse liver circadian miRNAs.
2015-06-30 | GSE59423 | GEO