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An Intrinsic Disorder Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [RNA-seq]

ABSTRACT: An Intrinsic Disorder Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [RNA-seq]

PROVIDER: PRJNA836761 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19154126_1.fastq.gz	Fastqsanger.gz
	SRR19154126_2.fastq.gz	Fastqsanger.gz
	SRR19154127_1.fastq.gz	Fastqsanger.gz
	SRR19154127_2.fastq.gz	Fastqsanger.gz
	SRR19154128_1.fastq.gz	Fastqsanger.gz

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An Intrinsic Disorder Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIA-PET]

Project description:Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBalpha, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein’s hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBalpha condensates are located at high-order transcriptional repressive hubs in the liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional repressive hubs and diminishes silencing of target genes by REV-ERBalpha. This work demonstrates physiological circadian protein condensates containing REV-ERBalpha whose IDR is required for hub formation and the control of rhythmic gene expression.

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An Intrinsic Disorder Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [RNA-seq]

Project description:Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBa, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein’s hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBa condensates are located at high-order transcriptional repressive hubs in the liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional repressive hubs and diminishes silencing of target genes by REV-ERBa. This work demonstrates physiological circadian protein condensates containing REV-ERBa whose IDR is required for hub formation and the control of rhythmic gene expression.

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An Intrinsic Disorder Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIA-PET]

Project description:An Intrinsic Disorder Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIA-PET]

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An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver

Project description:An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver

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An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIP-seq]

Project description:Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBalpha, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse Liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein’s hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBalpha condensates are located at high-order transcriptional repressive hubs in the Liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional repressive hubs and diminishes silencing of target genes by REV-ERBalpha. This work demonstrates physiological circadian protein condensates containing REV-ERBalpha whose IDR is required for hub formation and the control of rhythmic gene expression.

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An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIP-seq]

Project description:An Intrinsically Disordered Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [ChIP-seq]

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Control of rhythmic translation by the circadian clock

Project description:Evolutionary conserved biological rhythms play a fundamental role in the physiology and behavior of all light-sensitive organisms. Generation of rhythmic expression of clock-controlled genes is orchestrated by a molecular circadian clock constitutes by interconnected negative feedback loops of transcription factors. In this study, we want to characterize gene which also present a rhythmic translation through the characterization of genes with a rhythmic polysomal/total RNA ratio. Analyze of gene expression in liver total RNA and polysomal RNA harvested every 2 hrs during 2 series of 48 hrs, 2 mice per samples

2012-12-01 | E-GEOD-33726 | biostudies-arrayexpress

An intrinsically disordered region controlling condensation of a circadian clock component and rhythmic transcription in the liver.

Project description:Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBα, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein's hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBα condensates are located at high-order transcriptional repressive hubs in the liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional repressive hubs and diminishes silencing of target genes by REV-ERBα. This work demonstrates physiological circadian protein condensates containing REV-ERBα whose IDR is required for hub formation and the control of rhythmic gene expression.

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Rhythmic Food Intake Drives Rhythmic Gene Expression More Potently than the Hepatic Circadian Clock in Mice

Project description:Virtually every mammalian tissue exhibits rhythmic expression in thousands of genes, which activate tissue-specific processes at appropriate times of the day. Much of this rhythmic expression is thought to be driven cell-autonomously by molecular circadian clocks present throughout the body. However, increasing evidence suggests that systemic signals, and more specifically rhythmic food intake (RFI), can regulate rhythmic gene expression independently of the circadian clock. To determine the relative contribution of cell autonomous clocks versus RFI in the regulation of rhythmic gene expression, we developed a system that allows long-term manipulation of the daily rhythm of food intake in the mouse, and analyzed liver gene expression by RNA-Seq in mice fed ad libitum, only at night, or arrhythmically (mouse eating 1/8th of their daily food intake every 3 hours). We show that 70% of the cycling mouse liver transcriptome loses rhythmicity under arrhythmic feeding. Remarkably, this loss of rhythmic gene expression under arrhythmic feeding is independent of the liver circadian clock, which continues to exhibit normal oscillations in core clock gene expression. Many genes that lose rhythmicity participate in the regulation of metabolic processes such as lipogenesis and glycogenesis, likely contributing to an increased sensitivity to insulin that was observed in arrhythmically-fed mice. We also show that night-restricted feeding significantly increases the number of rhythmically expressed genes as well as the amplitude of the rhythms. Together, these results indicate that metabolic transcription factors control a large fraction of the rhythmic mouse liver transcriptome, and demonstrate that systemic signals driven by rhythmic food intake play a more important role than the cell-autonomous circadian clock in driving rhythms in liver gene expression and metabolic functions.

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Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver.

Project description:Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. Although such rhythms have been extensively studied at the level of transcription and mRNA accumulation, little is known about the accumulation patterns of proteins. Here, we quantified temporal profiles in the murine hepatic proteome under physiological light–dark conditions using stable isotope labeling by amino acids quantitative MS. To measure the daily accumulation of proteins, we designed an SILAC MS experiment, in which total protein extracts were harvested from C57BL/6J mice every 3 h for 2 d (eight samples per day). Relative protein abundance in each of 16 samples was quantified against a common reference sample labeled using the SILAC method. The generated mass spectra allowed the identification of a total of 5,827 distinct proteins, of which 70% yielded relative measurements in at least 8 of 16 samples. Our analysis identified over 5,000 proteins, of which several hundred showed robust diurnal oscillations with peak phases enriched in the morning and during the night and related to core hepatic physiological functions. Combined mathematical modeling of temporal protein and mRNA profiles indicated that proteins accumulate with reduced amplitudes and significant delays, consistent with protein half-life data. Moreover, a group comprising about one-half of the rhythmic proteins showed no corresponding rhythmic mRNAs, indicating significant translational or posttranslational diurnal control. Such rhythms were highly enriched in secreted proteins accumulating tightly during the night. Also, these rhythms persisted in clock-deficient animals subjected to rhythmic feeding, suggesting that food-related entrainment signals influence rhythms in circulating plasma factors

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