The organismal landscape of clock cells and circadian gene expression in Drosophila
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA975196 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24688641_1.fastq.gz | Fastqsanger.gz | |||
| SRR24688641_2.fastq.gz | Fastqsanger.gz | |||
| SRR24688642_1.fastq.gz | Fastqsanger.gz | |||
| SRR24688642_2.fastq.gz | Fastqsanger.gz | |||
| SRR24688643_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
Project description:Circadian rhythms time physiological and behavioral processes to 24-hour cycles. It is generally assumed that most cells contain self-sustained circadian clocks that drive circadian rhythms in gene expression that ultimately generating circadian rhythms in physiology. While those clocks supposedly act cell autonomously, current work suggests that in Drosophila some of them can be adjusted by the brain circadian pacemaker through neuropeptides, like the Pigment Dispersing Factor (PDF). Despite these findings and the ample knowledge of the molecular clockwork, it is still unknown how circadian gene expression in Drosophila is achieved across the body . Here, we used single-cell and bulk RNAseq data to identify cells within the fly that express core-clock components. Surprisingly, we found that less than a third of the cell types in the fly are enriched for core-clock genes. Moreover, we identified Lamina wild field (Lawf) and Ponx-neuro positive (Poxn) neurons as putative new circadian neurons. In addition, we found several cell types that don’t express core clock components but are highly enriched for cyclically expressed mRNAs. Strikingly, these cell types express the PDF receptor (Pdfr), suggesting that PDF drives rhythmic gene expression in many cell types in flies. Other cell types express both core circadian clock components and Pdfr, suggesting that in these cells, PDF regulates the phase of rhythmic gene expression. Together, our data suggest three different mechanisms generate daily gene expression in cells and tissues: an endogenous canonical molecular clock, PDF signaling-driven expression, or a combination of both.
2023-06-14 | GSE233184 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE39977: Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals [ChIP-seq] GSE39978: Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals [RNA-seq] Refer to individual Series
2012-08-31 | E-GEOD-39860 | biostudies-arrayexpress
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:Oscillatory lysosomal activity for disposal of the components of the cellular clock is essential to sustain organismal circadian rhythms
2021-10-05 | PXD019704 | 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 | PXD008862 |
Project description:The Drosophila circadian clock is driven by a transcriptional feedback loop in which the bHLH transcription factor CLOCK-CYCLE (CLK-CYC) binds E-boxes to transcribe genes encoding the PERIOD-TIMELESS (PER-TIM) repressor, which releases CLK-CYC from E-boxes to inhibit transcription. The bHLH-Orange transcription factor CLOCKWORK ORANGE (CWO) reinforces repression by binding E-boxes to displace CLK-CYC, but also acts through an unknown mechanism to promote CLK-CYC transcription. To determine how CWO activates CLK-CYC transcription, we identified CWO DNA binding targets that are upregulated in the absence of CWO repression, conserved in mammals and preferentially expressed in brain pacemaker neurons. Among the genes identified was the Drosophila ortholog of mammalian Clock Interacting Protein Circadian (Cipc) that acts to repress CLOCK-BMAL1 transcription. Reducing or eliminating Drosophila Cipc expression shortens circadian period while overexpressing Cipc lengthens circadian period in flies, consistent with previous analysis showing that Drosophila Cipc represses CLK-CYC transcription in S2 cell culture. Long period rhythms of cwo mutant flies are largely rescued when Cipc expression is reduced or eliminated, indicating that increased Cipc expression mediates period lengthening of cwo mutants. These results suggest a mechanism for CWO-dependent CLK-CYC activation: CWO inhibition of CIPC repression promotes CLK-CYC transcription. Such a mechanism may be conserved given that orthologs of cwo and Cipc carry out analogous roles in the mammalian circadian clock.
2021-07-23 | GSE165043 | GEO
Project description:Many different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs of Drosophila circadian neurons, we optimized a single cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.
2021-01-12 | GSE157504 | GEO
Project description:Influence of diet and neuronal clk (clock) activity on hemolymph proteomics. We have shown that as photoreceptors die (in the fly) they necrose, which results in their intercellular contents leaking into the hemolymph. We hypothesize that this process is regulated by diet and circadian clock control.
Analysis of differential protein expression in the hemolymph from flies reared on a high protein diet. Comparison of flies with and without a functional circadian clock within their photoreceptors.
Species/Strain: Drosophila, Elav-GeneSwitch-GAL4>UAS-Clk-DN1 (+/- RU486), female
2021-01-30 | MSV000086781 | MassIVE
Project description:The circadian system plays an essential role in regulating timing of body metabolism in humans. Indeed, circadian misalignments are strongly associated with high rates of metabolic disorders. Molecular makeup of the circadian oscillator can be deciphered in cells cultured in vitro, and these cellular rhythms are highly informative of the physiological circadian rhythm in vivo.
We aimed at assessing molecular clock properties in dermal fibroblasts established from the skin biopsies of seventeen Type 2 diabetic obese and non-obese patients and eleven healthy controls. Following in vitro synchronization, primary fibroblast cultures were subjected to continuous assessment of circadian bioluminescence profiles based on lentiviral luciferase reporters.
We observed a strong inverse correlation between HbA1c values and circadian period length within cells from the Type 2 diabetic group. RNA sequencing analysis conducted in this group samples revealed that ICAM1 encoding for the endothelial adhesion protein was differentially expressed between Type 2 diabetic compensated and non-compensated fibroblasts, and correlated with the period length. Furthermore, ICAM1 expression is driven by rhythmic CLOCK binding.
We provide for the first time a potential molecular link between severity of Type 2 diabetes and circadian clock machinery, which paves a way for further mechanistic understanding of circadian oscillator changes upon Type 2 diabetes in humans.
| EGAS00001003622 | EGA
Project description:CLOCK (CLK) is a master transcriptional regulator of the circadian clock in Drosophila. To identify CLK direct target genes and address circadian transcriptional regulation in Drosophila, we performed chromatin immunoprecipitation-tiling array assays (ChIP-chip) with a number of circadian proteins. CLK binding cycles on at least 800 sites with maximal binding in the early night. The CLK partner protein CYCLE (CYC) is on most of these sites. The CLK/CYC heterodimer is joined 4-6 hrs later by the transcriptional repressor PER, indicating that the majority of CLK targets are regulated similarly to core circadian genes (Menet et al. 2010). About 30% of target genes also show cycling Pol II binding. Many of these generate cycling RNAs despite not being documented in prior RNA cycling studies. This is due in part to different RNA isoforms and to fly head tissue heterogeneity. CLK has specific targets in different tissues, implying that important CLK partner proteins and/or mechanisms contribute to gene-specific and tissue-specific regulation.
2011-11-15 | GSE32613 | GEO