Clockwork orange-mediated control of sugar responsive transcription [time series]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA854146 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19898967.fastq.gz | Fastqsanger.gz | |||
| SRR19898968.fastq.gz | Fastqsanger.gz | |||
| SRR19898969.fastq.gz | Fastqsanger.gz | |||
| SRR19898970.fastq.gz | Fastqsanger.gz | |||
| SRR19898971.fastq.gz | Fastqsanger.gz |
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Project description:Feeding on high sugar diet reprograms metabolism, partially mediated through a gene regulatory network controlled by intracellular sugar sensor Mondo/ChREBP-Mlx. Sugar-induced gene expression changes include activation of genes encoding enzymes of glycolysis, pentose phosphate pathways, and de novo lipogenesis, collectively driving the flux of sugar-derived carbon into triacylglycerides. These sugar-induced metabolic changes are likely to trigger compensatory responses to avoid depletion of necessary metabolites, but they remain poorly characterized. Through a global temporal clustering analysis of sugar-induced gene expression in Drosophila we identify new gene expression programs controlled by sugar feeding. These include rapid and transient downregulation of ribosome biogenesis genes, known targets of transcription factor Myc. Through in silico motif predictions and experimental validation, we identify transcriptional repressor Clockwork orange (CWO) as a mediator of this response. CWO expression is directly activated by Mondo-Mlx and it counteracts Myc through repression of its expression as well as through binding to overlapping regulatory regions of ribosome biogenesis genes. Loss of CWO function leads to depletion of UDP-GlcNAc pools and impaired viability on high sugar diet. Analysis of CWO orthologs, BHLHE40 and BHLHE41, in mouse hepatocytes revealed a conserved role for BHLHE41 in repressing ribosome biogenesis genes. Collectively, our data uncover a gene regulatory circuit balancing the activities of lipid and protein biosynthesis to maintain homeostasis during high sugar feeding.
2023-06-01 | GSE207197 | GEO
Project description:Clockwork orange-mediated control of sugar responsive transcription
| PRJNA854137 | ENA
Project description:Feeding on high sugar diet reprograms metabolism, partially mediated through a gene regulatory network controlled by intracellular sugar sensor Mondo/ChREBP-Mlx. Sugar-induced gene expression changes include activation of genes encoding enzymes of glycolysis, pentose phosphate pathways, and de novo lipogenesis, collectively driving the flux of sugar-derived carbon into triacylglycerides. These sugar-induced metabolic changes are likely to trigger compensatory responses to avoid depletion of necessary metabolites, but they remain poorly characterized. Through a global temporal clustering analysis of sugar-induced gene expression in Drosophila we identify new gene expression programs controlled by sugar feeding. These include rapid and transient downregulation of ribosome biogenesis genes, known targets of transcription factor Myc. Through in silico motif predictions and experimental validation, we identify transcriptional repressor Clockwork orange (CWO) as a mediator of this response. CWO expression is directly activated by Mondo-Mlx and it counteracts Myc through repression of its expression as well as through binding to overlapping regulatory regions of ribosome biogenesis genes. Loss of CWO function leads to depletion of UDP-GlcNAc pools and impaired viability on high sugar diet. Analysis of CWO orthologs, BHLHE40 and BHLHE41, in mouse hepatocytes revealed a conserved role for BHLHE41 in repressing ribosome biogenesis genes. Collectively, our data uncover a gene regulatory circuit balancing the activities of lipid and protein biosynthesis to maintain homeostasis during high sugar feeding.
2023-06-01 | GSE207198 | GEO
Project description:Feeding on high sugar diet reprograms metabolism, partially mediated through a gene regulatory network controlled by intracellular sugar sensor Mondo/ChREBP-Mlx. Sugar-induced gene expression changes include activation of genes encoding enzymes of glycolysis, pentose phosphate pathways, and de novo lipogenesis, collectively driving the flux of sugar-derived carbon into triacylglycerides. These sugar-induced metabolic changes are likely to trigger compensatory responses to avoid depletion of necessary metabolites, but they remain poorly characterized. Through a global temporal clustering analysis of sugar-induced gene expression in Drosophila we identify new gene expression programs controlled by sugar feeding. These include rapid and transient downregulation of ribosome biogenesis genes, known targets of transcription factor Myc. Through in silico motif predictions and experimental validation, we identify transcriptional repressor Clockwork orange (CWO) as a mediator of this response. CWO expression is directly activated by Mondo-Mlx and it counteracts Myc through repression of its expression as well as through binding to overlapping regulatory regions of ribosome biogenesis genes. Loss of CWO function leads to depletion of UDP-GlcNAc pools and impaired viability on high sugar diet. Analysis of CWO orthologs, BHLHE40 and BHLHE41, in mouse hepatocytes revealed a conserved role for BHLHE41 in repressing ribosome biogenesis genes. Collectively, our data uncover a gene regulatory circuit balancing the activities of lipid and protein biosynthesis to maintain homeostasis during high sugar feeding.
2023-06-01 | GSE207196 | GEO
Project description:Clockwork orange-mediated control of sugar responsive transcription [cwo mutant]
| PRJNA854147 | ENA
Project description:Clockwork orange-mediated control of sugar responsive transcription [ChIP-seq]
| PRJNA854144 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-06-01 | GSE207199 | GEO
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:• To dissect how the genes are dynamically and differentially expressed during fruit development in sweet orange, a comprehensive transcriptomic study was performed in a pleiotropic mutant (MT) and its wild type (WT). • The detection of the fruit transcriptomic changes was conducted at five stages of fruit development by deep sequencing; the obtained millions of reliable tags were mapped on orange unigenes and subjected to cluster analysis and functional categorization. Sugar and organic acid contents were determined based on the prediction of differential biological processes. • The global clustering analysis revealed a total of 14 expression patterns for the genes involved in fruit development of sweet orange. More than 94% of the genes showed differential expression during fruit development. Comparative transcripts profiling between WT and MT revealed that between 410 and 634 genes were significantly differentially expressed at the five stages. Functional categorization indicated that TCA cycle, carotenoid biosynthesis, and pentose phosphate pathway (OPP) were among the most regulated pathways. • This study provided a dynamic-view of the transcriptome changes during fruit ripening in sweet orange; the results highlighted a set of molecular processes involved in the formation of the mutation trait in the orange fruits. Investigate the transcriptome changes during five fruit developmental stages of two sweet orange genotypes
2012-06-22 | E-GEOD-22505 | biostudies-arrayexpress
Project description:• To dissect how the genes are dynamically and differentially expressed during fruit development in sweet orange, a comprehensive transcriptomic study was performed in a pleiotropic mutant (MT) and its wild type (WT). • The detection of the fruit transcriptomic changes was conducted at five stages of fruit development by deep sequencing; the obtained millions of reliable tags were mapped on orange unigenes and subjected to cluster analysis and functional categorization. Sugar and organic acid contents were determined based on the prediction of differential biological processes. • The global clustering analysis revealed a total of 14 expression patterns for the genes involved in fruit development of sweet orange. More than 94% of the genes showed differential expression during fruit development. Comparative transcripts profiling between WT and MT revealed that between 410 and 634 genes were significantly differentially expressed at the five stages. Functional categorization indicated that TCA cycle, carotenoid biosynthesis, and pentose phosphate pathway (OPP) were among the most regulated pathways. • This study provided a dynamic-view of the transcriptome changes during fruit ripening in sweet orange; the results highlighted a set of molecular processes involved in the formation of the mutation trait in the orange fruits.
2012-06-22 | GSE22505 | GEO