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Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [ChIP-Seq]

ABSTRACT: Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [ChIP-Seq]

PROVIDER: PRJNA1059637 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27393261.fastq.gz	Fastqsanger.gz
	SRR27393262.fastq.gz	Fastqsanger.gz
	SRR27393263.fastq.gz	Fastqsanger.gz
	SRR27393264.fastq.gz	Fastqsanger.gz
	SRR27393265.fastq.gz	Fastqsanger.gz

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Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription.

Project description:Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription.

| PRJNA1059634 | ENA

Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [RNA-Seq 2]

Project description:Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [RNA-Seq 2]

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Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [RNA-Seq 1]

Project description:Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [RNA-Seq 1]

| PRJNA1059636 | ENA

Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [ChIP-Seq]

Project description:During fasting, bodily homeostasis is maintained due to hepatic production of glucose (via gluconeogenesis) and ketone bodies (via ketogenesis). The major hormones governing hepatic fuel production are glucagon and glucocorticoids who initiate a complex transcriptional program aimed at supporting gluconeogenesis and ketogenesis. Here, we found that in addition to the known metabolic genes induced by glucagon and glucocorticoids, these hormones each induce a set of genes encoding transcription factors (TFs) thereby initiating transcriptional cascades. Glucocorticoids activate the glucocorticoid receptor (GR) that induces the genes encoding two TFs - C/EBPβ and PPARα. Transcriptomic analysis combined with gene silencing revealed the role of C/EBPβ as an amplifier of hormone-induced gluconeogenesis. In contrast, the GR-PPARα cascade initiated a secondary transcriptional wave of genes supporting ketogenesis. We show that a dual treatment of glucocorticoids with a PPARα agonist leads to synergistic induction of ketogenic genes and that this induction is dependent on protein synthesis. Genome-wide analysis of enhancer dynamics revealed numerous enhancers activated by the GR-PPARα cascade. These enhancers are proximal to ketogenic genes, are enriched for the PPARα binding motif and show increased PPARα binding as profiled by ChIP-seq. In summary, this study reveals abundant TF cascades occurring during fasting. These cascades serve two separated purposes: the amplification of the primary gluconeogenic transcriptional program and the induction of a secondary gene program aimed at enhancing ketogenesis.

2024-08-18 | GSE252319 | GEO

Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [RNA-Seq 2]

2024-08-18 | GSE252318 | GEO

Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription. [RNA-Seq 1]

2024-08-18 | GSE252317 | GEO

Transcription factor cascades during fasting amplify gluconeogenesis and instigate a secondary wave of ketogenic gene transcription.

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-08-18 | GSE252320 | GEO

Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription

Project description:Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription

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ChIP-seq of transcription factors regulating the TLR-induced transcriptional cascades in macrophages

Project description:Toll-like receptors (TLRs) are responsible for sensing pathogen components, initiating cascades of signaling pathways, transcription factors, chromatin regulators, and activating thousands of genes contributing to diverse immune functions in macrophages. Conventional system approaches have been used to analyze TLR-induced transcriptional cascades. However, commonly used approaches possess a number of limitations, including a bias toward weakly induced genes, which are far more prevalent than strongly induced genes, and an inability to distinguish functionally important protein-DNA interactions identified by ChIP-seq from interactions that may be functionally insignificant. To develop a better understanding of a TLR-induced transcriptional cascade, we used more stringent criteria to analyze RNA-seq, ChIP-seq, and transcription factor binding motif data sets. Our analysis provided a number of insights into the regulation of an inducible transcriptional cascade. This stringent and quantitative strategy can effectively reveal gene-specific regulatory mechanisms from genome-wide studies.

2017-06-11 | GSE99895 | GEO

Jump-seq: Capture and amplify 5hmC Sites Whole Genome-Wide

Project description:We developed an efficient and precise method, which we name as Jump-seq, to capture and amplify 5hmC signal whole genome-wide, bridge the gap between base resolution (TAB-seq) and economic cost (hmC-seal).

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