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Impact of CAR agonist ligand TCPOBOP on transcription factor binding in adult male mouse liver

ABSTRACT: Impact of CAR agonist ligand TCPOBOP on transcription factor binding in adult male mouse liver

PROVIDER: PRJNA499057 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8128860_1.fastq.gz	Fastqsanger.gz
	SRR8128860_2.fastq.gz	Fastqsanger.gz
	SRR8128870_1.fastq.gz	Fastqsanger.gz
	SRR8128870_2.fastq.gz	Fastqsanger.gz
	SRR8128880_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Impact of CAR agonist ligand TCPOBOP on transcription factor binding in adult male mouse liver

Project description:Chromatin immunoprecipitation and sequencing for three transcription factors (RXRa, CEBPa, CEBPb) was performed on livers of male mice treated with vehicle or with TCPOBOP for either 3 h or 27 h. This dataset is part of a larger study, entitled “Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR”, which found that active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DNase hypersensitive sites (DHS) and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation.

2019-06-17 | GSE121915 | GEO

Impact of CAR agonist ligand TCPOBOP (27 hr time point) on H3-K27me3 marks in adult male mouse liver

Project description:Chromatin immunoprecipitation and sequencing for the H3K27me3 histone mark was performed on livers of male mice either treated with vehicle or with TCPOBOP for 27 h. This dataset is part of a larger study, entitled “Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR”, which found that active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DNase hypersensitive sites (DHS) and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation.

2019-06-17 | GSE121914 | GEO

Impact of CAR agonist ligand TCPOBOP (3 hr time point) on H3-K27me3 marks in adult male mouse liver

Project description:Chromatin immunoprecipitation and sequencing for the H3K27me3 histone mark was performed on livers of male mice either treated with vehicle or with TCPOBOP for 3 h. This dataset is part of a larger study, entitled “Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR”, which found that active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DNase hypersensitive sites (DHS) and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation.

2019-06-17 | GSE121913 | GEO

Impact of CAR agonist ligand TCPOBOP (3h and 27hr time points) on H3-K27me3 marks in adult male mouse liver

Project description:This SuperSeries is composed of the SubSeries listed below. This dataset is part of a larger study, entitled “Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR”, which found that active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DNase hypersensitive sites (DHS) and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation.

2019-06-17 | GSE121921 | GEO

Impact of CAR agonist ligand TCPOBOP (27 hr time point) on H3-K27me3 marks in adult male mouse liver

Project description:Impact of CAR agonist ligand TCPOBOP (27 hr time point) on H3-K27me3 marks in adult male mouse liver

| PRJNA499052 | ENA

Impact of CAR agonist ligand TCPOBOP (3 hr time point) on H3-K27me3 marks in adult male mouse liver

Project description:Impact of CAR agonist ligand TCPOBOP (3 hr time point) on H3-K27me3 marks in adult male mouse liver

| PRJNA499053 | ENA

STARR-seq library profiling 100 defined open chromatin regions (‘focused library’) in livers of male and female mice treated with the nuclear receptor CAR (Nr1i3) agonist ligand TCPOBOP.

Project description:Massively parallel reporter assays are widely used to discover functional enhancers but have largely been limited to transfected cell models, which are confounded by vector-induced innate immune responses and lack the physiologically relevant cellular and endogenous hormonal context and chromatin environment of complex mammalian tissues. Here, we combine hydrodynamic injection with a modified STARR-seq-based MPRA to determine condition-specific enhancer activity in mouse liver at scale. Strong liver enhancer activity was observed with STARR-seq libraries containing an Albumin minimal promoter but not when using a Super Core promoter or an origin of replication promoter. We prepared a focused STARR-seq library comprised of 100 PCR-amplified open chromatin regions nearby genes showing sex-biased expression or responsiveness to TCPOBOP, a xenobiotic and agonist ligand of the nuclear receptor CAR (Nr1i3). We assayed STARR-seq activity for the 100 genomic regions in male liver, in female liver and in TCPOBOP-treated male liver to quantitatively measure their intrinsic transcriptional activity under the 3 indicated biological conditions, and thereby identified enhancers whose activity is sex-dependent or xenobiotic-responsive.

2024-06-17 | GSE267041 | GEO

Liver lncRNA gene expression in response to CAR/PXR agonists

Project description:Gene expression in livers of male and female mice treated with the CAR agonist ligand TCPOBOP or the PXR agonist ligand PCN

2019-06-17 | GSE120851 | GEO

Impact of CAR agonist ligand TCPOBOP (3h and 27hr time points) on H3-K27me3 marks in adult male mouse liver

Project description:Impact of CAR agonist ligand TCPOBOP (3h and 27hr time points) on H3-K27me3 marks in adult male mouse liver

| PRJNA499062 | ENA

Modulation of the mouse liver epigenome following TCPOBOP exposure

Project description:Changes in the activating histone-H3 chromatin marks K4me1, K4me3, and K27ac were assayed in male mouse liver following exposure to TCPOBOP, an agonist ligand of the nuclear receptor CAR (constitutive androstane receptor). This work is part of a larger study, entitled: "Widespread Epigenetic Changes to the Enhancer Landscape of Mouse Liver Induced by a Specific Xenobiotic Agonist Ligand of the Nuclear Receptor CAR" (Tox Sci, 2019).

2020-04-28 | GSE104060 | GEO

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