GATA4 genome binding targets in adult mouse stomach
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA656821 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12440219.fastq.gz | Fastqsanger.gz | |||
| SRR12440220.fastq.gz | Fastqsanger.gz | |||
| SRR12440221.fastq.gz | Fastqsanger.gz | |||
| SRR12440222.fastq.gz | Fastqsanger.gz | |||
| SRR12440223.fastq.gz | Fastqsanger.gz |
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Project description:GATA4 facilitates its function as a transcriptional regulator by binding to promoter and enhancer regions of target genes in the glandular stomach.
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Project description:GATA4 regulates the liver development, but it's function and the gene transcriptional programs it regulates in the adult liver is unknown. In this study, we determined the genome-wide occupancy sites of GATA4 by performing ChIP-seq of whole livers. We have identified 4409 GATA4 enrichment peaks using two peak calling methods and irreproducible discovery rate (IDR) analysis. This corresponds to 3075 genes with GATA4 peaks within -5 kb of transcription start site (TSS) and +5 kb of transcription termination site (TTS). MEME analysis shows that approximately 90% of the peaks have the WGATAR motif, suggesting direct binding by GATA4. The peaks containing the WGATAR motif have a ChIP-seq higher tag enrichment score than peaks lacking the motif. Genome Regions Enrichment of Annotations Tool (GREAT) analysis of genes bound by GATA4 identified ontologies with liver specific functions. In summary, our study shows for the first time genome-wide occupancy profile of GATA4in the adult mouse liver. ChIP-sequencing of whole mouse livers from 2-3 month old mice
2013-11-07 | E-GEOD-49131 | biostudies-arrayexpress
Project description:GATA4 regulates the liver development, but it's function and the gene transcriptional programs it regulates in the adult liver is unknown. In this study, we determined the genome-wide occupancy sites of GATA4 by performing ChIP-seq of whole livers. We have identified 4409 GATA4 enrichment peaks using two peak calling methods and irreproducible discovery rate (IDR) analysis. This corresponds to 3075 genes with GATA4 peaks within -5 kb of transcription start site (TSS) and +5 kb of transcription termination site (TTS). MEME analysis shows that approximately 90% of the peaks have the WGATAR motif, suggesting direct binding by GATA4. The peaks containing the WGATAR motif have a ChIP-seq higher tag enrichment score than peaks lacking the motif. Genome Regions Enrichment of Annotations Tool (GREAT) analysis of genes bound by GATA4 identified ontologies with liver specific functions. In summary, our study shows for the first time genome-wide occupancy profile of GATA4in the adult mouse liver.
2013-11-07 | GSE49131 | GEO
Project description:GATA4 is a transcription factor known for its crucial role in the development of many tissues, including liver; however, its role in adult liver metabolism is unknown. Here, using high-throughput sequencing technologies, including assay for transposase-accessible chromatin with sequencing (ATAC-Seq), we identified GATA4 as a transcriptional regulator of metabolism in liver. GATA4 expression is elevated in response to refeeding, and its occupancy is increased at enhancers of genes linked to fatty acid and lipoprotein metabolism. Knocking out GATA4 in adult liver (Gata4LKO) decreased transcriptional activity at GATA4 binding sites especially during feeding. Gata4LKO mice have reduced plasma HDL cholesterol and increased liver triglyceride levels. The expression of a panel of genes involved in cholesterol export and triglyceride hydrolysis was downregulated and the expression of those involved in lipid uptake were upregulated in Gata4LKO liver, We further demonstrate that GATA4 collaborates with LXR liver. GATA4 shares a number of binding sites and direct transcriptional targets with LXRs, and loss of GATA4 impairs the hepatic transcriptional response to LXR agonist. Collectively, these results show that hepatic GATA4 contributes to the transcriptional control of hepatic and systemic lipid homeostasis.
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2014-01-09 | E-GEOD-53780 | biostudies-arrayexpress
Project description:Gata factors are amongst the genes expressed early on in the process of cardiogenesis. We used microarrays to examine the immediate early targets of Gata4 and Gata5 in the Xenopus leavis animal cap cardiogenesis model. We hope to use these data to examine the roles of Gata4 and Gata5 in cardiogenesis and also to begin to dissect out the common and distinct targets of Gata4 and Gata5. Keywords: genetic modification, gene overexpresison.
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Project description:Murine Adult Stomach Small RNA
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Project description:Cardiac hypertrophy is regulated by the zinc finger-containing DNA binding factors Gata4 and Gata6, both of which are required to mount a productive growth response of the adult heart. To determine if Gata4 and Gata6 are redundant or have non-overlapping roles, we performed cardiomyocyte-specific conditional gene deletions for Gata4 and Gata6 in conjunction with reciprocal replacement with a transgene encoding either Gata4 or Gata6, during the pressure overload response. We determined that Gata4 and Gata6 play a redundant and dosage-sensitive role in programming the hypertrophic growth response itself following pressure overload stimulation. However, non-redundant functions were identified as functional decompensation induced by either Gata4 or Gata6 deletion was not rescued by the reciprocal transgene, and only Gata4 heart-specific deletion produced a reduction in capillary density after pressure overload. Gene expression profiling from hearts of these gene-deleted mice showed both overlapping and unique transcriptional codes, with Gata4 exhibiting the strongest impact. These results indicate that Gata4 and Gata6 play a dosage-dependent and semi-redundant role in programming cardiac hypertrophy, but that each has a unique role in maintaining cardiac homeostasis and adaptation to injury that cannot be compensated by the other. Microarray-bassed gene expression profiling identified overlapping, distinct, and quantitatively/differentially regulated classes of Gata4 or Gata6 regulated genes. To determine if Gata4 and Gata6 are redundant or have non-overlapping roles in programming cardiac hypertrophic responses and adaptation to stress or injury, we performed cardiomyocyte-specific conditional gene deletions for Gata4 and Gata6 in conjunction with reciprocal replacement with a transgene encoding either Gata4 or Gata6, during the pressure overload response.
2014-01-01 | E-GEOD-52317 | biostudies-arrayexpress
Project description:Gata factors are amongst the genes expressed early on in the process of cardiogenesis. We used microarrays to examine the immediate early targets of Gata4 and Gata5 in the Xenopus leavis animal cap cardiogenesis model. We hope to use these data to examine the roles of Gata4 and Gata5 in cardiogenesis and also to begin to dissect out the common and distinct targets of Gata4 and Gata5. Experiment Overall Design: Xenopus leavis embryos were injected at the one cell stage with dexamethasone-inducible Gata4 or Gata5 mRNA constructs (to examine endodermal and mesodermal targets) or with Gata4 in the presence of Dkk1 (to examine mesodermal targets.) Embryos were cultured to stage 9, whereupon animal caps were excised and cultured for 2.5 hours in media containing dexamethasone to induce the constructs and cycloheximide to block de novo protein synthesis and thus give only immediate early targets.
2008-10-18 | E-GEOD-8496 | biostudies-arrayexpress
Project description:Cardiac hypertrophy is regulated by the zinc finger-containing DNA binding factors Gata4 and Gata6, both of which are required to mount a productive growth response of the adult heart. To determine if Gata4 and Gata6 are redundant or have non-overlapping roles, we performed cardiomyocyte-specific conditional gene deletions for Gata4 and Gata6 in conjunction with reciprocal replacement with a transgene encoding either Gata4 or Gata6, during the pressure overload response. We determined that Gata4 and Gata6 play a redundant and dosage-sensitive role in programming the hypertrophic growth response itself following pressure overload stimulation. However, non-redundant functions were identified as functional decompensation induced by either Gata4 or Gata6 deletion was not rescued by the reciprocal transgene, and only Gata4 heart-specific deletion produced a reduction in capillary density after pressure overload. Gene expression profiling from hearts of these gene-deleted mice showed both overlapping and unique transcriptional codes, with Gata4 exhibiting the strongest impact. These results indicate that Gata4 and Gata6 play a dosage-dependent and semi-redundant role in programming cardiac hypertrophy, but that each has a unique role in maintaining cardiac homeostasis and adaptation to injury that cannot be compensated by the other. Microarray-bassed gene expression profiling identified overlapping, distinct, and quantitatively/differentially regulated classes of Gata4 or Gata6 regulated genes.
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