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Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [ChIP-seq]

ABSTRACT: Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [ChIP-seq]

PROVIDER: PRJNA714666 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13970392_1.fastq.gz	Fastqsanger.gz
	SRR13970392_2.fastq.gz	Fastqsanger.gz
	SRR13970393_1.fastq.gz	Fastqsanger.gz
	SRR13970393_2.fastq.gz	Fastqsanger.gz

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Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

Project description:Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

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Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [RNA-seq]

Project description:Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [RNA-seq]

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Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [ATAC-seq]

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Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [RNA-seq]

Project description:Retinoic acid (RA) is a key signal for the specification of the pancreas. Still, the gene regulatory cascade triggered by RA in the endoderm remains poorly characterized. In this study, we investigated this regulatory network in zebrafish by combining RNA-seq, RAR ChIP-seq and ATAC-seq assays. By analysing the effect of RA and of the RA receptor (RAR) antagonist BMS439 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signalling. RAR ChIP-seq further defined the direct RAR target genes including the known hox genes as well as several pancreatic regulators like mnx1, insm1b, hnf1ba and gata6. Comparison of our zebrafish data with available murine RAR ChIP-seq data highlighted conserved direct target genes and revealed that some RAR sites are under strong evolutionary constraints. Among them, a novel highly conserved RAR-induced enhancer was identified downstream of the HoxB locus and driving expression in the nervous system and in the gut in a RA-dependant manner. Finally, ATAC-seq data unveiled the role of the RAR-direct targets Hnf1ba and Gata6 in opening chromatin at many regulatory loci upon RA treatment.

2021-03-16 | GSE168966 | GEO

Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [ChIP-seq]

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Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [ATAC-seq]

2021-03-16 | GSE168960 | GEO

Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics.

Project description:Retinoic acid (RA) is a key signal for the specification of the pancreas. Still, the gene regulatory cascade triggered by RA in the endoderm remains poorly characterized. In this study, we investigated this regulatory network in zebrafish by combining RNA-seq, RAR ChIP-seq and ATAC-seq assays. By analysing the effect of RA and of the RA receptor (RAR) inverse-agonist BMS493 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signalling. RAR ChIP-seq further defined the direct RAR target genes in zebrafish, including hox genes as well as several pancreatic regulators like mnx1, insm1b, hnf1ba and gata6. Comparison of zebrafish and murine RAR ChIP-seq data highlighted the conserved direct target genes and revealed that some RAR sites are under strong evolutionary constraints. Among them, a novel highly conserved RAR-induced enhancer was identified downstream of the HoxB locus and driving expression in the nervous system and in the gut in a RA-dependent manner. Finally, ATAC-seq data unveiled the role of the RAR-direct targets Hnf1ba and Gata6 in opening chromatin at many regulatory loci upon RA treatment.

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Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

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

2021-03-16 | GSE168969 | GEO

Retinoic acid induced expression of Hnf1β and Fzd4 is required for pancreas development in Xenopus laevis

Project description:Retinoic acid (RA) is required for pancreas specification in Xenopus and other vertebrates. However, the gene network that is directly induced by RA-signalling in this context remains to be defined. We identified the transcription factor Hnf1β and the Wnt-receptor Fzd4/Fzd4s as direct RA-target genes through RNA-sequencing of in vitro generated pancreatic explants. Functional analyses of Hnf1β and Fzd4/Fzd4s in programmed pancreatic explants and whole embryos revealed their requirement for pancreatic progenitor formation and differentiation. Hnf1β and Fzd4/Fzd4s thus appear to be involved in pre-patterning events of the embryonic endoderm allowing for pancreas formation.

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Retinoic acid signaling constrains the plasticity of Th1 cells and prevents development of pathogenic Th17 cells [Affymetrix experiments]

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