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

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

PROVIDER: PRJNA714679 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13972064.fastq.gz	Fastqsanger.gz
	SRR13972065.fastq.gz	Fastqsanger.gz
	SRR13972066.fastq.gz	Fastqsanger.gz
	SRR13972067.fastq.gz	Fastqsanger.gz
	SRR13972068.fastq.gz	Fastqsanger.gz

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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]

Project description: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 [ChIP-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]

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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.

| S-EPMC8608873 | biostudies-literature

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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Project description:CD4+ T cells differentiate into phenotypically distinct T-helper cells upon antigenic stimulation. Regulation of plasticity between these CD4+ T-cell lineages is critical for immune homeostasis and prevention of autoimmune diseases. However, the factors that regulate lineage stability are largely unknown. Here we investigate a role for retinoic acid (RA) in the regulation of lineage stability using T helper 1 (Th1) cells, traditionally considered the most phenotypically stable Th subset. We found that RA, through its receptor RARa, sustains stable expression of Th1 lineage specifying genes as well as repressing genes that instruct Th17 cell fate. RA signaling is essential for limiting Th1 cell conversion into Th17 effectors and for preventing pathogenic Th17 responses in vivo. Our studies identify RA-RARa as a key component of the regulatory network governing Th1 cell fate and define a new paradigm for the development of pathogenic Th17 cells. These findings have important implications for autoimmune diseases in which dysregulated Th1-Th17 responses are observed. IFN-gamma+ Th1 cells from IFNgeYFP reporter mouse; comparing dnRARa to WT

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