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| Status |
Public on Mar 16, 2021 |
| Title |
Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [RNA-seq] |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Combination of 24 RNA-seq samples. Non endodermal cells and endodermal cells (sox17:GFP +) from zebrafish embryos at 3 and 8 somites stage treated with DMO (control), retionic acid and BMS493 (RA antagonist) were generated in triplicates.
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| Contributor(s) |
López-Pérez AR, Balwierz PJ, Lenhard B, Muller F, Wardle FC, Manfroid I, Voz ML, Peers B |
| Citation(s) |
34811400 |
| |
| Submission date |
Mar 15, 2021 |
| Last update date |
Dec 07, 2021 |
| Contact name |
Ana Rosa López-Pérez |
| Organization name |
Navarrabiomed - Fundacion Migues Servet
|
| Lab |
Translational Bioinformatics
|
| Street address |
Calle Irunlarrea, 3
|
| City |
Pamplona |
| ZIP/Postal code |
31008 |
| Country |
Spain |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (24)
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| GSM5173158 |
Non endodermal cells 3 somites rep1 RNA-seq |
| GSM5173159 |
Non endodermal cells 3 somites rep2 RNA-seq |
| GSM5173160 |
Non endodermal cells 3 somites rep3 RNA-seq |
| GSM5173161 |
Endodermal cells treated with DMSO 3 somites rep1 RNA-seq |
| GSM5173162 |
Endodermal cells treated with DMSO 3 somites rep2 RNA-seq |
| GSM5173163 |
Endodermal cells treated with DMSO 3 somites rep3 RNA-seq |
| GSM5173164 |
Endodermal cells treated with RA 3 somites rep1 RNA-seq |
| GSM5173165 |
Endodermal cells treated with RA 3 somites rep2 RNA-seq |
| GSM5173166 |
Endodermal cells treated with RA 3 somites rep3 RNA-seq |
| GSM5173167 |
Endodermal cells treated with BMS 3 somites rep1 RNA-seq |
| GSM5173168 |
Endodermal cells treated with BMS 3 somites rep2 RNA-seq |
| GSM5173169 |
Endodermal cells treated with BMS 3 somites rep3 RNA-seq |
| GSM5173170 |
Non endodermal cells 8 somites rep1 RNA-seq |
| GSM5173171 |
Non endodermal cells 8 somites rep2 RNA-seq |
| GSM5173172 |
Non endodermal cells 8 somites rep3 RNA-seq |
| GSM5173173 |
Endodermal cells treated with DMSO 8 somites rep1 RNA-seq |
| GSM5173174 |
Endodermal cells treated with DMSO 8 somites rep2 RNA-seq |
| GSM5173175 |
Endodermal cells treated with DMSO 8 somites rep3 RNA-seq |
| GSM5173176 |
Endodermal cells treated with RA 8 somites rep1 RNA-seq |
| GSM5173177 |
Endodermal cells treated with RA 8 somites rep2 RNA-seq |
| GSM5173178 |
Endodermal cells treated with RA 8 somites rep3 RNA-seq |
| GSM5173179 |
Endodermal cells treated with BMS 8 somites rep1 RNA-seq |
| GSM5173180 |
Endodermal cells treated with BMS 8 somites rep2 RNA-seq |
| GSM5173181 |
Endodermal cells treated with BMS 8 somites rep3 RNA-seq |
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| This SubSeries is part of SuperSeries: |
| GSE168969 |
Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics |
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| Relations |
| BioProject |
PRJNA714676 |
| SRA |
SRP310759 |
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