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| Status |
Public on Jun 13, 2023 |
| Title |
Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development [Hi-ChIP] |
| Organism |
Danio rerio |
| Experiment type |
Other
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| Summary |
Retinoic acid (RA) functions as a ligand for the nuclear RA receptors (RARs), which regulate the expression of target genes by binding to RA response elements. RA signaling is required for multiple processes during chordate embryonic development, such as body axis extension, hindbrain antero-posterior patterning and forelimb bud initiation. Although some RA target genes have been identified, little is known about the genome-wide effects of RA signaling during in vivo embryonic development. Here we stimulate the RA pathway during development by treating zebrafish embryos with all-trans-RA (atRA), the most abundant form of RA, and use a combination of RNA-seq, ATAC-seq, ChIP-seq and HiChIP to gain insight into the molecular mechanisms by which RA signaling control target gene expression. We find that RA signaling is involved in anterior/posterior patterning and development of the central nervous system, participating in the transition from pluripotency to differentiation. atRA treatment also induces alterations in chromatin accessibility during early development and promotes chromatin binding of RARaa and the RA targets Hoxb1b, Meis2b and Sox3, which cooperate in central nervous system development. Finally, we show that RA induces a rewiring of chromatin architecture, with alterations in chromatin 3D interactions that are consistent with target gene expression. This is illustrated by the specific induction of anterior HoxB genes by RARs, among other examples. Altogether, our findings identify genome-wide targets of RA signaling during embryonic development and provide a molecular mechanism by which developmental signaling pathways regulate the expression of target genes by altering chromatin topology.
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| Overall design |
HiChIP assays of H3K4me3 in wild-type zebrafish whole embryos, at developmental stage 80% epiboly, with and without treatment with 0.1µM all-trans retinoic acid (atRA)
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| Web link |
https://doi.org/10.1101/2023.06.13.544553
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| Contributor(s) |
Moreno-Oñate M, Gallardo-Fuentes L, Martínez-García PM, Naranjo S, Jiménez-Gancedo S, Gómez-Skarmeta JL, Tena JJ, Santos-Pereira JM |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
May 30, 2023 |
| Last update date |
Dec 05, 2023 |
| Contact name |
José M. Santos-Pereira |
| Organization name |
IBiS, Universidad de Sevilla-CSIC
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| Street address |
Avda. Manuel Siurot s/n
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| City |
Seville |
| ZIP/Postal code |
41013 |
| Country |
Spain |
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| Platforms (1) |
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| Samples (4)
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| GSM7432730 |
HiChIP H3K4me3 80% epiboly stage, control, replicate 1 |
| GSM7432731 |
HiChIP H3K4me3 80% epiboly stage, control, replicate 2 |
| GSM7432732 |
HiChIP H3K4me3 80% epiboly stage, atRA, replicate 1 |
| GSM7432733 |
HiChIP H3K4me3 80% epiboly stage, atRA, replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE233698 |
Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development |
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| Relations |
| BioProject |
PRJNA977615 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE233697_HiChIP_H3K4me3_80epi_atRA_combined.hic |
194.8 Mb |
(ftp)(http) |
HIC |
| GSE233697_HiChIP_H3K4me3_80epi_control_combined.hic |
149.5 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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