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Series GSE233689 Query DataSets for GSE233689
Status Public on Jun 13, 2023
Title Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development [RNA-seq]
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
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.
Overall design RNA-seq assays in wild-type zebrafish whole embryos, at developmental stages 80% epiboly, 12 somites and 24 hpf, with and without treatment with 0.1µM all-trans retinoic acid (atRA)
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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
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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
Street address Avda. Manuel Siurot s/n
City Seville
ZIP/Postal code 41013
Country Spain
Platforms (1)
GPL21741 Illumina HiSeq 4000 (Danio rerio)
Samples (18)
GSM7432609 RNA-seq 80% epiboly stage, control, replicate 1
GSM7432610 RNA-seq 80% epiboly stage, control, replicate 2
GSM7432611 RNA-seq 80% epiboly stage, control, replicate 3
This SubSeries is part of SuperSeries:
GSE233698 Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development
BioProject PRJNA977604

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Supplementary file Size Download File type/resource
GSE233689_RAW.tar 2.4 Gb (http)(custom) TAR (of BW, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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