Artículo
Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development
Autor/es | Moreno Oñate, Marta
Gallardo Fuentes, Lourdes Martínez García, Pedro M. Naranjo, Silvia Jiménez Gancedo, Sandra Tena, Juan J. Santos Pereira, José María |
Departamento | Universidad de Sevilla. Departamento de Biología Celular |
Fecha de publicación | 2024-04-24 |
Fecha de depósito | 2024-06-18 |
Publicado en |
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Resumen | Retinoic acid (RA) is the ligand of RA receptors (RARs), transcription factors that bind to RA response elements. RA signaling is required for multiple processes during embryonic development, including body axis extension, ... Retinoic acid (RA) is the ligand of RA receptors (RARs), transcription factors that bind to RA response elements. RA signaling is required for multiple processes during embryonic development, including 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 by treating zebrafish embryos with all-trans-RA (atRA) and use a combination of RNA-seq, ATAC-seq, ChIP-seq and HiChIP to gain insight into the molecular mechanisms by which exogenously induced RA signaling controls gene expression. We find that RA signaling is involved in anterior/posterior patterning, central nervous system development, and the transition from pluripotency to differentiation. AtRA treatment also alters chromatin accessibility during early development and promotes chromatin binding of RARαa and the RA targets Hoxb1b, Meis2b and Sox3, which cooperate in central nervous system development. Finally, we show that exogenous RA induces a rewiring of chromatin architecture, with alterations in chromatin 3D interactions involving target genes. Altogether, our findings identify genome-wide targets of RA signaling and provide a molecular mechanism by which developmental signaling pathways regulate target gene expression by altering chromatin topology. |
Agencias financiadoras | Ministerio de Ciencia e Innovación (MICIN). España Excelencia María de Maeztu Junta de Andalucía Universidad de Sevilla |
Identificador del proyecto | PID2019- 103921GB-I00
PID2022-141288NB-I00 CEX2020-001088-M ProyExcel_00363 EMC21_00188 DOC_00397 82927599 |
Cita | Moreno Oñate, M., Gallardo Fuentes, L., Martínez García, P.M., Naranjo, S., Jiménez Gancedo, S., Tena, J.J. y Santos Pereira, J.M. (2024). Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development. Nucleic Acids Research, 52 (7), 3682-3701. https://doi.org/10.1093/nar/gkae065. |
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Rewiring of the epigenome.pdf | 2.826Mb | [PDF] | Ver/ | Versión publicada |