A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large...

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Detalles Bibliográficos
Autores: Abassah-Oppong, S., Zoia, M., Mannion, Brandon J., Rouco, Raquel, Tissières, Virginie, Spurrell, Cailyn H., Roland, Virginia, Darbellay, Fabrice, Itum, Anja, Gamart, Julie, Festa-Daroux, Tabitha A., Sullivan, Carly S., Kosicki, Michael, Rodríguez-Carballo, Eddie, Fukuda-Yuzawa, Yoko, Hunter, Riana D., Novak, Catherine S., Plajzer-Frick, Ingrid, Tran, Stella, Akiyama, Jennifer A., Dickel, Diane E., López-Ríos, Javier, Barozzi, Iros, Andrey, Guillaume, Visel, Axel, Pennacchio, Len A., Cobb, J., Osterwalder, Marco
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/372247
Acceso en línea:http://hdl.handle.net/10261/372247
Access Level:acceso abierto
Palabra clave:Body patterning
Epigenomics
Gene regulation
Transcriptional regulatory elements
Descripción
Sumario:Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size. Here, we explore the cis-regulatory architecture of a gene desert flanking the Shox2 gene, which encodes a transcription factor indispensable for proximal limb, craniofacial, and cardiac pacemaker development. We identify the gene desert as a regulatory hub containing more than 15 distinct enhancers recapitulating anatomical subdomains of Shox2 expression. Ablation of the gene desert leads to embryonic lethality due to Shox2 depletion in the cardiac sinus venosus, caused in part by the loss of a specific distal enhancer. The gene desert is also required for stylopod morphogenesis, mediated via distributed proximal limb enhancers. In summary, our study establishes a multi-layered role of the Shox2 gene desert in orchestrating pleiotropic developmental expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.

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