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 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.
Authors
- Axel Visel (ORCID: https://orcid.org/0000-0002-4130-7784)
- Javier López-Rı́os (ORCID: https://orcid.org/0000-0001-6731-3798)
- Cailyn H. Spurrell (ORCID: https://orcid.org/0000-0003-0681-3697)
- John Cobb (ORCID: https://orcid.org/0000-0002-1053-2604)
- Y. Fukuda (ORCID: https://orcid.org/0000-0002-9887-9820)
- Samuel Abassah‐Oppong (ORCID: https://orcid.org/0000-0001-6051-2559)
- Riana D. Hunter (ORCID: https://orcid.org/0000-0002-2888-1079)
- Diane E. Dickel (ORCID: https://orcid.org/0000-0001-5497-6824)
- Stella Tran (ORCID: https://orcid.org/0000-0001-5226-2238)
- L Pennacchio (ORCID: https://orcid.org/0000-0002-8748-3732)
- Catherine S. Novak
- Eddie Rodríguez-Carballo (ORCID: https://orcid.org/0000-0003-4321-508X)
- Guillaume Andrey (ORCID: https://orcid.org/0000-0002-0911-4907)
- Fabrice Darbellay (ORCID: https://orcid.org/0000-0001-6942-3325)
- Brandon J. Mannion (ORCID: https://orcid.org/0000-0002-1149-3790)
- Michael Kosicki (ORCID: https://orcid.org/0000-0001-7173-8852)
- Marco Osterwalder (ORCID: https://orcid.org/0000-0002-1969-2313)
- Ingrid Plajzer-Frick
- Raquel Rouco (ORCID: https://orcid.org/0000-0002-0657-0704)
- Virginia Roland (ORCID: https://orcid.org/0000-0002-5154-3959)
- Jennifer A. Akiyama (ORCID: https://orcid.org/0000-0002-0667-9355)
- Virginie Tissières (ORCID: https://orcid.org/0000-0003-4276-5514)
- Iros Barozzi (ORCID: https://orcid.org/0000-0003-0690-3473)
- Julie Gamart
- Matteo Zoia (ORCID: https://orcid.org/0000-0002-0040-0085)
- Tabitha A. Festa-Daroux (ORCID: https://orcid.org/0000-0003-4289-8704)
- Carly S. Sullivan (ORCID: https://orcid.org/0000-0002-6217-6293)
- Anja Itum
Institutions
- University of Geneva (CH)
- University of Bern (CH)
- Bern University of Applied Sciences (CH)
- Lawrence Berkeley National Laboratory (US)
- University of California, Merced (US)
- University of Calgary (CA)
- Joint Genome Institute (US)
- Universidad Loyola Andalucía (ES)
- University Hospital of Bern (CH)
- Universidad Iberoamericana (DO)
- Comprehensive Cancer Center Vienna (AT)
- Centro Andaluz de Biología del Desarrollo (ES)
- Medical University of Vienna (AT)
- Fort Hays State University (US)
- Junta de Andalucía (ES)
- Universidad Pablo de Olavide (ES)
- University of California, Berkeley (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-10-10
- DOI
- https://doi.org/10.1038/s41467-024-53009-7
- Citations
- 7
- Primary Topic
- Developmental Biology and Gene Regulation
- Type
- article
- Field-Weighted Citation Impact
- 1.64
Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Natural Sciences and Engineering Research Council of Canada