Identification of ancestral gnathostome Gli3 enhancers with activity in mammals

Shahid Ali, Muhammad Abrar, Irfan Hussain, Fatima Batool, Rabail Zehra Raza, Hizran Khatoon, Matteo Zoia, Axel Visel, Neil H. Shubin, Marco Osterwalder, Amir Ali Abbasi

Research output: Contribution to journalArticlepeer-review


Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15–21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. These results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.

Original languageEnglish
Pages (from-to)75-88
Number of pages14
JournalDevelopment Growth and Differentiation
Issue number1
Publication statusPublished - Jan 2024
Externally publishedYes


  • CNEs
  • Gli family
  • Gli3
  • elephant shark
  • enhancers
  • gar
  • gnathostomes
  • transgenesis
  • zebrafish


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