ArticleScientific reports2012
Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties.
Article in Scientific reports, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 34 citations in OpenAlex.
- The application of irreversible genomic states to define and trace ancient cell type homologies.EvoDevo · 2025Article
- Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease.Frontiers in cell and developmental biology · 2021Review
- Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications.Molecular biology and evolution · 2020Article
- Hedgehog-FGF signaling axis patterns anterior mesoderm during gastrulation.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.eLife · 2018Article
- Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation.Nature communications · 2017Article
- Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle.Genome biology and evolution · 2016Article
- Cis-regulatory architecture of a brain signaling center predates the origin of chordates.Nature genetics · 2016Article
- Genome-wide analysis of functional and evolutionary features of tele-enhancers.G3 (Bethesda, Md.) · 2014Article
- Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates.PloS one · 2014Article
- Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression.BMC genomics · 2012Article
- Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.Genome research · 2012Article
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Authors and funding
6 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The origin and evolution of the complex regulatory landscapes of some vertebrate developmental genes, often spanning hundreds of Kbp and including neighboring genes, remain poorly understood. The Sonic Hedgehog (Shh) genomic regulatory block (GRB) is one of the best functionally characterized examples, with several discrete enhancers reported within its introns, vast upstream gene-free region and neighboring genes (Lmbr1 and Rnf32). To investigate the origin and evolution of this GRB, we sequenced and characterized the Hedgehog (Hh) loci from three invertebrate chordate amphioxus species, which share several early expression domains with Shh. Using phylogenetic footprinting within and between chordate lineages, and reporter assays in zebrafish probing >30 Kbp of amphioxus Hh, we report large sequence and functional divergence between both groups. In addition, we show that the linkage of Shh to Lmbr1 and Rnf32, necessary for the unique gnatostomate-specific Shh limb expression, is a vertebrate novelty occurred between the two whole-genome duplications.
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