Parallel evolution of ameloblastic scpp genes in bony and cartilaginous vertebrates

Xenopus tropicalis osteoblast-specific open chromatin regions reveal promoters and enhancers involved in human skeletal phenotypes and shed light on early vertebrate evolution

While understanding the genetic underpinnings of osteogenesis has far-reaching implications for skeletal diseases and evolution, a comprehensive characterization of the osteoblastic regulatory landscape in non-mammalian vertebrates is still lacking. Here, we compared the ATAC-Seq profile of Xenopus tropicalis (Xt) osteoblasts to a variety of non mineralizing control tissues, and identified osteoblast-specific nucleosome free regions (NFRs) at 527 promoters and 6747 distal regions. Sequence analyses, Gene Ontology, RNA-Seq and ChIP-Seq against four key histone marks confirmed that the distal regions correspond to bona fide osteogenic transcriptional enhancers exhibiting a shared regulatory logic with mammals. We report 425 regulatory regions conserved with human and globally associated to skeletogenic genes. Of these, 35 regions have been shown to impact human skeletal phenotypes by GWAS, including one trps1 enhancer and the runx2 promoter, two genes which are respectively involved in trichorhinophalangeal syndrome type I and cleidocranial dysplasia. Intriguingly, 60 osteoblastic NFRs also align to the genome of the elephant shark, a species lacking osteoblasts and bone tissue. To tackle this paradox, we chose to focus on dlx5 because its conserved promoter, known to integrate regulatory inputs during mammalian osteogenesis, harbours an osteoblast-specific NFR in both frog and human. Hence, we show that dlx5 is expressed in Xt and elephant shark odontoblasts, supporting a common cellular and genetic origin of bone and dentine. Taken together, our work (i) unravels the Xt osteogenic regulatory landscape, (ii) illustrates how cross-species comparisons harvest data relevant to human biology and (iii) reveals that a set of genes including bnc2, dlx5, ebf3, mir199a, nfia, runx2 and zfhx4 drove the development of a primitive form of mineralized skeletal tissue deep in the vertebrate lineage.

Evolution, development, and regeneration of tooth-like epithelial appendages in sharks

Sharks and their relatives are typically covered in highly specialized epithelial appendages embedded in the skin called dermal denticles; ancient tooth-like units (odontodes) composed of dentine and enamel-like tissues. These 'skin teeth' are remarkably similar to oral teeth of vertebrates and share comparable morphological and genetic signatures. Here we review the histological and morphological data from embryonic sharks to uncover characters that unite all tooth-like elements (odontodes), including teeth and skin denticles in sharks. In addition, we review the differences between the skin and oral odontodes that reflect their varied capacity for renewal. Our observations have begun to decipher the developmental and genetic shifts that separate these seemingly similar dental units, including elements of the regenerative nature in both oral teeth and the emerging skin denticles from the small-spotted catshark (Scyliorhinus canicula) and other chondrichthyan models. Ultimately, we ask what defines a tooth at both the molecular and morphological level. These insights aim to help us understand how nature makes, replaces and evolves a vast array of odontodes.

Emergence of saliva protein genes in the secretory calcium-binding phosphoprotein (SCPP) locus and accelerated evolution in primates

Genes within the secretory calcium-binding phosphoprotein (SCPP) family evolved in conjunction with major evolutionary milestones: the formation of a calcified skeleton in vertebrates, the emergence of tooth enamel in fish, and the introduction of lactation in mammals. The SCPP gene family also contains genes expressed primarily and abundantly in human saliva. Here, we explored the evolution of the saliva-related SCPP genes by harnessing currently available genomic and transcriptomic resources. Our findings provide insights into the expansion and diversification of SCPP genes, notably identifying previously undocumented convergent gene duplications. In primate genomes, we found additional duplication and diversification events that affected genes coding for proteins secreted in saliva. These saliva-related SCPP genes exhibit signatures of positive selection in the primate lineage while the other genes in the same locus remain conserved. We found that regulatory shifts and gene turnover events facilitated the accelerated gain of salivary expression. Collectively, our results position the SCPP gene family as a hotbed of evolutionary innovation, suggesting the potential role of dietary and pathogenic pressures in the adaptive diversification of the saliva composition in primates, including humans.

Ganoin and acrodin formation on scales and teeth in spotted gar: A vital role of enamelin in the unique process of enamel mineralization

Gars and bichirs develop scales and teeth with ancient actinopterygian characteristics. Their scale surface and tooth collar are covered with enamel, also known as ganoin, whereas the tooth cap is equipped with an enamel-like tissue, acrodin. Here, we investigated the formation and mineralization of the ganoin and acrodin matrices in spotted gar, and the evolution of the scpp5, ameloblastin (ambn), and enamelin (enam) genes, which encode matrix proteins of ganoin. Results suggest that, in bichirs and gars, all these genes retain structural characteristics of their orthologs in stem actinopterygians, presumably reflecting the presence of ganoin on scales and teeth. During scale formation, Scpp5 and Enam were initially found in the incipient ganoin matrix and the underlying collagen matrix, whereas Ambn was detected mostly in a surface region of the well-developed ganoin matrix. Although collagen is the principal acrodin matrix protein, Scpp5 was detected within the matrix. Similarities in timings of mineralization and the secretion of Scpp5 suggest that acrodin evolved by the loss of the matrix secretory stage of ganoin formation: dentin formation is immediately followed by the maturation stage. The late onset of Ambn secretion during ganoin formation implies that Ambn is not essential for mineral ribbon formation, the hallmark of the enamel matrix. Furthermore, Scpp5 resembles amelogenin that is not important for the initial formation of mineral ribbons in mammals. It is thus likely that the evolution of ENAM was vital to the origin of the unique mineralization process of the enamel matrix.

Dental structure and tooth attachment modes in the common fangtooth Anoplogaster cornuta (Valenciennes, 1833) (Actinopterygii; Trachichthyiformes; Anoplogastridae)

We studied the structure and attachment modes of the teeth of adult Anoplogaster cornuta using light- and scanning-electron microscopic techniques. All teeth were monocuspid, composed solely of orthodentin, and lacked a covering enameloid cap. Fourteen teeth were present in the oral jaws, with three teeth each on the left and right premaxilla and four teeth each on the left and right dentary. The anteriormost premaxillary and dentary teeth were considerably larger than the more posteriorly located ones. The oral jaw teeth were transparent, non-depressible and firmly ankylosed to their respective dentigerous bone by a largely anosteocytic bone of attachment. No evidence for replacement of the large oral jaw teeth was found in the analyzed adult specimens. The bone of attachment exhibited lower calcium and phosphorus concentrations and a higher Ca/P ratio than the orthodentin. The connection between dentinal tooth shaft and bone of attachment was stabilized by a collar of mineralized collagen fibers. In contrast to the oral jaw teeth, the pharyngeal teeth exhibited a ring-like fibrous attachment to their supporting bones. This mode of attachment provides the teeth with some lateral mobility and allows their depression relative to their supporting bones, which may facilitate intra-pharyngeal prey transport. In contrast, a firm ankylosis was observed in numerous small teeth located on the branchial arches. The function of these teeth is presumably to increase the tightness of the pharyngeal basket and thereby the retention of small prey items in a species living in a habitat with only sparse food supply. Our findings corroborate earlier statements on the tooth attachment modes of the oral jaw teeth of Anoplogaster cornuta, but provide new findings for the attachment modes of pharyngeal teeth in this species.