Khor JM , Ettensohn CA .

Figure 1. Molecular phylogeny of Alx proteins (adapted from McGonnell et al., 2011; Koga et al., 2016). Branch lengths are arbitrary. Sk, Saccoglossus kowalevskii (acorn worm); Lv, Lytechinus variegatus (euechinoid sea urchin); Hp, Hemicentrotus pulcherrimus (euechinoid sea urchin); Sp, Strongylocentrotus purpuratus (euechinoid sea urchin); Mr, Metacrinus rotundus (sea lily); Ak, Amphipholis kochii (brittle star); Pm, Patiria miniata (sea star); Ppc, Patiria pectinifera (sea star); Bf, Branchiostoma floridae (lancelet); Dr, Danio rerio (zebrafish); Xt, Xenopus tropicalis (frog); Ac, Anolis carolinensis (lizard); Hs, Homo sapiens (human); Mm, Mus musculus (mouse).

Figure 2. Activation of Alx1 in euechinoids (S. purpuratus) and regulatory inputs into primary mesenchyme cell (PMC) effector genes. Only a small number of more than 420 effector genes differentially expressed in PMCs (Rafiq et al., 2014) is shown here. A large subset of effector genes receives regulatory inputs from both Ets1 and Alx1 (Rafiq et al., 2014). Positive regulatory inputs by Ets1 and Alx1 into msp130, sm50, and vegf-Ig-10 are described in (Oliveri et al., 2008). Direct targets of the sea urchin Alx1 (Khor et al., 2019) define a genetic subcircuit that impinges on almost all aspect of PMC morphogenesis, including directional cell migration, extracellular matrix (ECM) remodeling, cell-cell fusion, and biomineralization. Dashed arrows indicate interactions that may be indirect. For additional information regarding the developmental functions of the specific effector genes shown here, see Shashikant et al. (2018) and references therein.

Adomako-Ankomah, Growth factor-mediated mesodermal cell guidance and skeletogenesis during sea urchin gastrulation. 2013, Pubmed, Echinobase

Adomako-Ankomah, Growth factor-mediated mesodermal cell guidance and skeletogenesis during sea urchin gastrulation. 2013, Pubmed , Echinobase
Akiyama, Osteo-chondroprogenitor cells are derived from Sox9 expressing precursors. 2005, Pubmed
Amore, cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo. 2006, Pubmed , Echinobase
Barsi, Genome-wide assessment of differential effector gene use in embryogenesis. 2015, Pubmed , Echinobase
Bertola, Vertical transmission of a frontonasal phenotype caused by a novel ALX4 mutation. 2013, Pubmed
Beverdam, Severe nasal clefting and abnormal embryonic apoptosis in Alx3/Alx4 double mutant mice. 2001, Pubmed
Beverdam, Expression patterns of group-I aristaless-related genes during craniofacial and limb development. 2001, Pubmed
Bhattacherjee, CBP/p300 and associated transcriptional co-activators exhibit distinct expression patterns during murine craniofacial and neural tube development. 2009, Pubmed
Bluteau, VEGF and VEGF receptors are differentially expressed in chondrocytes. 2007, Pubmed
Bolean, Biophysical aspects of biomineralization. 2017, Pubmed
Bothe, The molecular setup of the avian head mesoderm and its implication for craniofacial myogenesis. 2006, Pubmed
Bothe, Dynamic control of head mesoderm patterning. 2011, Pubmed
Brazeau, Endochondral bone in an Early Devonian 'placoderm' from Mongolia. 2020, Pubmed
Brenig, A 20 bp Duplication in Exon 2 of the Aristaless-Like Homeobox 4 Gene (ALX4) Is the Candidate Causative Mutation for Tibial Hemimelia Syndrome in Galloway Cattle. 2015, Pubmed
Brew, The tissue inhibitors of metalloproteinases (TIMPs): an ancient family with structural and functional diversity. 2010, Pubmed
Cameron, Biomineral ultrastructure, elemental constitution and genomic analysis of biomineralization-related proteins in hemichordates. 2012, Pubmed , Echinobase
Capellini, Scapula development is governed by genetic interactions of Pbx1 with its family members and with Emx2 via their cooperative control of Alx1. 2010, Pubmed
Carlevaro, Vascular endothelial growth factor (VEGF) in cartilage neovascularization and chondrocyte differentiation: auto-paracrine role during endochondral bone formation. 2000, Pubmed
Cattell, A new mechanistic scenario for the origin and evolution of vertebrate cartilage. 2011, Pubmed
Cervantes-Diaz, Evolutionary origin of endochondral ossification: the transdifferentiation hypothesis. 2017, Pubmed
Chan, Polydactylous limbs in Strong's Luxoid mice result from ectopic polarizing activity. 1995, Pubmed
Cheung, Acquisition of multipotent and migratory neural crest cells in vertebrate evolution. 2019, Pubmed
Cole, A review of diversity in the evolution and development of cartilage: the search for the origin of the chondrocyte. 2011, Pubmed
Czarkwiani, Expression of skeletogenic genes during arm regeneration in the brittle star Amphiura filiformis. 2013, Pubmed , Echinobase
Dash, The development, patterning and evolution of neural crest cell differentiation into cartilage and bone. 2020, Pubmed
Dee, Defective neural crest migration revealed by a Zebrafish model of Alx1-related frontonasal dysplasia. 2013, Pubmed
Du, Characterization of Fam20C expression in odontogenesis and osteogenesis using transgenic mice. 2015, Pubmed
Duan, Vegfa regulates perichondrial vascularity and osteoblast differentiation in bone development. 2015, Pubmed
Duloquin, Localized VEGF signaling from ectoderm to mesenchyme cells controls morphogenesis of the sea urchin embryo skeleton. 2007, Pubmed , Echinobase
Dylus, Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution. 2018, Pubmed , Echinobase
Dylus, Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. 2016, Pubmed , Echinobase
El-Ruby, Identification of a novel homozygous ALX4 mutation in two unrelated patients with frontonasal dysplasia type-2. 2018, Pubmed
Erkenbrack, Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses. 2015, Pubmed , Echinobase
Erkenbrack, A Conserved Role for VEGF Signaling in Specification of Homologous Mesenchymal Cell Types Positioned at Spatially Distinct Developmental Addresses in Early Development of Sea Urchins. 2017, Pubmed , Echinobase
Erkenbrack, Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity. 2019, Pubmed , Echinobase
Ettensohn, The gene regulatory control of sea urchin gastrulation. 2020, Pubmed , Echinobase
Ettensohn, The evolution of a new cell type was associated with competition for a signaling ligand. 2019, Pubmed , Echinobase
Ettensohn, Alx1, a member of the Cart1/Alx3/Alx4 subfamily of Paired-class homeodomain proteins, is an essential component of the gene network controlling skeletogenic fate specification in the sea urchin embryo. 2003, Pubmed , Echinobase
Ettensohn, Gene regulatory networks and developmental plasticity in the early sea urchin embryo: alternative deployment of the skeletogenic gene regulatory network. 2007, Pubmed , Echinobase
Fondon, Molecular origins of rapid and continuous morphological evolution. 2004, Pubmed
Forlino, A diastrophic dysplasia sulfate transporter (SLC26A2) mutant mouse: morphological and biochemical characterization of the resulting chondrodysplasia phenotype. 2005, Pubmed
FORSTHOEFEL, THE EMBRYOLOGICAL DEVELOPMENT OF THE EFFECTS OF STRONG'S LUXOID GENE IN THE MOUSE. 1963, Pubmed
Gao, Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution. 2008, Pubmed , Echinobase
Gao, Juvenile skeletogenesis in anciently diverged sea urchin clades. 2015, Pubmed , Echinobase
Garg, Alx4 relays sequential FGF signaling to induce lacrimal gland morphogenesis. 2017, Pubmed
Gerber, VEGF couples hypertrophic cartilage remodeling, ossification and angiogenesis during endochondral bone formation. 1999, Pubmed
Goh, Collagenous Extracellular Matrix Biomaterials for Tissue Engineering: Lessons from the Common Sea Urchin Tissue. 2017, Pubmed , Echinobase
Green, Multifaceted signaling regulators of chondrogenesis: Implications in cartilage regeneration and tissue engineering. 2015, Pubmed
Haila, SLC26A2 (diastrophic dysplasia sulfate transporter) is expressed in developing and mature cartilage but also in other tissues and cell types. 2001, Pubmed
Hao, Dentin matrix protein 4, a novel secretory calcium-binding protein that modulates odontoblast differentiation. 2007, Pubmed
Hirasawa, Evolution of the vertebrate skeleton: morphology, embryology, and development. 2015, Pubmed
Hu, A SLC4 family bicarbonate transporter is critical for intracellular pH regulation and biomineralization in sea urchin embryos. 2018, Pubmed , Echinobase
Hudson, Alx-4, a transcriptional activator whose expression is restricted to sites of epithelial-mesenchymal interactions. 1998, Pubmed
Hughes, Otopetrin 1 is required for otolith formation in the zebrafish Danio rerio. 2004, Pubmed
Hughes, Otopetrin 1 activation by purinergic nucleotides regulates intracellular calcium. 2007, Pubmed
Hurle, Non-syndromic vestibular disorder with otoconial agenesis in tilted/mergulhador mice caused by mutations in otopetrin 1. 2003, Pubmed
Ingersoll, Matrix metalloproteinase inhibitors disrupt spicule formation by primary mesenchyme cells in the sea urchin embryo. 1998, Pubmed , Echinobase
Jackson, Pseudoachondroplasia and multiple epiphyseal dysplasia: a 7-year comprehensive analysis of the known disease genes identify novel and recurrent mutations and provides an accurate assessment of their relative contribution. 2012, Pubmed
Jacobsen, Bone formation during distraction osteogenesis is dependent on both VEGFR1 and VEGFR2 signaling. 2008, Pubmed
Jacome-Galarza, Developmental origin, functional maintenance and genetic rescue of osteoclasts. 2019, Pubmed
Jandzik, Evolution of the new vertebrate head by co-option of an ancient chordate skeletal tissue. 2015, Pubmed
Jin, MMP-2 functions as a negative regulator of chondrogenic cell condensation via down-regulation of the FAK-integrin beta1 interaction. 2007, Pubmed
Kaucka, Evolution and development of the cartilaginous skull: From a lancelet towards a human face. 2019, Pubmed
Kawasaki, Genetic basis for the evolution of vertebrate mineralized tissue. 2004, Pubmed
Kayserili, ALX4 dysfunction disrupts craniofacial and epidermal development. 2009, Pubmed
Keating, The nature of aspidin and the evolutionary origin of bone. 2018, Pubmed
Khor, Functional divergence of paralogous transcription factors supported the evolution of biomineralization in echinoderms. 2017, Pubmed , Echinobase
Khor, Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis. 2019, Pubmed , Echinobase
Killian, SpSM30 gene family expression patterns in embryonic and adult biomineralized tissues of the sea urchin, Strongylocentrotus purpuratus. 2010, Pubmed , Echinobase
Kim, Regulation of cellular calcium in vestibular supporting cells by otopetrin 1. 2010, Pubmed
Koga, Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton. 2016, Pubmed , Echinobase
Kuijper, Genetics of shoulder girdle formation: roles of Tbx15 and aristaless-like genes. 2005, Pubmed
Kuijper, Function and regulation of Alx4 in limb development: complex genetic interactions with Gli3 and Shh. 2005, Pubmed
Kuratani, Evolution of the Vertebrate Cranium: Viewed from Hagfish Developmental Studies. 2016, Pubmed
Lamichhaney, Evolution of Darwin's finches and their beaks revealed by genome sequencing. 2015, Pubmed
Le Douarin, Piecing together the vertebrate skull. 2012, Pubmed
Lefebvre, Roles and regulation of SOX transcription factors in skeletogenesis. 2019, Pubmed
Li, Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms. 2020, Pubmed , Echinobase
Liang, TIMP-1 inhibits proliferation and osteogenic differentiation of hBMSCs through Wnt/β-catenin signaling. 2019, Pubmed
Liao, Clinical and molecular characterization of a transmitted reciprocal translocation t(1;12)(p32.1;q21.3) in a family co-segregating with mental retardation, language delay, and microcephaly. 2011, Pubmed
Liu, Specific ablation of mouse Fam20C in cells expressing type I collagen leads to skeletal defects and hypophosphatemia. 2017, Pubmed
Livingston, A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus. 2006, Pubmed , Echinobase
Lyons, Aristaless-Like Homeobox protein 1 (ALX1) variant associated with craniofacial structure and frontonasal dysplasia in Burmese cats. 2016, Pubmed
Mackie, Endochondral ossification: how cartilage is converted into bone in the developing skeleton. 2008, Pubmed
Marin, Organic matrices in metazoan calcium carbonate skeletons: Composition, functions, evolution. 2016, Pubmed
Marín-Llera, Understanding the Cellular and Molecular Mechanisms That Control Early Cell Fate Decisions During Appendicular Skeletogenesis. 2019, Pubmed
Martik, Regulatory Logic Underlying Diversification of the Neural Crest. 2017, Pubmed
Matsubara, Upstream regulation for initiation of restricted Shh expression in the chick limb bud. 2017, Pubmed
Mavrogiannis, Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype. 2006, Pubmed
McCauley, Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms. 2012, Pubmed , Echinobase
McClay, Gastrulation in the sea urchin. 2020, Pubmed , Echinobase
McDougall, The evolution of mollusc shells. 2018, Pubmed
McGonnell, Evolution of the Alx homeobox gene family: parallel retention and independent loss of the vertebrate Alx3 gene. 2011, Pubmed
McIntyre, Branching out: origins of the sea urchin larval skeleton in development and evolution. 2014, Pubmed , Echinobase
Meulemans, Insights from amphioxus into the evolution of vertebrate cartilage. 2007, Pubmed
Morgulis, Possible cooption of a VEGF-driven tubulogenesis program for biomineralization in echinoderms. 2019, Pubmed , Echinobase
Morino, Heterochronic activation of VEGF signaling and the evolution of the skeleton in echinoderm pluteus larvae. 2012, Pubmed , Echinobase
Murdock, Evolutionary origins of animal skeletal biomineralization. 2011, Pubmed
Murshed, Mechanism of Bone Mineralization. 2018, Pubmed
Noden, Relations and interactions between cranial mesoderm and neural crest populations. 2005, Pubmed
Oliveri, Global regulatory logic for specification of an embryonic cell lineage. 2008, Pubmed , Echinobase
Percival, Angiogenesis and intramembranous osteogenesis. 2013, Pubmed
Piacentino, RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins. 2016, Pubmed , Echinobase
Poulet, Overexpression of TIMP-3 in Chondrocytes Produces Transient Reduction in Growth Plate Length but Permanently Reduces Adult Bone Quality and Quantity. 2016, Pubmed
Qu, Alx-4: cDNA cloning and characterization of a novel paired-type homeodomain protein. 1997, Pubmed
Qu, Polydactyly and ectopic ZPA formation in Alx-4 mutant mice. 1997, Pubmed
Rafaelsen, Exome sequencing reveals FAM20c mutations associated with fibroblast growth factor 23-related hypophosphatemia, dental anomalies, and ectopic calcification. 2013, Pubmed
Rafiq, The genomic regulatory control of skeletal morphogenesis in the sea urchin. 2012, Pubmed , Echinobase
Rafiq, Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins. 2014, Pubmed , Echinobase
Rice, Progression of calvarial bone development requires Foxc1 regulation of Msx2 and Alx4. 2003, Pubmed
Richardson, Expression of an embryonic spicule matrix gene in calcified tissues of adult sea urchins. 1989, Pubmed , Echinobase
Roe, Inhibitors of metalloendoproteases block spiculogenesis in sea urchin primary mesenchyme cells. 1989, Pubmed , Echinobase
Rose, A Tale of Two Joints: The Role of Matrix Metalloproteases in Cartilage Biology. 2016, Pubmed
Rothstein, The molecular basis of neural crest axial identity. 2018, Pubmed
Rychel, Evolution and development of the chordates: collagen and pharyngeal cartilage. 2006, Pubmed
Rychel, Development and evolution of chordate cartilage. 2007, Pubmed
Santagati, Cranial neural crest and the building of the vertebrate head. 2003, Pubmed
Saotome, Structures of the otopetrin proton channels Otop1 and Otop3. 2019, Pubmed
Seidahmed, Report of a case of Raine syndrome and literature review. 2015, Pubmed
Sharma, Regulative deployment of the skeletogenic gene regulatory network during sea urchin development. 2011, Pubmed , Echinobase
Shashikant, From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms. 2018, Pubmed , Echinobase
Shubin, Deep homology and the origins of evolutionary novelty. 2009, Pubmed
Simões-Costa, Establishing neural crest identity: a gene regulatory recipe. 2015, Pubmed
Simpson, Mutations in FAM20C are associated with lethal osteosclerotic bone dysplasia (Raine syndrome), highlighting a crucial molecule in bone development. 2007, Pubmed
Söllner, Mutated otopetrin 1 affects the genesis of otoliths and the localization of Starmaker in zebrafish. 2004, Pubmed
Square, A gene expression map of the larval Xenopus laevis head reveals developmental changes underlying the evolution of new skeletal elements. 2015, Pubmed
Square, The origin and diversification of the developmental mechanisms that pattern the vertebrate head skeleton. 2017, Pubmed
Superti-Furga, A chondrodysplasia family produced by mutations in the diastrophic dysplasia sulfate transporter gene: genotype/phenotype correlations. 1996, Pubmed
Suzuki, Comparative analysis of fibrillar and basement membrane collagen expression in embryos of the sea urchin, Strongylocentrotus purpuratus. 1997, Pubmed , Echinobase
Tagliabracci, Secreted kinase phosphorylates extracellular proteins that regulate biomineralization. 2012, Pubmed
Takahashi, The role of Alx-4 in the establishment of anteroposterior polarity during vertebrate limb development. 1998, Pubmed
Takeyari, Hypophosphatemic osteomalacia and bone sclerosis caused by a novel homozygous mutation of the FAM20C gene in an elderly man with a mild variant of Raine syndrome. 2014, Pubmed
Tarazona, The genetic program for cartilage development has deep homology within Bilateria. 2016, Pubmed
ten Berge, Mouse Alx3: an aristaless-like homeobox gene expressed during embryogenesis in ectomesenchyme and lateral plate mesoderm. 1998, Pubmed
Tuckermann, Collagenase-3 (MMP-13) and integral membrane protein 2a (Itm2a) are marker genes of chondrogenic/osteoblastic cells in bone formation: sequential temporal, and spatial expression of Itm2a, alkaline phosphatase, MMP-13, and osteocalcin in the mouse. 2000, Pubmed
Twigg, Frontorhiny, a distinctive presentation of frontonasal dysplasia caused by recessive mutations in the ALX3 homeobox gene. 2009, Pubmed
Ullah, Exome sequencing revealed a novel nonsense variant in ALX3 gene underlying frontorhiny. 2018, Pubmed
Uz, Disruption of ALX1 causes extreme microphthalmia and severe facial clefting: expanding the spectrum of autosomal-recessive ALX-related frontonasal dysplasia. 2010, Pubmed
Valente, Malformation of cortical and vascular development in one family with parietal foramina determined by an ALX4 homeobox gene mutation. 2004, Pubmed
Veis, Organic matrix-related mineralization of sea urchin spicules, spines, test and teeth. 2011, Pubmed , Echinobase
Vogel, Amelogenesis imperfecta and other biomineralization defects in Fam20a and Fam20c null mice. 2012, Pubmed
Wang, Expression of FAM20C in the osteogenesis and odontogenesis of mouse. 2010, Pubmed
Wang, Gene profiling of head mesoderm in early zebrafish development: insights into the evolution of cranial mesoderm. 2019, Pubmed
Wang, Inactivation of a novel FGF23 regulator, FAM20C, leads to hypophosphatemic rickets in mice. 2012, Pubmed
Whittaker, The echinoderm adhesome. 2006, Pubmed , Echinobase
Wilt, Biomineralization of the spicules of sea urchin embryos. 2002, Pubmed , Echinobase
Wood, Problems in Fish-to-Tetrapod Transition: Genetic Expeditions Into Old Specimens. 2018, Pubmed
Wuyts, The ALX4 homeobox gene is mutated in patients with ossification defects of the skull (foramina parietalia permagna, OMIM 168500). 2000, Pubmed
Yagnik, ALX4 gain-of-function mutations in nonsyndromic craniosynostosis. 2012, Pubmed
Yajima, Implication of HpEts in gene regulatory networks responsible for specification of sea urchin skeletogenic primary mesenchyme cells. 2010, Pubmed , Echinobase
Yamasu, Functional organization of DNA elements regulating SM30alpha, a spicule matrix gene of sea urchin embryos. 1999, Pubmed , Echinobase
Yang, Hypertrophic chondrocytes can become osteoblasts and osteocytes in endochondral bone formation. 2014, Pubmed
York, The origin and evolution of vertebrate neural crest cells. 2020, Pubmed
Young, Genetics of scapula and pelvis development: An evolutionary perspective. 2019, Pubmed
Zhao, Prenatal folic acid treatment suppresses acrania and meroanencephaly in mice mutant for the Cart1 homeobox gene. 1996, Pubmed
Zhao, The gene for the homeodomain-containing protein Cart-1 is expressed in cells that have a chondrogenic potential during embryonic development. 1994, Pubmed
Zhuravlev, The two phases of the Cambrian Explosion. 2018, Pubmed