Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs

Perspectives on Principles of Cellular Behavior from the Biophysics of Protists

Cells are the fundamental unit of biological organization. Although it may be easy to think of them as little more than the simple building blocks of complex organisms such as animals, single cells are capable of behaviors of remarkable apparent sophistication. This is abundantly clear when considering the diversity of form and function among the microbial eukaryotes, the protists. How might we navigate this diversity in the search for general principles of cellular behavior? Here, we review cases in which the intensive study of protists from the perspective of cellular biophysics has driven insight into broad biological questions of morphogenesis, navigation and motility, and decision making. We argue that applying such approaches to questions of evolutionary cell biology presents rich, emerging opportunities. Integrating and expanding biophysical studies across protist diversity, exploiting the unique characteristics of each organism, will enrich our understanding of general underlying principles.

Developmental regulation of conserved non-coding element evolution provides insights into limb loss in squamates

Limb loss shows recurrent phenotypic evolution across squamate lineages. Here, based on three de novo-assembled genomes of limbless lizards from different lineages, we showed that divergence of conserved non-coding elements (CNEs) played an important role in limb development. These CNEs were associated with genes required for limb initiation and outgrowth, and with regulatory signals in the early stage of limb development. Importantly, we identified the extensive existence of insertions and deletions (InDels) in the CNEs, with the numbers ranging from 111 to 756. Most of these CNEs with InDels were lineage-specific in the limbless squamates. Nearby genes of these InDel CNEs were important to early limb formation, such as Tbx4, Fgf10, and Gli3. Based on functional experiments, we found that nucleotide mutations and InDels both affected the regulatory function of the CNEs. Our study provides molecular evidence underlying limb loss in squamate reptiles from a developmental perspective and sheds light on the importance of regulatory element InDels in phenotypic evolution.

Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes

Changes in gene expression represent an important source of phenotypic innovation. Yet how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing integrative analyses of epigenetic and transcriptional data in mole and mouse, we identified the co-option of SALL1 expression in mole ovotestes formation. Chromosome conformation capture analyses highlight a striking conservation of the 3D organization at the SALL1 locus, but an evolutionary divergence of enhancer activity. Interspecies reporter assays support the capability of mole-specific enhancers to activate transcription in urogenital tissues. Through overexpression experiments in transgenic mice, we further demonstrate the capability of SALL1 to induce kidney-related gene programs, which are a signature of mole ovotestes. Our results highlight the co-option of gene expression, through changes in enhancer activity, as a plausible mechanism for the evolution of traits.

Distinct patterning responses of wing and leg neuromuscular systems to different preaxial polydactylies

The tetrapod limb has long served as a paradigm to study vertebrate pattern formation and evolutionary diversification. The distal part of the limb, the so-called autopod, is of particular interest in this regard, given the numerous modifications in both its morphology and behavioral motor output. While the underlying alterations in skeletal form have received considerable attention, much less is known about the accompanying changes in the neuromuscular system. However, modifications in the skeleton need to be properly integrated with both muscle and nerve patterns, to result in a fully functional limb. This task is further complicated by the distinct embryonic origins of the three main tissue types involved-skeleton, muscles and nerves-and, accordingly, how they are patterned and connected with one another during development. To evaluate the degree of regulative crosstalk in this complex limb patterning process, here we analyze the developing limb neuromuscular system of Silkie breed chicken. These animals display a preaxial polydactyly, due to a polymorphism in the limb regulatory region of the Sonic Hedgehog gene. Using lightsheet microscopy and 3D-reconstructions, we investigate the neuromuscular patterns of extra digits in Silkie wings and legs, and compare our results to Retinoic Acid-induced polydactylies. Contrary to previous findings, Silkie autopod muscle patterns do not adjust to alterations in the underlying skeletal topology, while nerves show partial responsiveness. We discuss the implications of tissue-specific sensitivities to global limb patterning cues for our understanding of the evolution of novel forms and functions in the distal tetrapod limb.

Frem1 activity is regulated by Sonic hedgehog signaling in the cranial neural crest mesenchyme during midfacial morphogenesis

BACKGROUND

Frem1 has been linked to human face shape variation, dysmorphology, and malformation, but little is known about its regulation and biological role in facial development.

RESULTS

During midfacial morphogenesis in mice, we observed Frem1 expression in the embryonic growth centers that form the median upper lip, nose, and palate. Expansive spatial gradients of Frem1 expression in the cranial neural crest cell (cNCC) mesenchyme of these tissues suggested transcriptional regulation by a secreted morphogen. Accordingly, Frem1 expression paralleled that of the conserved Sonic Hedgehog (Shh) target gene Gli1 in the cNCC mesenchyme. Suggesting direct transcriptional regulation by Shh signaling, we found that Frem1 expression is induced by SHH ligand stimulation or downstream pathway activation in cNCCs and observed GLI transcription factor binding at the Frem1 transcriptional start site during midfacial morphogenesis. Finally, we found that FREM1 is sufficient to induce cNCC proliferation in a concentration-dependent manner and that Shh pathway antagonism reduces Frem1 expression during pathogenesis of midfacial hypoplasia.

CONCLUSIONS

By demonstrating that the Shh signaling pathway regulates Frem1 expression in cNCCs, these findings provide novel insight into the mechanisms underlying variation in midfacial morphogenesis.

The little skate genome and the evolutionary emergence of wing-like fins

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins-including gene expression, chromatin occupancy and three-dimensional conformation-we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

Evolutionary genetics of flipper forelimb and hindlimb loss from limb development-related genes in cetaceans

Background

Cetacean hindlimbs were lost and their forelimb changed into flippers characterized by webbed digits and hyperphalangy, thus allowing them to adapt to a completely aquatic environment. However, the underlying molecular mechanism behind cetacean limb development remains poorly understood.

Results

In the present study, we explored the evolution of 16 limb-related genes and their cis-regulatory elements in cetaceans and compared them with that of other mammals. TBX5, a forelimb specific expression gene, was identified to have been under accelerated evolution in the ancestral branches of cetaceans. In addition, 32 cetacean-specific changes were examined in the SHH signaling network (SHH, PTCH1, TBX5, BMPs and SMO), within which mutations could yield webbed digits or an additional phalange. These findings thus suggest that the SHH signaling network regulates cetacean flipper formation. By contrast, the regulatory activity of the SHH gene enhancer—ZRS in cetaceans—was significantly lower than in mice, which is consistent with the cessation of SHH gene expression in the hindlimb bud during cetacean embryonic development. It was suggested that the decreased SHH activity regulated by enhancer ZRS might be one of the reasons for hindlimb degeneration in cetaceans. Interestingly, a parallel / convergent site (D42G) and a rapidly evolving CNE were identified in marine mammals in FGF10 and GREM1, respectively, and shown to be essential to restrict limb bud size; this is molecular evidence explaining the convergence of flipper-forelimb and shortening or degeneration of hindlimbs in marine mammals.

Conclusions

We did evolutionary analyses of 16 limb-related genes and their cis-regulatory elements in cetaceans and compared them with those of other mammals to provide novel insights into the molecular basis of flipper forelimb and hindlimb loss in cetaceans.

Gene expression changes during the evolution of the tetrapod limb

Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb development have been discerned over the past century using a combination of classical embryological and molecular methods, only recent advances made it possible to identify and study the regulatory changes that have contributed to the evolution of the tetrapod appendage. These advances include the expansion of the model repertoire from traditional genetic model species to non-conventional ones, a proliferation of predictive mathematical models that describe gene interactions, an explosion in genomic data and the development of high-throughput methodologies. These revolutionary innovations make it possible to identify specific mutations that are behind specific transitions in limb evolution. Also, as we continue to apply them to more and more extant species, we can expect to gain a fine-grained view of this evolutionary transition that has been so consequential for our species as well.

A limb bud morphogen bites the dust

Hedgehog signaling has traditionally been considered to be a morphogen for digits. In this issue of Developmental Cell, Zhu et al. show that a brief exposure to Sonic Hedgehog is sufficient for digit specification, and this finding suggests that it is not acting as a direct morphogen but rather as an initiator of this process.

THE FORELIMBS OF ALVAREZSAUROIDEA (DINOSAURIA: THEROPODA): INSIGHT FROM EVOLUTIONARY TERATOLOGY

Alvarezsauroidea (Tetanurae) are non-avian theropod dinosaurs whose forelimb evolution is characterised by overdevelopment of digit I, at the expense of the other two digits, complemented by a drastic forelimb shortening in derived species (Parvicursorinae). These variations are recognised as evolutionary developmental anomalies. Evolutionary teratology hence leads to a double diagnosis with 1) macrodactyly of digit I and microdactyly of digits II and III, plus 2) anterior micromelia. The teratological macrodactyly/microdactyly coupling evolved first. Developmental mechanisms disturbing limb proportion are thought to be convergent with those of other Tetanurae (Tyrannosauridae, Carcharodontosauridae). As for the manual anomalies, both are specific to Alvarezsauroidea (macrodactyly/microdactyly) and inherited (digit loss/reduction). While considering the frame-shift theory, posterior digits develop before the most anterior one. There would therefore be a decrease in the area devoted to digits II (condensation 3) and III (condensation 4), in connection with the Shh signalling pathway, interacting with other molecular players such as the GLI 3 protein and the Hox system. Developmental independence of digit I (condensation 2) would contribute to generate a particular morphology. Macrodactyly would be linked to a variation in Hoxd-13, impacting Gli3 activity, increasing cell proliferation. The loss/reduction of digital ray/phalanges (digits II and III), would be associated to Shh activity, a mechanism inherited from the theropodan ancestry. The macrodactyly/macrodactyly coupling, and then anterior micromelia, fundamentally changed the forelimb mechanical function, compared to the 'classical' grasping structure of basal representatives and other theropods. The distal ossification of the macrodactylian digit has been identified as physiological, implying the use of the structure. However, the debate of a particular 'adaptive' use is pointless since the ecology of an organism is interactively complex, being both at the scale of the individual and dependent on circumstances. Other anatomical features also allow for compensation and a different predation (cursorial hindlimbs). This article is protected by copyright. All rights reserved.

GLI transcriptional repression is inert prior to Hedgehog pathway activation

The Hedgehog (HH) pathway regulates a spectrum of developmental processes through the transcriptional mediation of GLI proteins. GLI repressors control tissue patterning by preventing sub-threshold activation of HH target genes, presumably even before HH induction, while lack of GLI repression activates most targets. Despite GLI repression being central to HH regulation, it is unknown when it first becomes established in HH-responsive tissues. Here, we investigate whether GLI3 prevents precocious gene expression during limb development. Contrary to current dogma, we find that GLI3 is inert prior to HH signaling. While GLI3 binds to most targets, loss of Gli3 does not increase target gene expression, enhancer acetylation or accessibility, as it does post-HH signaling. Furthermore, GLI repression is established independently of HH signaling, but after its onset. Collectively, these surprising results challenge current GLI pre-patterning models and demonstrate that GLI repression is not a default state for the HH pathway.

GLI repression has been presumed to be the default transcriptional state and important for pre-patterning tissues. Challenging current models, the authors show that GLI3 repression is inert in the limb bud before the onset of Hedgehog signaling.

Ossification pattern of the unusual pisiform in two-toed (Choloepus) and three-toed sloths (Bradypus)

Two-toed (Choloepus sp.) and three-toed (Bradypus sp.) sloths possess short, rounded pisiforms that are rare among mammals and differ from other members of Xenarthra like the giant anteater (Myrmecophaga tridactyla) which retain elongated, rod-like pisiforms in common with most mammals. Using photographs, radiographs, and μCT, we assessed ossification patterns in the pisiform and the paralogous tarsal, the calcaneus, for two-toed sloths, three-toed sloths, and giant anteaters to determine the process by which pisiform reduction occurs in sloths and compare it to other previously studied examples of pisiform reduction in humans and orangutans. Both extant sloth genera achieve pisiform reduction through the loss of a secondary ossification center and the likely disruption of the associated growth plate based on an unusually porous subchondral surface. This represents a third unique mechanism of pisiform reduction among mammals, along with primary ossification center loss in humans and retention of two ossification centers with likely reduced growth periods in orangutans. Given the remarkable similarities between two-toed and three-toed sloth pisiform ossification patterns and the presence of pisiform reduction in fossil sloths, extant sloth pisiform morphology does not appear to represent a recent convergent adaptation to suspensory locomotion, but instead is likely to be an ancestral trait of Folivora that emerged early in the radiation of extant and fossil sloths.

(Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss

Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. The multiple routes to appendage reduction and loss suggest that adaptive loss of function phenotypes might arise routinely through changes in expression of key developmental genes.

Conserved and species-specific chromatin remodeling and regulatory dynamics during mouse and chicken limb bud development

Chromatin remodeling and genomic alterations impact spatio-temporal regulation of gene expression, which is central to embryonic development. The analysis of mouse and chicken limb development provides important insights into the morphoregulatory mechanisms, however little is known about the regulatory differences underlying their morphological divergence. Here, we identify the underlying shared and species-specific epigenomic and genomic variations. In mouse forelimb buds, we observe striking synchrony between the temporal dynamics of chromatin accessibility and gene expression, while their divergence in chicken wing buds uncovers species-specific regulatory heterochrony. In silico mapping of transcription factor binding sites and computational footprinting establishes the developmental time-restricted transcription factor-DNA interactions. Finally, the construction of target gene networks for HAND2 and GLI3 transcriptional regulators reveals both conserved and species-specific interactions. Our analysis reveals the impact of genome evolution on the regulatory interactions orchestrating vertebrate limb bud morphogenesis and provides a molecular framework for comparative Evo-Devo studies.

The vertebrate limb bud is a paradigm to uncover the fundamental mechanisms that govern embryogenesis and evolutionary diversification. Here the authors compare mouse and chicken limb bud development to study the impact of genome evolution on conserved and divergent gene regulatory interactions.

Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity

Precise cis-regulatory control of gene expression is essential for normal embryogenesis and tissue development. The BMP antagonist Gremlin1 (Grem1) is a key node in the signalling system that coordinately controls limb bud development. Here, we use mouse reverse genetics to identify the enhancers in the Grem1 genomic landscape and the underlying cis-regulatory logics that orchestrate the spatio-temporal Grem1 expression dynamics during limb bud development. We establish that transcript levels are controlled in an additive manner while spatial regulation requires synergistic interactions among multiple enhancers. Disrupting these interactions shows that altered spatial regulation rather than reduced Grem1 transcript levels prefigures digit fusions and loss. Two of the enhancers are evolutionary ancient and highly conserved from basal fishes to mammals. Analysing these enhancers from different species reveal the substantial spatial plasticity in Grem1 regulation in tetrapods and basal fishes, which provides insights into the fin-to-limb transition and evolutionary diversification of pentadactyl limbs.

The BMP antagonist Gremlin1 balances BMP and SHH signalling, endowing limb bud development with robustness. Here, the authors identify enhancers controlling Grem1 levels in an additive, and spatial regulation in a synergistic manner, providing digit patterning with cis-regulatory robustness and evolutionary plasticity.

Primordial Germ Cell Specification in Vertebrate Embryos: Phylogenetic Distribution and Conserved Molecular Features of Preformation and Induction

The differentiation of primordial germ cells (PGCs) occurs during early embryonic development and is critical for the survival and fitness of sexually reproducing species. Here, we review the two main mechanisms of PGC specification, induction, and preformation, in the context of four model vertebrate species: mouse, axolotl, Xenopus frogs, and zebrafish. We additionally discuss some notable molecular characteristics shared across PGC specification pathways, including the shared expression of products from three conserved germline gene families, DAZ (Deleted in Azoospermia) genes, nanos-related genes, and DEAD-box RNA helicases. Then, we summarize the current state of knowledge of the distribution of germ cell determination systems across kingdom Animalia, with particular attention to vertebrate species, but include several categories of invertebrates - ranging from the "proto-vertebrate" cephalochordates to arthropods, cnidarians, and ctenophores. We also briefly highlight ongoing investigations and potential lines of inquiry that aim to understand the evolutionary relationships between these modes of specification.

Selection on phalanx development in the evolution of the bird wing

The frameshift hypothesis is a widely-accepted model of bird wing evolution. This hypothesis postulates a shift in positional values, or molecular-developmental identity, that caused a change in digit phenotype. The hypothesis synthesised developmental and palaeontological data on wing digit homology. The 'most anterior digit' (MAD) hypothesis presents an alternative view based on changes in transcriptional regulation in the limb. The molecular evidence for both hypotheses is that the most anterior digit expresses Hoxd13 but not Hoxd11 and Hoxd12. This digit I 'signature' is thought to characterise all amniotes. Here, we studied Hoxd expression patterns in a phylogenetic sample of 18 amniotes. Instead of a conserved molecular signature in digit I, we find wide variation of Hoxd11, Hoxd12 and Hoxd13 expression in digit I. Patterns of apoptosis, and Sox9 expression, a marker of the phalanx-forming region, suggest that phalanges were lost from wing digit IV because of early arrest of the phalanx-forming region followed by cell death. Finally, we show that multiple amniote lineages lost phalanges with no frameshift. Our findings suggest that the bird wing evolved by targeted loss of phalanges under selection. Consistent with our view, some recent phylogenies based on dinosaur fossils eliminate the need to postulate a frameshift in the first place. We suggest that the phenotype of the Archaeopteryx lithographica wing is also consistent with phalanx loss. More broadly, our results support a gradualist model of evolution based on tinkering with developmental gene expression.

Gene Regulatory and Expression Differences between Mouse and Pig Limb Buds Provide Insights into the Evolutionary Emergence of Artiodactyl Traits

Digit loss/reductions are evolutionary adaptations in cursorial mammals such as pigs. To gain mechanistic insight into these processes, we performed a comparative molecular analysis of limb development in mouse and pig embryos, which revealed a loss of anterior-posterior polarity during distal progression of pig limb bud development. These alterations in pig limb buds are paralleled by changes in the mesenchymal response to Sonic hedgehog (SHH) signaling, which is altered upstream of the reduction and loss of Fgf8 expression in the ectoderm that overlaps the reduced and vestigial digit rudiments of the pig handplate, respectively. Furthermore, genome-wide open chromatin profiling using equivalent developmental stages of mouse and pig limb buds reveals the functional divergence of about one-third of the regulatory genome. This study uncovers widespread alterations in the regulatory landscapes of genes essential for limb development that likely contributed to the morphological diversion of artiodactyl limbs from the pentadactyl archetype of tetrapods.

Regulation of vertebrate forelimb development and wing reduction in the flightless emu

The vertebrate limb is a dynamic structure which has evolved into many diverse forms to facilitate complex behavioral adaptations. The principle molecular and cellular processes that underlie development of the vertebrate limb are well characterized. However, how these processes are altered to drive differential limb development between vertebrates is less well understood. Several vertebrate models are being utilized to determine the developmental basis of differential limb morphogenesis, though these typically focus on later patterning of the established limb bud and may not represent the complete developmental trajectory. Particularly, heterochronic limb development can occur prior to limb outgrowth and patterning but receives little attention. This review summarizes the genetic regulation of vertebrate forelimb diversity, with particular focus on wing reduction in the flightless emu as a model for examining limb heterochrony. These studies highlight that wing reduction is complex, with heterochronic cellular and genetic events influencing the major stages of limb development. Together, these studies provide a broader picture of how different limb morphologies may be established during development.

The mole genome reveals regulatory rearrangements associated with adaptive intersexuality

Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. These include a tandem triplication involving CYP17A1, a gene controlling androgen synthesis, and an intrachromosomal inversion involving the pro-testicular growth factor gene FGF9, which is heterochronically expressed in mole ovotestes. Transgenic mice with a knock-in mole CYP17A1 enhancer or overexpressing FGF9 showed phenotypes recapitulating mole sexual features. Our results highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.

Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks

Despite a common understanding that Gli TFs are utilized to convey a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. Using the mouse model (Mus musculus), we demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the basic helix-loop-helix TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, 'divergent' Gli-binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.

Hedgehog signaling controls segmentation dynamics and diversity via msx1 in a spider embryo

Hedgehog (Hh) signaling plays fundamental roles in animal body patterning. Understanding its mechanistic complexity requires simple tractable systems that can be used for these studies. In the early spider embryo, Hh signaling mediates the formation of overall anterior-posterior polarity, yet it remains unclear what mechanisms link the initial Hh signaling activity with body axis segmentation, in which distinct periodic stripe-forming dynamics occur depending on the body region. We performed genome-wide searches for genes that transcriptionally respond to altered states of Hh signaling. Characterization of genes negatively regulated by Hh signaling suggested that msx1, encoding a conserved transcription factor, functions as a key segmentation gene. Knockdown of msx1 prevented all dynamic processes causing spatial repetition of stripes, including temporally repetitive oscillations and bi-splitting, and temporally nonrepetitive tri-splitting. Thus, Hh signaling controls segmentation dynamics and diversity via msx1 These genome-wide data from an invertebrate illuminate novel mechanistic features of Hh-based patterning.

Polydactyly Patient Carried a Mutation of PTCH1 Which Has Been Identified in Nevoid Basal Cell Nevus Syndrome

Polydactyly frequently exhibits autosomal dominant inheritance, which is characterized by supernumerary fingers or toes. The growth of the limb was controlled by three signaling pathways in three-dimensional axis. Sonic Hedgehog signaling, which controls the anterior to posterior (radial to ulnar) orientation has been suspected to be a main cause for polydactyly. To determine the pathogenesis of the patients with polydactyly, we recruited a polydactyly family with two patients. Taking advantage of next-generation sequencing technology, we applied whole-exome sequencing and Sanger sequencing to the proband and her daughter. The analysis of the whole-exome sequencing showed a heterozygous missense mutation c.3617G>A (p.R1206H) in the PTCH1 gene. The results of Sanger sequencing also verified this mutation. Our research discovered a candidate gene of polydactyly-PTCH1. We are the first to point out the relationship between polydactyly and PTCH1 mutation in human. As the PTCH1 gene mutations have been identified in nevoid basal cell nevus syndrome (NBCCS), and polydactyly is one phenotype of NBCCS, it may provide a new clue to the study of the genotype-phenotype correlations between the PTCH1 gene mutations and NBCCS.

Developmental constraints on fin diversity

The fish fin is a breathtaking repository full of evolutionary diversity, novelty, and convergence. Over 500 million years, the adaptation to novel habitats has provided landscapes of fin diversity. Although comparative anatomy of evolutionarily divergent patterns over centuries has highlighted the fundamental architectures and evolutionary trends of fins, including convergent evolution, the developmental constraints on fin evolution, which bias the evolutionary trajectories of fin morphology, largely remain elusive. Here, we review the evolutionary history, developmental mechanisms, and evolutionary underpinnings of paired fins, illuminating possible developmental constraints on fin evolution. Our compilation of anatomical and genetic knowledge of fin development sheds light on the canalized and the unpredictable aspects of fin shape in evolution. Leveraged by an arsenal of genomic and genetic tools within the working arena of spectacular fin diversity, evolutionary developmental biology embarks on the establishment of conceptual framework for developmental constraints, previously enigmatic properties of evolution.

The tissues and regulatory pattern of limb chondrogenesis

Initial limb chondrogenesis offers the first differentiated tissues that resemble the mature skeletal anatomy. It is a developmental progression of three tissues. The limb begins with undifferentiated mesenchyme-1, some of which differentiates into condensations-2, and this tissue then transforms into cartilage-3. Each tissue is identified by physical characteristics of cell density, shape, and extracellular matrix composition. Tissue specific regimes of gene regulation underlie the diagnostic physical and chemical properties of these three tissues. These three tissue based regimes co-exist amid a background of other gene regulatory regimes within the same tissues and time-frame of limb development. The bio-molecular indicators of gene regulation reveal six identifiable patterns. Three of these patterns describe the unique bio-molecular indicators of each of the three tissues. A fourth pattern shares bio-molecular indicators between condensation and cartilage. Finally, a fifth pattern is composed of bio-molecular indicators that are found in undifferentiated mesenchyme prior to any condensation differentiation, then these bio-molecular indicators are upregulated in condensations and downregulated in undifferentiated mesenchyme. The undifferentiated mesenchyme that remains in between the condensations and cartilage, the interdigit, contains a unique set of bio-molecular indicators that exhibit dynamic behaviour during chondrogenesis and therefore argue for its own inclusion as a tissue in its own right and for more study into this process of differentiation.

Digit ratio and length asymmetry in calves' limbs

This study considered possible sexual dimorphism in the relative lengths of the second, third and fourth digits (digit ratio), in calves. Furthermore, a different length of the bone structures of the third (3D) and of the fourth (4D) digits has been examined as an evolutionary adaptation to locomotion on soft ground. The length of the digital bones of the right fore-limb of 33 females and 15 male calves was measured in vivo using a portable X-ray machine. The vestigial structure of the second digit (2D), and 3D and 4D, from metacarpus to the third phalanx were considered in a mixed model, as well as some ratios between 2D and different parts of 3D or 4D (2D:3D and 2D:4D). A covariate for the mean finger length was considered for digit ratios to control for possible biases due to shape allometry. Shorter first phalanx and trotter were found in 3D than in 4D, and the reverse for the third phalanx. The 2D was significantly shorter in females, as well as the second phalanges of 3D and 4D. Significant sex differences in 2D:3D and 2D:4D were found for some digit parts of 3D and 4D and for the first phalanges of 3D:4D. These ratios were always shorter in females, in contrast to that found in most mammals. The asymmetry between 3D and 4D could mean a functional adaptation for locomotion. Sex differences in 2D:4D and 3D:4D were found, but with a reverse pattern than in most mammal species (males > females rather than males < females). In this regard digit ratio in calves was similar to that of Old World monkeys. This study is the first investigation of digit ratio in Ungulates, whose limbs differ from the limbs of most mammals, maintaining five digits. The reverse pattern of sex differences (digit ratios: males> females) could be due to the peculiar nature of the vestigial dewclaw of 2D and to the hormone patterns acting on this digit during development, but further research is required around this topic.

Development of the chick wing and leg neuromuscular systems and their plasticity in response to changes in digit numbers

The tetrapod limb has long served as a paradigm to study vertebrate pattern formation. During limb morphogenesis, a number of distinct tissue types are patterned and subsequently must be integrated to form coherent functional units. For example, the musculoskeletal apparatus of the limb requires the coordinated development of the skeletal elements, connective tissues, muscles and nerves. Here, using light-sheet microscopy and 3D-reconstructions, we concomitantly follow the developmental emergence of nerve and muscle patterns in chicken wings and legs, two appendages with highly specialized locomotor outputs. Despite a comparable flexor/extensor-arrangement of their embryonic muscles, wings and legs show a rotated innervation pattern for their three main motor nerve branches. To test the functional implications of these distinct neuromuscular topologies, we challenge their ability to adapt and connect to an experimentally altered skeletal pattern in the distal limb, the autopod. Our results show that, unlike autopod muscle groups, motor nerves are unable to fully adjust to a changed peripheral organisation, potentially constrained by their original projection routes. As the autopod has undergone substantial morphological diversifications over the course of tetrapod evolution, our results have implications for the coordinated modification of the distal limb musculoskeletal apparatus, as well as for our understanding of the varying degrees of motor functionality associated with human hand and foot malformations.

Evidence of five digits in embryonic horses and developmental stabilization of tetrapod digit number

Previous work comparing the developmental mechanisms involved in digit reduction in horses with other mammals reported that horses have only a 'single digit', with two flanking metapodials identified as remnants of digit II and IV. Here we show that early Equus embryos go through a stage with five digit condensations, and that the flanking splint metapodials result from fusions of the two anterior digits I and II and the two posterior digits IV and V, in a striking parallel between ontogeny and phylogeny. Given that even this most extreme case of digit reduction exhibits primary pentadactyly, we re-examined the initial stages of digit condensation of all digit-reduced tetrapods where data are available and found that in all cases, five or four digits initiate (four with digit I missing). The persistent pentadactyl initiation in the horse and other digit-reduced modern taxa underscores a durable developmental stability at the initiation of digits. The digit evodevo model may help illuminate the biological circumstances under which organ systems become highly stabilized versus highly plastic.

The Evolution of a Single Toe in Horses: Causes, Consequences, and the Way Forward

Horses are a classic example of macroevolution in three major traits-large body size, tall-crowned teeth (hypsodonty), and a single toe (monodactyly)-but how and why monodactyly evolved is still poorly understood. Existing hypotheses usually connect digit reduction in horses to the spread and eventual dominance of open-habitat grasslands, which took over from forests during the Cenozoic; digit reduction has been argued to be an adaptation for speed, locomotor economy, stability, and/or increased body size. In this review, we assess the evidence for these (not necessarily mutually exclusive) hypotheses from a variety of related fields, including paleoecology, phylogenetic comparative methods, and biomechanics. Convergent evolution of digit reduction, including in litopterns and artiodactyls, is also considered. We find it unlikely that a single evolutionary driver was responsible for the evolution of monodactyly, because changes in body size, foot posture, habitat, and substrate are frequently found to influence one another (and to connect to broader potential drivers, such as changing climate). We conclude with suggestions for future research to help untangle the complex dynamics of this remarkable morphological change in extinct horses. A path forward should combine regional paleoecology studies, quantitative biomechanical work, and make use of convergence and modern analogs to estimate the relative contributions of potential evolutionary drivers for digit reduction.

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

Transcriptional repression needs to be rapidly reversible during embryonic development. This extends to the Hedgehog pathway, which primarily serves to counter GLI repression by processing GLI proteins into transcriptional activators. In investigating the mechanisms underlying GLI repression, we find that a subset of GLI binding regions, termed HH-responsive enhancers, specifically loses acetylation in the absence of HH signaling. These regions are highly enriched around HH target genes and primarily drive HH-specific transcriptional activity in the mouse limb bud. They also retain H3K27ac enrichment in limb buds devoid of GLI activator and repressor, indicating that their activity is primarily regulated by GLI repression. Furthermore, the Polycomb repression complex is not active at most of these regions, suggesting it is not a major mechanism of GLI repression. We propose a model for tissue-specific enhancer activity in which an HDAC-associated GLI repression complex regulates target genes by altering the acetylation status at enhancers.

Evolution of epimorphosis in mammals

Mammalian epimorphic regeneration is rare and digit tip regeneration in mice is the best-studied model for a multi-tissue regenerative event that involves blastema formation. Digit tip regeneration parallels human fingertip regeneration, thus understanding the details of this response can provide insight into developing strategies to expand the potential of human regeneration. Following amputation, the digit stump undergoes a strong histolytic response involving osteoclast-mediated bone degradation that is spatially and temporally linked to the expansion of blastema osteoprogenitor cells. Blastemal differentiation occurs via direct intramembranous ossification. Although robust, digit regeneration is imperfect: The amputated cortical bone is replaced with woven bone and there is excessive bone regeneration restricted to the dorsal-ventral axis. Ontogenetic and phylogenetic analysis of digit regeneration in amphibians and mammals raise the possibility that mammalian blastema is a product of convergent evolution and we hypothesize that digit tip regeneration evolved from a nonregenerative precondition. A model is proposed in which the mammalian blastema evolved in part from an adaptation of two bone repair strategies (the bone remodeling cycle and fracture healing) both of which are conserved across tetrapod vertebrates. The view that epimorphic regeneration evolved in mammals from a nonregenerative precondition is supported by recent studies demonstrating that complex regenerative responses can be induced from a number of different nonregenerative amputation wounds by specific modification of the healing response.

The formation of the thumb requires direct modulation of Gli3 transcription by Hoxa13

In the tetrapod limb, the digits (fingers or toes) are the elements most subject to morphological diversification in response to functional adaptations. However, despite their functional importance, the mechanisms controlling digit morphology remain poorly understood. Here we have focused on understanding the special morphology of the thumb (digit 1), the acquisition of which was an important adaptation of the human hand. To this end, we have studied the limbs of the Hoxa13 mouse mutant that specifically fail to form digit 1. We show that, consistent with the role of Hoxa13 in Hoxd transcriptional regulation, the expression of Hoxd13 in Hoxa13 mutant limbs does not extend into the presumptive digit 1 territory, which is therefore devoid of distal Hox transcripts, a circumstance that can explain its agenesis. The loss of Hoxd13 expression, exclusively in digit 1 territory, correlates with increased Gli3 repressor activity, a Hoxd negative regulator, resulting from increased Gli3 transcription that, in turn, is due to the release from the negative modulation exerted by Hox13 paralogs on Gli3 regulatory sequences. Our results indicate that Hoxa13 acts hierarchically to initiate the formation of digit 1 by reducing Gli3 transcription and by enabling expansion of the 5'Hoxd second expression phase, thereby establishing anterior-posterior asymmetry in the handplate. Our work uncovers a mutual antagonism between Gli3 and Hox13 paralogs that has important implications for Hox and Gli3 gene regulation in the context of development and evolution.

Attenuated Fgf Signaling Underlies the Forelimb Heterochrony in the Emu Dromaius novaehollandiae

Powered flight was fundamental to the establishment and radiation of birds. However, flight has been lost multiple times throughout avian evolution. Convergent losses of flight within the ratites (flightless paleognaths, including the emu and ostrich) often coincide with reduced wings. Although there is a wealth of anatomical knowledge for several ratites, the genetic mechanisms causing these changes remain debated. Here, we use a multidisciplinary approach employing embryological, genetic, and genomic techniques to interrogate the mechanisms underlying forelimb heterochrony in emu embryos. We show that the initiation of limb formation, an epithelial to mesenchymal transition (EMT) in the lateral plate mesoderm (LPM) and myoblast migration into the LPM, occur at equivalent stages in the emu and chick. However, the emu forelimb fails to subsequently proliferate. The unique emu forelimb expression of Nkx2.5, previously associated with diminished wing development, initiates after this stage (concomitant with myoblast migration into the LPM) and is therefore unlikely to cause this developmental delay. In contrast, RNA sequencing of limb tissue reveals significantly lower Fgf10 expression in the emu forelimb. Artificially increasing Fgf10 expression in the emu LPM induces ectodermal Fgf8 expression and a limb bud. Analyzing open chromatin reveals differentially active regulatory elements near Fgf10 and Sall-1 in the emu wing, and the Sall-1 enhancer activity is dependent on a likely Fgf-mediated Ets transcription factor-binding site. Taken together, our results suggest that regulatory changes result in lower expression of Fgf10 and a concomitant failure to express genes required for limb proliferation in the early emu wing bud.

Convergent metatarsal fusion in jerboas and chickens is mediated by similarities and differences in the patterns of osteoblast and osteoclast activities

In many vertebrate animals that run or leap, the metatarsals and/or metacarpals of the distal limb are fused into a single larger element, likely to resist fracture due to high ground-reaction forces during locomotion. Although metapodial fusion evolved independently in modern birds, ungulates, and jerboas, the developmental basis has only been explored in chickens, which diverged from the mammalian lineage approximately 300 million years ago. Here, we use a bipedal rodent, the lesser Egyptian jerboa (Jaculus jaculus), to understand the cellular processes of metatarsal fusion in a mammal, and we revisit the developing chicken to assess similarities and differences in the localization of osteoblast and osteoclast activities. In both species, adjacent metatarsals align along flat surfaces, osteoblasts cross the periosteal membrane to unite the three elements in a single circumference, and osteoclasts resorb bone at the interfaces leaving a single marrow cavity. However, the pattern of osteoclast activity differs in each species; osteoclasts are highly localized to resorb bone at the interfaces of neighboring jerboa metatarsals and are distributed throughout the endosteum of chicken metatarsals. Each species, therefore, provides an opportunity to understand mechanisms that pattern osteoblast and osteoclast activities to alter bone shape during development and evolution.

A single-cell transcriptomic atlas of the developing chicken limb

BACKGROUND

Through precise implementation of distinct cell type specification programs, differentially regulated in both space and time, complex patterns emerge during organogenesis. Thanks to its easy experimental accessibility, the developing chicken limb has long served as a paradigm to study vertebrate pattern formation. Through decades' worth of research, we now have a firm grasp on the molecular mechanisms driving limb formation at the tissue-level. However, to elucidate the dynamic interplay between transcriptional cell type specification programs and pattern formation at its relevant cellular scale, we lack appropriately resolved molecular data at the genome-wide level. Here, making use of droplet-based single-cell RNA-sequencing, we catalogue the developmental emergence of distinct tissue types and their transcriptome dynamics in the distal chicken limb, the so-called autopod, at cellular resolution.

RESULTS

Using single-cell RNA-sequencing technology, we sequenced a total of 17,628 cells coming from three key developmental stages of chicken autopod patterning. Overall, we identified 23 cell populations with distinct transcriptional profiles. Amongst them were small, albeit essential populations like the apical ectodermal ridge, demonstrating the ability to detect even rare cell types. Moreover, we uncovered the existence of molecularly distinct sub-populations within previously defined compartments of the developing limb, some of which have important signaling functions during autopod pattern formation. Finally, we inferred gene co-expression modules that coincide with distinct tissue types across developmental time, and used them to track patterning-relevant cell populations of the forming digits.

CONCLUSIONS

We provide a comprehensive functional genomics resource to study the molecular effectors of chicken limb patterning at cellular resolution. Our single-cell transcriptomic atlas captures all major cell populations of the developing autopod, and highlights the transcriptional complexity in many of its components. Finally, integrating our data-set with other single-cell transcriptomics resources will enable researchers to assess molecular similarities in orthologous cell types across the major tetrapod clades, and provide an extensive candidate gene list to functionally test cell-type-specific drivers of limb morphological diversification.

'Building a perfect body': control of vertebrate organogenesis by PBX-dependent regulatory networks

Pbx genes encode transcription factors that belong to the TALE (three-amino-acid loop extension) superclass of homeodomain proteins. We have witnessed a surge in information about the roles of this gene family as leading actors in the transcriptional control of development. PBX proteins represent a clear example of how transcription factors can regulate developmental processes by combinatorial properties, acting within multimeric complexes to implement activation or repression of transcription depending on their interaction partners. Here, we revisit long-emphasized functions of PBX transcription factors as cofactors for HOX proteins, major architects of the body plan. We further discuss new knowledge on roles of PBX proteins in different developmental contexts as upstream regulators of Hox genes-as factors that interact with non-HOX proteins and can work independently of HOX-as well as potential pioneer factors. Committed to building a perfect body, PBX proteins govern regulatory networks that direct essential morphogenetic processes and organogenesis in vertebrate development. Perturbations of PBX-dependent networks can cause human congenital disease and cancer.

A proteomic approach identifies SAFB-like transcription modulator (SLTM) as a bidirectional regulator of GLI family zinc finger transcription factors

In Sonic hedgehog (SHH) signaling, GLI family zinc finger (GLI)-mediated diverse gene transcription outcomes are strictly regulated and are important for SHH function in both development and disease. However, how the GLI factors differentially regulate transcription in response to variable SHH activities is incompletely understood. Here, using a newly generated, tagged Gli3 knock-in mouse (Gli3^TAP ), we performed proteomic analyses and identified the chromatin-associated SAFB-like transcription modulator (SLTM) as a GLI-interacting protein that context-dependently regulates GLI activities. Using immunoprecipitation and immunoblotting, RT-quantitative PCR, and ChIP assays, we show that SLTM interacts with all three GLI proteins and that its cellular levels are regulated by SHH. We also found that SLTM enhances GLI3 binding to chromatin and increases GLI3 repressor (GLI3R) form protein levels. In a GLI3-dependent manner, SLTM promoted the formation of a repressive chromatin environment and functioned as a GLI3 co-repressor. In the absence of GLI3 or in the presence of low GLI3 levels, SLTM co-activated GLI activator (GLIA)-mediated target gene activation and cell differentiation. Moreover, in vivo Sltm deletion generated through CRISPR/Cas9-mediated gene editing caused perinatal lethality and SHH-related abnormal ventral neural tube phenotypes. We conclude that SLTM regulates GLI factor binding to chromatin and contributes to the transcriptional outcomes of SHH signaling via a novel molecular mechanism.

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits.

Cis-regulatory elements are important factors for morphological changes. Here, the authors show widespread divergence of limb and eye regulatory elements in limb loss in snakes and eye degeneration in subterranean mammals respectively.

The skeletal ontogeny of Astatotilapia burtoni - a direct-developing model system for the evolution and development of the teleost body plan

Background

The experimental approach to the evolution and development of the vertebrate skeleton has to a large extent relied on “direct-developing” amniote model organisms, such as the mouse and the chicken. These organisms can however only be partially informative where it concerns secondarily lost features or anatomical novelties not present in their lineages. The widely used anamniotes Xenopus and zebrafish are “indirect-developing” organisms that proceed through an extended time as free-living larvae, before adopting many aspects of their adult morphology, complicating experiments at these stages, and increasing the risk for lethal pleiotropic effects using genetic strategies.

Results

Here, we provide a detailed description of the development of the osteology of the African mouthbrooding cichlid Astatotilapia burtoni, primarily focusing on the trunk (spinal column, ribs and epicentrals) and the appendicular skeleton (pectoral, pelvic, dorsal, anal, caudal fins and scales), and to a lesser extent on the cranium. We show that this species has an extremely “direct” mode of development, attains an adult body plan within 2 weeks after fertilization while living off its yolk supply only, and does not pass through a prolonged larval period.

Conclusions

As husbandry of this species is easy, generation time is short, and the species is amenable to genetic targeting strategies through microinjection, we suggest that the use of this direct-developing cichlid will provide a valuable model system for the study of the vertebrate body plan, particularly where it concerns the evolution and development of fish or teleost specific traits. Based on our results we comment on the development of the homocercal caudal fin, on shared ontogenetic patterns between pectoral and pelvic girdles, and on the evolution of fin spines as novelty in acanthomorph fishes. We discuss the differences between “direct” and “indirect” developing actinopterygians using a comparison between zebrafish and A. burtoni development.

Evolutionary emergence of the rac3b/rfng/sgca regulatory cluster refined mechanisms for hindbrain boundaries formation

Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cable assembly at hindbrain boundaries. We show that the novel rac3b/rfng/sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis-regulatory interactions. By combining 4C-seq, ATAC-seq, transgenesis, and CRISPR-induced deletions, we characterized this regulatory domain, identifying hindbrain boundary-specific cis-regulatory elements. Our results suggest that the capacity of boundaries to act as an elastic mesh for segregating rhombomeric cells evolved by cooption of critical genes to a novel regulatory block, refining the mechanisms for hindbrain segmentation.

Noncanonical Hox, Etv4, and Gli3 gene activities give insight into unique limb patterning in salamanders

Limb development in salamanders is unique among tetrapods in significant ways. Not only can salamanders regenerate lost limbs repeatedly and throughout their lives, but also the preaxial zeugopodial element and digits form before the postaxial ones and, hence, with a reversed polarity compared to all other tetrapods. Moreover, in salamanders with free-swimming larval stages, as exemplified by the axolotl (Ambystoma mexicanum), each digit buds independently, instead of undergoing a paddle stage. Here, we report gene expression patterns of Hoxa and d clusters, and other crucial transcription factors during axolotl limb development. During early phases of limb development, expression patterns are mostly similar to those reported for amniotes and frogs. Likewise, Hoxd and Shh regulatory landscapes are largely conserved. However, during late digit-budding phases, remarkable differences are present: (i) the Hoxd13 expression domain excludes developing digits I and IV, (ii) we expand upon previous observation that Hoxa11 expression, which traditionally marks the zeugopodium, extends distally into the developing digits, and (iii) Gli3 and Etv4 show prolonged expression in developing digits. Our findings identify derived patterns in the expression of key transcription factors during late phases of salamander limb development, and provide the basis for a better understanding of the unique patterning of salamander limbs.

Gli1 promotes colorectal cancer metastasis in a Foxm1-dependent manner by activating EMT and PI3K-AKT signaling

Colorectal cancer(CRC) is one of the most commonly diagnosed cancers in human beings and metastasis is the main death reason. Recently, Gli1 has been reported to be a key regulator of various cancer biologies and genes expressions. However, the detailed molecular mechanism of Gli1 in CRC metastasis remains largely unknown. In this study, we aimed to investigate the role of Gli1 in CRC metastasis. We used qRT-PCR, Immunohistochemistry and Western blot to test the expression levels of Gli1, Foxm1 and other target genes in the tissues and cells; Lentivirus stable transfection to change the expression levels of Gli1 and Foxm1; Wound-healing, cell invasion, migration assays and tail vein metastatic assay to test the role of Gli1 in CRC metastasis in vitro and vivo. We demonstrated that Gli1 was significantly overexpressed in colorectal cancer tissues and cells. Foxm1 level had a positive correlation with Gli1. Furthermore, we found that Gli1 promotes colorectal cancer cells metastasis in a Foxm1-dependent manner by activating EMT and PI3K-AKT signaling. Thus, we proved that Gli1 plays important role in CRC metastasis and provided a new visual field on the therapy of CRC metastasis.

Mechanics of evolutionary digit reduction in fossil horses (Equidae)

Digit reduction is a major trend that characterizes horse evolution, but its causes and consequences have rarely been quantitatively tested. Using beam analysis on fossilized centre metapodials, we tested how locomotor bone stresses changed with digit reduction and increasing body size across the horse lineage. Internal bone geometry was captured from 13 fossil horse genera that covered the breadth of the equid phylogeny and the spectrum of digit reduction and body sizes, from Hyracotherium to Equus To account for the load-bearing role of side digits, a novel, continuous measure of digit reduction was also established-toe reduction index (TRI). Our results show that without accounting for side digits, three-toed horses as late as Parahippus would have experienced physiologically untenable bone stresses. Conversely, when side digits are modelled as load-bearing, species at the base of the horse radiation through Equus probably maintained a similar safety factor to fracture stress. We conclude that the centre metapodial compensated for evolutionary digit reduction and body mass increases by becoming more resistant to bending through substantial positive allometry in internal geometry. These results lend support to two historical hypotheses: that increasing body mass selected for a single, robust metapodial rather than several smaller ones; and that, as horse limbs became elongated, the cost of inertia from the side toes outweighed their utility for stabilization or load-bearing.

Evolution of antero-posterior patterning of the limb: Insights from the chick

The developing limbs of chicken embryos have served as pioneering models for understanding pattern formation for over a century. The ease with which chick wing and leg buds can be experimentally manipulated, while the embryo is still in the egg, has resulted in the discovery of important developmental organisers, and subsequently, the signals that they produce. Sonic hedgehog (Shh) is produced by mesenchyme cells of the polarizing region at the posterior margin of the limb bud and specifies positional values across the antero-posterior axis (the axis running from the thumb to the little finger). Detailed experimental embryology has revealed the fundamental parameters required to specify antero-posterior positional values in response to Shh signaling in chick wing and leg buds. In this review, the evolution of the avian wing and leg will be discussed in the broad context of tetrapod paleontology, and more specifically, ancestral theropod dinosaur paleontology. How the parameters that dictate antero-posterior patterning could have been modulated to produce the avian wing and leg digit patterns will be considered. Finally, broader speculations will be made regarding what the antero-posterior patterning of chick limbs can tell us about the evolution of other digit patterns, including those that were found in the limbs of the earliest tetrapods.

Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13

The combinatorial expression of Hox genes along the body axes is a major determinant of cell fate and plays a pivotal role in generating the animal body plan. Loss of HOXA13 and HOXD13 transcription factors (HOX13) leads to digit agenesis in mice, but how HOX13 proteins regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here, we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13^−/−; Hoxd13^−/−limbs. Our results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.

Timing the developmental origins of mammalian limb diversity

Mammals have highly diverse limbs that have contributed to their occupation of almost every niche. Researchers have long been investigating the development of these diverse limbs, with the goals of identifying developmental processes and potential biases that shape mammalian limb diversity. To date, researchers have used techniques ranging from the genomic to the anatomic to investigate the developmental processes shaping the limb morphology of mammals from five orders (Marsupialia, Chiroptera, Rodentia, Cetartiodactyla, and Perissodactyla). Results of these studies suggest that the differential expression of genes controlling diverse cellular processes underlies mammalian limb diversity. Results also suggest that the earliest development of the limb tends to be conserved among mammalian species, while later limb development tends to be more variable. This research has established the mammalian limb as a model system for evolutionary developmental biology, and set the stage for more in-depth, cross-disciplinary research into the genetic controls, tissue-level cellular behaviors, and selective pressures that have driven the developmental evolution of mammalian limbs. Ideally, these studies will be performed in a diverse suite of mammalian species within a comparative, phylogenetic framework.

John Saunders' ZPA, Sonic hedgehog and digit identity - How does it really all work?

Among John Saunders' many seminal contributions to developmental biology, his discovery of the limb 'zone of polarizing activity' (ZPA) is arguably one of the most memorable and ground-breaking. This discovery introduced the limb as a premier model for understanding developmental patterning and promoted the concept of patterning by a morphogen gradient. In the 50 years since the discovery of the ZPA, Sonic hedgehog (Shh) has been identified as the ZPA factor and the basic components of the signaling pathway and many aspects of its regulation have been elucidated. Although much has also been learned about how it regulates growth, the mechanism by which Shh patterns the limb, how it acts to instruct digit 'identity', nevertheless remains an enigma. This review focuses on what has been learned about Shh function in the limb and the outstanding puzzles that remain to be solved.