1
|
Surette E, Donahue J, Robinson S, McKenna D, Martinez CS, Fitzgerald B, Karlstrom RO, Cumplido N, McMenamin SK. Adult caudal fin shape is imprinted in the embryonic fin fold. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603744. [PMID: 39071346 PMCID: PMC11275767 DOI: 10.1101/2024.07.16.603744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Appendage shape is formed during development (and re-formed during regeneration) according to spatial and temporal cues that orchestrate local cellular morphogenesis. The caudal fin is the primary appendage used for propulsion in most fish species, and exhibits a range of distinct morphologies adapted for different swimming strategies, however the molecular mechanisms responsible for generating these diverse shapes remain mostly unknown. In zebrafish, caudal fins display a forked shape, with longer supportive bony rays at the periphery and shortest rays at the center. Here, we show that a premature, transient pulse of sonic hedgehog a (shha) overexpression during late embryonic development results in excess proliferation and growth of the central rays, causing the adult caudal fin to grow into a triangular, truncate shape. Both global and regional ectopic shha overexpression are sufficient to alter fin shape, and forked shape may be rescued by subsequent treatment with an antagonist of the canonical Shh pathway. The induced truncate fins show a decreased fin ray number and fail to form the hypural diastema that normally separates the dorsal and ventral fin lobes. While forked fins regenerate their original forked morphology, truncate fins regenerate truncate, suggesting that positional memory of the fin rays can be permanently altered by a transient treatment during embryogenesis. Ray finned fish have evolved a wide spectrum of caudal fin morphologies, ranging from truncate to forked, and the current work offers insights into the developmental mechanisms that may underlie this shape diversity.
Collapse
|
2
|
Harshan P, Sukumaran S, Gopalakrishnan A. De novo transcriptome for Chiloscyllium griseum, a long-tail carpet shark of the Indian waters. Sci Data 2024; 11:285. [PMID: 38461175 PMCID: PMC10924892 DOI: 10.1038/s41597-024-03093-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/27/2024] [Indexed: 03/11/2024] Open
Abstract
Sharks have thrived in the oceans for 400 million years, experienced five extinctions and evolved into today's apex predators. However, enormous genome size, poor karyotyping and limited tissue sampling options are the bottlenecks in shark research. Sharks of the family Orectolobiformes act as model species in transcriptome research with exceptionally high reproductive fecundity, catch prominence and oviparity. The present study illustrates a de novo transcriptome for an adult grey bamboo shark, Chiloscyllium griseum (Chondrichthyes; Hemiscyllidae) using paired-end RNA sequencing. Around 150 million short Illumina reads were obtained from five different tissues and assembled using the Trinity assembler. 70,647 hits on Uniprot by BLASTX was obtained after the transcriptome annotation. The data generated serve as a basis for transcriptome-based population genetic studies and open up new avenues in the field of comparative transcriptomics and conservation biology.
Collapse
Affiliation(s)
- Pooja Harshan
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
- Cochin University of Science and Technology, South Kalamassery, Ernakulam, Kerala, 682022, India.
| | - Sandhya Sukumaran
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- Marine Biotechnology, Fish Nutrition and Health Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| |
Collapse
|
3
|
da Silva JPCB, Vaz DFB. Morphology and phylogenetic significance of the pelvic articular region in elasmobranchs (Chondrichthyes). Cladistics 2023; 39:155-197. [PMID: 36856203 DOI: 10.1111/cla.12528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 03/02/2023] Open
Abstract
The morphology of paired fins is commonly overlooked in morphological studies, particularly the pelvic girdle and fins. Consequently, previous phylogenetic studies incorporating morphological data used few skeletal characters from this complex. In this paper, the phylogenetic significance of pelvic articular characters for elasmobranchs is discussed in light of the morphological variation observed in 130 species, the most comprehensive study exploring the morphology of the pelvic girdle done so far. The 10 morphological characters proposed herein for the pelvic articulation were incorporated into a molecular matrix of NADH2 sequences and submitted to an analysis of maximum parsimony employing extended implied weighting. The most stable tree was selected based on the distortion coefficients, SPR distances (subtree pruning and regrafting) and fit values. Some of the striking synapomorphies recovered within elasmobranchs include the presence of an articular surface for the first enlarged pelvic radial supporting Elasmobranchii and the pelvic articular region for the basipterygium extending from the posterolatral margin of the pelvic girdle over its lateral surface in Echinorhinus + Hexanchiformes. Additionally, the proposed characters and their distributions are discussed considering the relationships recovered and also compared with previous morphological and molecular phylogenetic hypotheses.
Collapse
Affiliation(s)
- João Paulo C B da Silva
- Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Castelo Branco, João Pessoa, 58051-900, Brazil
| | - Diego F B Vaz
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, 02143, USA.,Biorepository Collaboratorium Guam EPSCoR, Marine Laboratory, University of Guam, 303 University Dr, UOG Station, Mangilao, GU, 96923, USA
| |
Collapse
|
4
|
Trofka A, Huang BL, Zhu J, Heinz WF, Magidson V, Shibata Y, Shi YB, Tarchini B, Stadler HS, Kabangu M, Al Haj Baddar NW, Voss SR, Mackem S. Genetic basis for an evolutionary shift from ancestral preaxial to postaxial limb polarity in non-urodele vertebrates. Curr Biol 2021; 31:4923-4934.e5. [PMID: 34610275 DOI: 10.1016/j.cub.2021.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/30/2021] [Accepted: 09/03/2021] [Indexed: 11/24/2022]
Abstract
In most tetrapod vertebrates, limb skeletal progenitors condense with postaxial dominance. Posterior elements (such as ulna and fibula) appear prior to their anterior counterparts (radius and tibia), followed by digit-appearance order with continuing postaxial polarity. The only exceptions are urodele amphibians (salamanders), whose limb elements develop with preaxial polarity and who are also notable for their unique ability to regenerate complete limbs as adults. The mechanistic basis for this preaxial dominance has remained an enigma and has even been proposed to relate to the acquisition of novel genes involved in regeneration. However, recent fossil evidence suggests that preaxial polarity represents an ancestral rather than derived state. Here, we report that 5'Hoxd (Hoxd11-d13) gene deletion in mouse is atavistic and uncovers an underlying preaxial polarity in mammalian limb formation. We demonstrate this shift from postaxial to preaxial dominance in mouse results from excess Gli3 repressor (Gli3R) activity due to the loss of 5'Hoxd-Gli3 antagonism and is associated with cell-cycle changes promoting precocious cell-cycle exit in the anterior limb bud. We further show that Gli3 knockdown in axolotl results in a shift to postaxial dominant limb skeleton formation, as well as expanded paddle-shaped limb-bud morphology and ensuing polydactyly. Evolutionary changes in Gli3R activity level, which also played a key role in the fin-to-limb transition, appear to be fundamental to the shift from preaxial to postaxial polarity in formation of the tetrapod limb skeleton.
Collapse
Affiliation(s)
- Anna Trofka
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Bau-Lin Huang
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yuki Shibata
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver NICHD, Bethesda, MD, USA
| | - Yun-Bo Shi
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver NICHD, Bethesda, MD, USA
| | | | - H Scott Stadler
- Division of Skeletal Biology, Shriners Hospitals for Children, Portland, OR, USA; Department of Orthopaedics and Rehabilitation, Oregon Health & Science University, Portland, OR, USA
| | - Mirindi Kabangu
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, USA
| | - Nour W Al Haj Baddar
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, USA
| | - S Randal Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, USA.
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA.
| |
Collapse
|
5
|
The Shh/ Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits. Proc Natl Acad Sci U S A 2021; 118:2100575118. [PMID: 34750251 PMCID: PMC8673081 DOI: 10.1073/pnas.2100575118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
In this study, we show that the inactivation of the gli3 gene in medaka fish results in the formation of larger dorsal and paired fins. These mutant fins display multiple radial bones and fin rays which resemble polydactyly in Gli3-deficient mice. Our molecular and genetic analyses indicate that the size of fish fins is controlled by an ancient mechanism mediated by SHH-GLI signaling that appeared prior to the evolutionary appearance of paired fins. We also show that the key regulatory networks that mediate the expansion of digit progenitor cells in tetrapods were already in place in the fins of the last common ancestor between ray and lobe-finned fishes, suggesting an ancient similarity between distal fins and digits. One of the central problems of vertebrate evolution is understanding the relationship among the distal portions of fins and limbs. Lacking comparable morphological markers of these regions in fish and tetrapods, these relationships have remained uncertain for the past century and a half. Here we show that Gli3 functions in controlling the proliferative expansion of distal progenitors are shared among dorsal and paired fins as well as tetrapod limbs. Mutant knockout gli3 fins in medaka (Oryzias latipes) form multiple radials and rays, in a pattern reminiscent of the polydactyly observed in Gli3-null mutant mice. In limbs, Gli3 controls both anterior–posterior patterning and cell proliferation, two processes that can be genetically uncoupled. In situ hybridization, quantification of proliferation markers, and analysis of regulatory regions reveal that in paired and dorsal fins, gli3 plays a main role in controlling proliferation but not in patterning. Moreover, gli3 down-regulation in shh mutant fins rescues fin loss in a manner similar to how Gli3 deficiency restores digits in the limbs of Shh mutant mouse embryos. We hypothesize that the Gli3/Shh gene pathway preceded the origin of paired appendages and was originally involved in modulating cell proliferation. Accordingly, the distal regions of dorsal fins, paired fins, and limbs retain a deep regulatory and functional homology that predates the origin of paired appendages.
Collapse
|
6
|
Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity. Nat Commun 2021; 12:5557. [PMID: 34548488 PMCID: PMC8455560 DOI: 10.1038/s41467-021-25810-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
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.
Collapse
|
7
|
Bones of contention: skeletal patterning across the fin-to-limb transition. Cell 2021; 184:854-856. [PMID: 33606983 DOI: 10.1016/j.cell.2021.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The fin-to-limb transition has long fascinated evolutionary biologists, but a unifying theory as to its developmental origins has remained elusive. New work by Hawkins and colleagues demonstrates the surprising potential of teleost fins to exhibit a Hox-regulated limb-like skeletal pattern, shedding new light on the evolution of proximo-distal patterning processes.
Collapse
|
8
|
Conserved Mechanisms, Novel Anatomies: The Developmental Basis of Fin Evolution and the Origin of Limbs. DIVERSITY 2021. [DOI: 10.3390/d13080384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The transformation of paired fins into tetrapod limbs is one of the most intensively scrutinized events in animal evolution. Early anatomical and embryological datasets identified distinctive morphological regions within the appendage and posed hypotheses about how the loss, gain, and transformation of these regions could explain the observed patterns of both extant and fossil appendage diversity. These hypotheses have been put to the test by our growing understanding of patterning mechanisms that regulate formation of the appendage axes, comparisons of gene expression data from an array of phylogenetically informative taxa, and increasingly sophisticated and elegant experiments leveraging the latest molecular approaches. Together, these data demonstrate the remarkable conservation of developmental mechanisms, even across phylogenetically and morphologically disparate taxa, as well as raising new questions about the way we view homology, evolutionary novelty, and the often non-linear connection between morphology and gene expression. In this review, we present historical hypotheses regarding paired fin evolution and limb origins, summarize key aspects of central appendage patterning mechanisms in model and non-model species, address how modern comparative developmental data interface with our understanding of appendage anatomy, and highlight new approaches that promise to provide new insight into these well-traveled questions.
Collapse
|
9
|
Höch R, Schneider RF, Kickuth A, Meyer A, Woltering JM. Spiny and soft-rayed fin domains in acanthomorph fish are established through a BMP- gremlin- shh signaling network. Proc Natl Acad Sci U S A 2021; 118:e2101783118. [PMID: 34230098 PMCID: PMC8307853 DOI: 10.1073/pnas.2101783118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With over 18,000 species, the Acanthomorpha, or spiny-rayed fishes, form the largest and arguably most diverse radiation of vertebrates. One of the key novelties that contributed to their evolutionary success are the spiny rays in their fins that serve as a defense mechanism. We investigated the patterning mechanisms underlying the differentiation of median fin Anlagen into discrete spiny and soft-rayed domains during the ontogeny of the direct-developing cichlid fish Astatotilapia burtoni Distinct transcription factor signatures characterize these two fin domains, whereby mutually exclusive expression of hoxa13a/b with alx4a/b and tbx2b marks the spine to soft-ray boundary. The soft-ray domain is established by BMP inhibition via gremlin1b, which synergizes in the posterior fin with shh secreted from a zone of polarizing activity. Modulation of BMP signaling by chemical inhibition or gremlin1b CRISPR/Cas9 knockout induces homeotic transformations of spines into soft rays and vice versa. The expression of spine and soft-ray genes in nonacanthomorph fins indicates that a combination of exaptation and posterior expansion of an ancestral developmental program for the anterior fin margin allowed the evolution of robustly individuated spiny and soft-rayed domains. We propose that a repeated exaptation of such pattern might underly the convergent evolution of anterior spiny-fin elements across fishes.
Collapse
Affiliation(s)
- Rebekka Höch
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Ralf F Schneider
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Alison Kickuth
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Joost M Woltering
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz 78457, Germany
| |
Collapse
|
10
|
Onimaru K, Tatsumi K, Tanegashima C, Kadota M, Nishimura O, Kuraku S. Developmental hourglass and heterochronic shifts in fin and limb development. eLife 2021; 10:62865. [PMID: 33560225 PMCID: PMC7932699 DOI: 10.7554/elife.62865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
How genetic changes are linked to morphological novelties and developmental constraints remains elusive. Here, we investigate genetic apparatuses that distinguish fish fins from tetrapod limbs by analyzing transcriptomes and open-chromatin regions (OCRs). Specifically, we compared mouse forelimb buds with the pectoral fin buds of an elasmobranch, the brown-banded bamboo shark (Chiloscyllium punctatum). A transcriptomic comparison with an accurate orthology map revealed both a mass heterochrony and hourglass-shaped conservation of gene expression between fins and limbs. Furthermore, open-chromatin analysis suggested that access to conserved regulatory sequences is transiently increased during mid-stage limb development. During this stage, stage-specific and tissue-specific OCRs were also enriched. Together, early and late stages of fin/limb development are more permissive to mutations than middle stages, which may have contributed to major morphological changes during the fin-to-limb evolution. We hypothesize that the middle stages are constrained by regulatory complexity that results from dynamic and tissue-specific transcriptional controls. Animals come in all shapes and sizes. This diversity arose through genetic mutations during evolution, but it is unclear exactly how these variations led to the formation of new shapes. There is increasing evidence to suggest that not all shapes are possible and that variability between animals is limited by a phenomenon known as “developmental constraint”. These limitations direct parts of the body towards a specific shape as they develop in the embryo. Therefore, understanding the mechanisms underlying these developmental constraints could help explain how different body shapes evolved. The limbs of humans and other mammals evolved from the fins of fish, and this transition is often used to study the role developmental constraints play in evolution. This is an ideal model as there is already a detailed fossil record mapping this evolutionary event, and data pinpointing some of the genes involved in the development of limbs and fins. But this data is incomplete, and a full comparison between the genes activated in the fin and the limb during embryonic development had not been achieved. This is because most fish used for research have undergone recent genetic changes, making it hard to spot which genetic differences are linked to the evolution of the limb. To overcome this barrier, Onimaru et al. compared genetic data from the developing limbs of mice to the developing fins of the brown-banded bamboo shark, which evolves much slower than other fish. This revealed that although many genes commonly played a role in the development of the fin and the limb in the embryo, the activity of these shared genes was not the same. For example, genes that switched on in the late stages of limb development, switched off in the late stages of fin development. But in the middle of development, those differences were relatively small and both species activated very similar sets of genes. Many of these genes were pleiotropic, which means they have important roles in other tissues and therefore mutate less often. This suggests that the mid-stage of limb development is under the strongest level of constraint. Darwin’s theory of natural selection explains that mutations drive evolution. But the theory cannot predict what kinds of new body shapes new mutations will produce. Understanding how the activity levels of different genes affect development could help to fill this knowledge gap. This has potential medical applications, for example, understanding why some genetic changes cause more serious problems than others. This work suggests that mutations in genes that are active during the mid-stage of limb development may have the most serious impact.
Collapse
Affiliation(s)
- Koh Onimaru
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,Laboratory for Bioinformatics Research, RIKEN BDR, Wako City, Japan.,Molecular Oncology Laboratory, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Kaori Tatsumi
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| |
Collapse
|
11
|
Ali S, Arif I, Iqbal A, Hussain I, Abrar M, Khan MR, Shubin N, Abbasi AA. Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Dev Dyn 2021; 250:669-683. [PMID: 33381902 PMCID: PMC9292287 DOI: 10.1002/dvdy.291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/03/2022] Open
Abstract
Background The zinc finger‐containing transcription factor Gli2, is a key mediator of Hedgehog (Hh) signaling and participates in embryonic patterning of various organs including the central nervous system (CNS) and limbs. Abnormal expression of Gli2 can impede the transcription of Hh target genes through disruption of proper balance between Gli2 and Gli3 functions. Therefore, delineation of enhancers that are required for complementary roles of Glis would allow the interrogation of those pathogenic variants that cause gene dysregulation, and a corresponding abnormal phenotype. Previously, we reported tissue‐specific enhancers for Gli family including Gli2 through direct tetrapod‐teleost comparisons. Results Here, we employed the sequence alignments of slowly evolving spotted gar and elephant shark and have identified six novel conserved noncoding elements in human GLI2 containing locus. Zebrafish‐based transgenic assays revealed that combined action of these autonomous CNEs reflects many aspects of Gli2 specific endogenous transcriptional activity, including CNS and pectoral fins. Conclusion Taken together with our previous findings, this study suggests that Hh‐signaling controlled deployment of Gli2 activity in embryonic patterning arose in the common ancestor of gnathostomes. These GLI2 specific cis‐regulatory modules will help to identify DNA variants that probably reside outside of coding intervals and are associated with congenital anomalies. We performed a phylogenetic footprint analyses of human GLI2 containing locus by incorporating relatively slowly evolving gar and elephant shark genomes and have identified multiple novel conserved non‐coding elements (CNEs) that were not predicted by direct human‐teleostcomparisons. Comparative analyses suggest that majority of the GLI2 associated CNEs identified in the present data and reported previously arose in the common ancestor of gnathostomes but lost in teleosts, presumably because of fast teleost sequence evolution. Functional testing of GLI2 associated CNEs by employing zebrafish based transgenic reporter assays revealed their tissue specific cis‐regulatory potential that corresponds with the results based on whole‐mount in situ hybridization analysis of gli2 mRNA in zebrafish. The delineated set of GLI2 associated enhancers can be further interrogated to determine their role in canonical Hh signaling, gene dysregulation, and a corresponding congenital anomaly.
Collapse
Affiliation(s)
- Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irum Arif
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Ayesha Iqbal
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Islamabad, Pakistan
| | - Neil Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| |
Collapse
|
12
|
Barske L, Fabian P, Hirschberger C, Jandzik D, Square T, Xu P, Nelson N, Yu HV, Medeiros DM, Gillis JA, Crump JG. Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer. Proc Natl Acad Sci U S A 2020; 117:24876-24884. [PMID: 32958671 PMCID: PMC7547273 DOI: 10.1073/pnas.2011531117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Whereas the gill chambers of jawless vertebrates open directly into the environment, jawed vertebrates evolved skeletal appendages that drive oxygenated water unidirectionally over the gills. A major anatomical difference between the two jawed vertebrate lineages is the presence of a single large gill cover in bony fishes versus separate covers for each gill chamber in cartilaginous fishes. Here, we find that these divergent patterns correlate with the pharyngeal arch expression of Pou3f3 orthologs. We identify a deeply conserved Pou3f3 arch enhancer present in humans through sharks but undetectable in jawless fish. Minor differences between the bony and cartilaginous fish enhancers account for their restricted versus pan-arch expression patterns. In zebrafish, mutation of Pou3f3 or the conserved enhancer disrupts gill cover formation, whereas ectopic pan-arch Pou3f3b expression generates ectopic skeletal elements resembling the multimeric covers of cartilaginous fishes. Emergence of this Pou3f3 arch enhancer >430 Mya and subsequent modifications may thus have contributed to the acquisition and diversification of gill covers and respiratory strategies during gnathostome evolution.
Collapse
Affiliation(s)
- Lindsey Barske
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033;
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Peter Fabian
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | | | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
- Department of Zoology, Comenius University in Bratislava, 84215 Bratislava, Slovakia
| | - Tyler Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Pengfei Xu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Nellie Nelson
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Haoze Vincent Yu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
| | - J Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
- Marine Biological Laboratory, Woods Hole, MA 02543
| | - J Gage Crump
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, W. M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033;
| |
Collapse
|
13
|
Woltering JM, Irisarri I, Ericsson R, Joss JMP, Sordino P, Meyer A. Sarcopterygian fin ontogeny elucidates the origin of hands with digits. SCIENCE ADVANCES 2020; 6:eabc3510. [PMID: 32875118 PMCID: PMC7438105 DOI: 10.1126/sciadv.abc3510] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/09/2020] [Indexed: 05/03/2023]
Abstract
How the hand and digits originated from fish fins during the Devonian fin-to-limb transition remains unsolved. Controversy in this conundrum stems from the scarcity of ontogenetic data from extant lobe-finned fishes. We report the patterning of an autopod-like domain by hoxa13 during fin development of the Australian lungfish, the most closely related extant fish relative of tetrapods. Differences from tetrapod limbs include the absence of digit-specific expansion of hoxd13 and hand2 and distal limitation of alx4 and pax9, which potentially evolved through an enhanced response to shh signaling in limbs. These developmental patterns indicate that the digit program originated in postaxial fin radials and later expanded anteriorly inside of a preexisting autopod-like domain during the evolution of limbs. Our findings provide a genetic framework for the transition of fins into limbs that supports the significance of classical models proposing a bending of the tetrapod metapterygial axis.
Collapse
Affiliation(s)
- Joost M. Woltering
- Zoology and Evolutionary Biology, Department of Biology, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
| | - Iker Irisarri
- Zoology and Evolutionary Biology, Department of Biology, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
| | | | | | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
| |
Collapse
|
14
|
Fowler DA, Larsson HCE. The tissues and regulatory pattern of limb chondrogenesis. Dev Biol 2020; 463:124-134. [PMID: 32417169 DOI: 10.1016/j.ydbio.2020.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022]
Abstract
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.
Collapse
Affiliation(s)
- Donald A Fowler
- Redpath Museum, McGill University, 859 Sherbrooke St W, Montréal, QC, H3A 0C4, Canada; Department of Biology, McGill University, Stewart Biology Building, 1205 Docteur Penfield, Montréal, QC, H3A 1B1, Canada.
| | - Hans C E Larsson
- Redpath Museum, McGill University, 859 Sherbrooke St W, Montréal, QC, H3A 0C4, Canada.
| |
Collapse
|
15
|
Onimaru K. The evolutionary origin of developmental enhancers in vertebrates: Insights from non‐model species. Dev Growth Differ 2020; 62:326-333. [DOI: 10.1111/dgd.12662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Koh Onimaru
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research (BDR) Wako CitySaitama Japan
| |
Collapse
|
16
|
Stewart TA, Lemberg JB, Taft NK, Yoo I, Daeschler EB, Shubin NH. Fin ray patterns at the fin-to-limb transition. Proc Natl Acad Sci U S A 2020; 117:1612-1620. [PMID: 31888998 PMCID: PMC6983361 DOI: 10.1073/pnas.1915983117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The fin-to-limb transition was marked by the origin of digits and the loss of dermal fin rays. Paleontological research into this transformation has focused on the evolution of the endoskeleton, with little attention paid to fin ray structure and function. To address this knowledge gap, we study the dermal rays of the pectoral fins of 3 key tetrapodomorph taxa-Sauripterus taylori (Rhizodontida), Eusthenopteron foordi (Tristichopteridae), and Tiktaalik roseae (Elpistostegalia)-using computed tomography. These data show several trends in the lineage leading to digited forms, including the consolidation of fin rays (e.g., reduced segmentation and branching), reduction of the fin web, and unexpectedly, the evolution of asymmetry between dorsal and ventral hemitrichia. In Eusthenopteron, dorsal rays cover the preaxial endoskeleton slightly more than ventral rays. In Tiktaalik, dorsal rays fully cover the third and fourth mesomeres, while ventral rays are restricted distal to these elements, suggesting the presence of ventralized musculature at the fin tip analogous to a fleshy "palm." Asymmetry is also observed in cross-sectional areas of dorsal and ventral rays. Eusthenopteron dorsal rays are slightly larger than ventral rays; by contrast, Tiktaalik dorsal rays can be several times larger than ventral rays, and degree of asymmetry appears to be greater at larger sizes. Analysis of extant osteichthyans suggests that cross-sectional asymmetry in the dermal rays of paired fins is plesiomorphic to crown group osteichthyans. The evolution of dermal rays in crownward stem tetrapods reflects adaptation for a fin-supported elevated posture and resistance to substrate-based loading prior to the origin of digits.
Collapse
Affiliation(s)
- Thomas A Stewart
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637;
| | - Justin B Lemberg
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637
| | - Natalia K Taft
- Department of Biological Sciences, University of Wisconsin-Parkside, Kenosha, WI 53141
| | - Ihna Yoo
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637
| | - Edward B Daeschler
- Department of Vertebrate Zoology, Academy of Natural Sciences of Drexel University, Philadelphia, PA 19103
| | - Neil H Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637;
| |
Collapse
|
17
|
Dynamic and self-regulatory interactions among gene regulatory networks control vertebrate limb bud morphogenesis. Curr Top Dev Biol 2020; 139:61-88. [DOI: 10.1016/bs.ctdb.2020.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
18
|
Young JJ, Grayson P, Edwards SV, Tabin CJ. Attenuated Fgf Signaling Underlies the Forelimb Heterochrony in the Emu Dromaius novaehollandiae. Curr Biol 2019; 29:3681-3691.e5. [PMID: 31668620 DOI: 10.1016/j.cub.2019.09.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/21/2019] [Accepted: 09/06/2019] [Indexed: 11/19/2022]
Abstract
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.
Collapse
Affiliation(s)
- John J Young
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Clifford J Tabin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
19
|
Kawahata K, Cordeiro IR, Ueda S, Sheng G, Moriyama Y, Nishimori C, Yu R, Koizumi M, Okabe M, Tanaka M. Evolution of the avian digital pattern. Sci Rep 2019; 9:8560. [PMID: 31189916 PMCID: PMC6561939 DOI: 10.1038/s41598-019-44913-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/23/2019] [Indexed: 11/26/2022] Open
Abstract
Variation in digit number has occurred multiple times in the history of archosaur evolution. The five digits of dinosaur limbs were reduced to three in bird forelimbs, and were further reduced in the vestigial forelimbs of the emu. Regulation of digit number has been investigated previously by examining genes involved in anterior-posterior patterning in forelimb buds among emu (Dromaius novaehollandiae), chicken (Gallus gallus) and zebra finch (Taeniopygia guttata). It was described that the expression of posterior genes are conserved among these three birds, whereas expression of anterior genes Gli3 and Alx4 varied significantly. Here we re-examined the expression pattern of Gli3 and Alx4 in the forelimb of emu, chicken and zebra finch. We found that Gli3 is expressed in the anterior region, although its range varied among species, and that the expression pattern of Alx4 in forelimb buds is broadly conserved in a stage-specific manner. We also found that the dynamic expression pattern of the BMP antagonist Gremlin1 (Grem1) in limb buds, which is critical for autopodial expansion, was consistent with the digital pattern of emu, chicken and zebra finch. Furthermore, in emu, variation among individuals was observed in the width of Grem1 expression in forelimb buds, as well as in the adult skeletal pattern. Our results support the view that the signalling system that regulates the dynamic expression of Grem1 in the limb bud contributes substantially to variations in avian digital patterns.
Collapse
Affiliation(s)
- Kenta Kawahata
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | | | - Shogo Ueda
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Guojun Sheng
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,RIKEN Center for Developmental Biology, Kobe, Japan
| | - Yuuta Moriyama
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Department of Physics and Mathematics, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Chika Nishimori
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Reiko Yu
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makoto Koizumi
- Laboratory Animal Facilities, The Jikei University School of Medicine, Tokyo, Japan
| | - Masataka Okabe
- Department of Anatomy, The Jikei University School of Medicine, Tokyo, Japan
| | - Mikiko Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
| |
Collapse
|
20
|
Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M, Edwards SV. Convergent regulatory evolution and loss of flight in paleognathous birds. Science 2019; 364:74-78. [DOI: 10.1126/science.aat7244] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 02/27/2019] [Indexed: 01/05/2023]
Abstract
A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.
Collapse
|
21
|
Ueda S, Cordeiro IR, Moriyama Y, Nishimori C, Kai KI, Yu R, Nakato R, Shirahige K, Tanaka M. Cux2 refines the forelimb field by controlling expression of Raldh2 and Hox genes. Biol Open 2019; 8:bio.040584. [PMID: 30651234 PMCID: PMC6398465 DOI: 10.1242/bio.040584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In vertebrates, two pairs of buds that give rise to the fore- and hindlimbs form at discrete positions along the rostral-caudal axis of the body. The mechanism responsible for the positioning of the limb buds is still largely unknown. Here we show a novel function for Cut homeobox transcription factor 2 (Cux2), the ortholog of Drosophila cut, in refining the forelimb field during chick development. Cux2 is expressed in the forelimb field before the emergence of the limb buds. Knocking down the expression of Cux2 using small interfering RNA (siRNA) resulted in a caudal shift of the forelimb bud, whereas misexpression of Cux2 or the constitutively active Cux2-VP16 caused a rostral shift of the forelimb bud or reduction of the forelimb field along the anterior-posterior axis. Further functional analyses revealed that expression of Hoxb genes and retinaldehyde dehydrogenase 2 (Raldh2), which are involved in limb positioning, are directly activated by Cux2 in the lateral plate mesoderm. Our data suggest that Cux2 in the lateral plate mesoderm refines the forelimb field via regulation of Raldh2 and Hoxb genes in chicken embryos. Summary: Cux2 in the lateral plate mesoderm refines the forelimb field via regulation of Raldh2 and Hoxb genes in chicken embryos.
Collapse
Affiliation(s)
- Shogo Ueda
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Ingrid Rosenburg Cordeiro
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Yuuta Moriyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Chika Nishimori
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Kei-Ichi Kai
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Reiko Yu
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Ryoichiro Nakato
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Mikiko Tanaka
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| |
Collapse
|
22
|
Kawakami H, Johnson A, Fujita Y, Swearer A, Wada N, Kawakami Y. Characterization of cis-regulatory elements for Fgf10 expression in the chick embryo. Dev Dyn 2018; 247:1253-1263. [PMID: 30325084 DOI: 10.1002/dvdy.24682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/28/2018] [Accepted: 10/11/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Fgf10 is expressed in various tissues and organs, such as the limb bud, heart, inner ear, and head mesenchyme. Previous studies identified Fgf10 enhancers for the inner ear and heart. However, Fgf10 enhancers for other tissues have not been identified. RESULTS By using primary culture chick embryo lateral plate mesoderm cells, we compared activities of deletion constructs of the Fgf10 promoter region, cloned into a promoter-less luciferase reporter vector. We identified a 0.34-kb proximal promoter that can activate luciferase expression. Then, we cloned 11 evolutionarily conserved sequences located within or outside of the Fgf10 gene into the 0.34-kb promoter-luciferase vector, and tested their activities in vitro using primary cultured cells. Two sequences showed the highest activities. By using the Tol2 system and electroporation into chick embryos, activities of the 0.34-kb promoter with and without the two sequences were tested in vivo. No activities were detected in limb buds. However, the 0.34-kb promoter exhibited activities in the dorsal midline of the brain, while Fgf10 is detected in broader region in the brain. The two noncoding sequences negatively acted on the 0.34-kb promoter in the brain. CONCLUSIONS The proximal 0.34-kb promoter has activities to drive expression in restricted areas of the brain. Developmental Dynamics 247:1253-1263, 2018. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota.,Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota.,Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota
| | - Austin Johnson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota
| | - Yu Fujita
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba, Japan
| | - Avery Swearer
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota
| | - Naoyuki Wada
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba, Japan
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota.,Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota.,Developmental Biology Center, University of Minnesota, Minneapolis, Minnesota
| |
Collapse
|
23
|
Swenson JD, Klomp J, Fisher RA, Crow KD. How the Devil Ray Got Its Horns: The Evolution and Development of Cephalic Lobes in Myliobatid Stingrays (Batoidea: Myliobatidae). Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
24
|
Onimaru K, Tatsumi K, Shibagaki K, Kuraku S. A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra. Sci Data 2018; 5:180197. [PMID: 30295671 PMCID: PMC6174923 DOI: 10.1038/sdata.2018.197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/14/2018] [Indexed: 11/25/2022] Open
Abstract
Although cartilaginous fishes have played crucial roles in various fields, including evolutionary biology, marine ecology, bioresources, and aquarium exhibitions, molecular information for these species is poorly available. The present study reports a transcriptome assembly from an embryo of the zebra bullhead shark (Heterodontus zebra), produced by paired-end RNA sequencing. Transcriptome data is generated with a de novo transcriptome assembler, Trinity. Amino acid sequences are predicted from the assemblies, using TransDecoder. Because cartilaginous fishes serve as the outgroup of bony vertebrates, the data would contribute to comparative analyses of a various biological fields. In addition, this study would be useful for conservation biology, such as transcriptome-based population genetics.
Collapse
Affiliation(s)
- Koh Onimaru
- Phyloinformatics unit, RIKEN Center for Life Science Technologies (CLST), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, Japan
| | - Kaori Tatsumi
- Phyloinformatics unit, RIKEN Center for Life Science Technologies (CLST), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, Japan
| | - Kazuhiro Shibagaki
- Ibaraki Prefectural Oarai Aquarium, 8252-3, Isohama-machi, Oarai-machi, Higashiibaraki-gun, Ibaraki, Japan
| | - Shigehiro Kuraku
- Phyloinformatics unit, RIKEN Center for Life Science Technologies (CLST), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, Japan
| |
Collapse
|
25
|
Wood TWP, Nakamura T. Problems in Fish-to-Tetrapod Transition: Genetic Expeditions Into Old Specimens. Front Cell Dev Biol 2018; 6:70. [PMID: 30062096 PMCID: PMC6054942 DOI: 10.3389/fcell.2018.00070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/15/2018] [Indexed: 12/30/2022] Open
Abstract
The fish-to-tetrapod transition is one of the fundamental problems in evolutionary biology. A significant amount of paleontological data has revealed the morphological trajectories of skeletons, such as those of the skull, vertebrae, and appendages in vertebrate history. Shifts in bone differentiation, from dermal to endochondral bones, are key to explaining skeletal transformations during the transition from water to land. However, the genetic underpinnings underlying the evolution of dermal and endochondral bones are largely missing. Recent genetic approaches utilizing model organisms—zebrafish, frogs, chickens, and mice—reveal the molecular mechanisms underlying vertebrate skeletal development and provide new insights for how the skeletal system has evolved. Currently, our experimental horizons to test evolutionary hypotheses are being expanded to non-model organisms with state-of-the-art techniques in molecular biology and imaging. An integration of functional genomics, developmental genetics, and high-resolution CT scanning into evolutionary inquiries allows us to reevaluate our understanding of old specimens. Here, we summarize the current perspectives in genetic programs underlying the development and evolution of the dermal skull roof, shoulder girdle, and appendages. The ratio shifts of dermal and endochondral bones, and its underlying mechanisms, during the fish-to-tetrapod transition are particularly emphasized. Recent studies have suggested the novel cell origins of dermal bones, and the interchangeability between dermal and endochondral bones, obscuring the ontogenetic distinction of these two types of bones. Assimilation of ontogenetic knowledge of dermal and endochondral bones from different structures demands revisions of the prevalent consensus in the evolutionary mechanisms of vertebrate skeletal shifts.
Collapse
Affiliation(s)
- Thomas W P Wood
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Tetsuya Nakamura
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| |
Collapse
|
26
|
Onimaru K, Motone F, Kiyatake I, Nishida K, Kuraku S. A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum). Dev Dyn 2018; 247:712-723. [PMID: 29396887 PMCID: PMC5947634 DOI: 10.1002/dvdy.24623] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 12/12/2017] [Accepted: 01/25/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Studying cartilaginous fishes (chondrichthyans) has helped us understand vertebrate evolution and diversity. However, resources such as genome sequences, embryos, and detailed staging tables are limited for species within this clade. To overcome these limitations, we have focused on a species, the brownbanded bamboo shark (Chiloscyllium punctatum), which is a relatively common aquarium species that lays eggs continuously throughout the year. In addition, because of its relatively small genome size, this species is promising for molecular studies. RESULTS To enhance biological studies of cartilaginous fishes, we establish a normal staging table for the embryonic development of the brownbanded bamboo shark. Bamboo shark embryos take around 118 days to reach the hatching period at 25°C, which is approximately 1.5 times as fast as the small-spotted catshark (Scyliorhinus canicula) takes. Our staging table divides the embryonic period into 38 stages. Furthermore, we found culture conditions that allow early embryos to grow in partially opened egg cases. CONCLUSIONS In addition to the embryonic staging table, we show that bamboo shark embryos exhibit relatively fast embryonic growth and are amenable to culture, key characteristics that enhance their experimental utility. Therefore, the present study is a foundation for cartilaginous fish research. Developmental Dynamics 247:712-723, 2018. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Koh Onimaru
- Phyloinformatics UnitRIKEN Center for Life Science Technologies (CLST)HyogoJapan
| | - Fumio Motone
- Phyloinformatics UnitRIKEN Center for Life Science Technologies (CLST)HyogoJapan
- Graduate School of Science and TechnologyKwansei Gakuin UniversityHyogoJapan
| | | | | | - Shigehiro Kuraku
- Phyloinformatics UnitRIKEN Center for Life Science Technologies (CLST)HyogoJapan
| |
Collapse
|
27
|
Tulenko FJ, Massey JL, Holmquist E, Kigundu G, Thomas S, Smith SME, Mazan S, Davis MC. Fin-fold development in paddlefish and catshark and implications for the evolution of the autopod. Proc Biol Sci 2018; 284:rspb.2016.2780. [PMID: 28539509 DOI: 10.1098/rspb.2016.2780] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/24/2017] [Indexed: 01/04/2023] Open
Abstract
The evolutionary origin of the autopod involved a loss of the fin-fold and associated dermal skeleton with a concomitant elaboration of the distal endoskeleton to form a wrist and digits. Developmental studies, primarily from teleosts and amniotes, suggest a model for appendage evolution in which a delay in the AER-to-fin-fold conversion fuelled endoskeletal expansion by prolonging the function of AER-mediated regulatory networks. Here, we characterize aspects of paired fin development in the paddlefish Polyodon spathula (a non-teleost actinopterygian) and catshark Scyliorhinus canicula (chondrichthyan) to explore aspects of this model in a broader phylogenetic context. Our data demonstrate that in basal gnathostomes, the autopod marker HoxA13 co-localizes with the dermoskeleton component And1 to mark the position of the fin-fold, supporting recent work demonstrating a role for HoxA13 in zebrafish fin ray development. Additionally, we show that in paddlefish, the proximal fin and fin-fold mesenchyme share a common mesodermal origin, and that components of the Shh/LIM/Gremlin/Fgf transcriptional network critical to limb bud outgrowth and patterning are expressed in the fin-fold with a profile similar to that of tetrapods. Together these data draw contrast with hypotheses of AER heterochrony and suggest that limb-specific morphologies arose through evolutionary changes in the differentiation outcome of conserved early distal patterning compartments.
Collapse
Affiliation(s)
- Frank J Tulenko
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA.,Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - James L Massey
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309, USA
| | - Elishka Holmquist
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Gabriel Kigundu
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sarah Thomas
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sylvie Mazan
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, UMR7232, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marcus C Davis
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| |
Collapse
|
28
|
Paço A, Freitas R. Hox D genes and the fin-to-limb
transition: Insights from fish studies. Genesis 2017; 56. [DOI: 10.1002/dvg.23069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/14/2017] [Accepted: 09/08/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Ana Paço
- IBMC - Instituto de Biologia Celular e Molecular; Porto Portugal
- I3S - Instituto de Investigação e Inovação em Saúde; Porto Portugal
- Universidade do Porto; Porto Portugal
| | - Renata Freitas
- IBMC - Instituto de Biologia Celular e Molecular; Porto Portugal
- I3S - Instituto de Investigação e Inovação em Saúde; Porto Portugal
- Universidade do Porto; Porto Portugal
| |
Collapse
|
29
|
Zhu J, Mackem S. John Saunders' ZPA, Sonic hedgehog and digit identity - How does it really all work? Dev Biol 2017; 429:391-400. [PMID: 28161524 PMCID: PMC5540801 DOI: 10.1016/j.ydbio.2017.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/28/2017] [Accepted: 02/01/2017] [Indexed: 01/02/2023]
Abstract
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.
Collapse
Affiliation(s)
- Jianjian Zhu
- Cancer and Developmental Biology Laboratory, CCR, NCI, Frederick, MD 21702, United States
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, CCR, NCI, Frederick, MD 21702, United States.
| |
Collapse
|
30
|
Tanaka M. Alterations in anterior-posterior patterning and its accompanying changes along the proximal-distal axis during the fin-to-limb transition. Genesis 2017; 56. [PMID: 28834131 DOI: 10.1002/dvg.23053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 11/07/2022]
Abstract
The evolution from fins to limbs was one of the most successful innovations for vertebrates, allowing them to vastly expand their behaviors and habitats. Fossil records suggest that morphological changes occurred not only along the proximal-distal axis included appearance of the autopod, but also occurred along the anterior-posterior axis included reductions in the size and number of basal bones and digits. This review focuses on recent progress in developmental and genetic studies aimed at elucidating the mechanisms underlying alteration of anterior-posterior patterning and its accompanying changes along the proximal-distal axis during the fin-to-limb transition.
Collapse
Affiliation(s)
- Mikiko Tanaka
- Department of Life Science and Technology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| |
Collapse
|
31
|
Miyake T, Kumamoto M, Iwata M, Sato R, Okabe M, Koie H, Kumai N, Fujii K, Matsuzaki K, Nakamura C, Yamauchi S, Yoshida K, Yoshimura K, Komoda A, Uyeno T, Abe Y. The pectoral fin muscles of the coelacanthLatimeria chalumnae: Functional and evolutionary implications for the fin-to-limb transition and subsequent evolution of tetrapods. Anat Rec (Hoboken) 2016; 299:1203-23. [DOI: 10.1002/ar.23392] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 05/25/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Tsutomu Miyake
- The Graduate School of Science and Technology; Keio University; Tokyo Japan
- Department of Anatomy; The Jikei University School of Medicine; Tokyo Japan
| | | | | | - Ryuichi Sato
- Institute of Biomechanical Control Systems; Kanazawa Institute of Technology; Hakusan Japan
| | - Masataka Okabe
- Department of Anatomy; The Jikei University School of Medicine; Tokyo Japan
| | - Hiroshi Koie
- Department of Veterinary Medicine; Nihon University; Fujisawa Japan
| | - Nori Kumai
- Research Center of Computational Mechanics (RCCM), Inc; Tokyo Japan
| | - Kenichi Fujii
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | - Koji Matsuzaki
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | - Chiho Nakamura
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | | | - Kosuke Yoshida
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | | | - Akira Komoda
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| | - Teruya Uyeno
- National Museum of Nature and Science; Tokyo Japan
| | - Yoshitaka Abe
- Aquamarine Fukushima; Marine Science Museum; Iwaki Japan
| |
Collapse
|
32
|
Onimaru K, Marcon L, Musy M, Tanaka M, Sharpe J. The fin-to-limb transition as the re-organization of a Turing pattern. Nat Commun 2016; 7:11582. [PMID: 27211489 PMCID: PMC4879262 DOI: 10.1038/ncomms11582] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 04/11/2016] [Indexed: 12/22/2022] Open
Abstract
A Turing mechanism implemented by BMP, SOX9 and WNT has been proposed to control mouse digit patterning. However, its generality and contribution to the morphological diversity of fins and limbs has not been explored. Here we provide evidence that the skeletal patterning of the catshark Scyliorhinus canicula pectoral fin is likely driven by a deeply conserved Bmp–Sox9–Wnt Turing network. In catshark fins, the distal nodular elements arise from a periodic spot pattern of Sox9 expression, in contrast to the stripe pattern in mouse digit patterning. However, our computer model shows that the Bmp–Sox9–Wnt network with altered spatial modulation can explain the Sox9 expression in catshark fins. Finally, experimental perturbation of Bmp or Wnt signalling in catshark embryos produces skeletal alterations which match in silico predictions. Together, our results suggest that the broad morphological diversity of the distal fin and limb elements arose from the spatial re-organization of a deeply conserved Turing mechanism. Mouse digit patterning is controlled by a Turing network of Bmp, Sox9, and Wnt. Here, Onimaru et al. show that fin patterning in the catshark, Scyliorhinus canicula, is controlled by the same network with a different spatial organization; thus, the Turing network is deeply conserved in limb development.
Collapse
Affiliation(s)
- Koh Onimaru
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Luciano Marcon
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marco Musy
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mikiko Tanaka
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - James Sharpe
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
| |
Collapse
|
33
|
Rasch LJ, Martin KJ, Cooper RL, Metscher BD, Underwood CJ, Fraser GJ. An ancient dental gene set governs development and continuous regeneration of teeth in sharks. Dev Biol 2016; 415:347-370. [PMID: 26845577 DOI: 10.1016/j.ydbio.2016.01.038] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/11/2016] [Accepted: 01/29/2016] [Indexed: 12/20/2022]
Abstract
The evolution of oral teeth is considered a major contributor to the overall success of jawed vertebrates. This is especially apparent in cartilaginous fishes including sharks and rays, which develop elaborate arrays of highly specialized teeth, organized in rows and retain the capacity for life-long regeneration. Perpetual regeneration of oral teeth has been either lost or highly reduced in many other lineages including important developmental model species, so cartilaginous fishes are uniquely suited for deep comparative analyses of tooth development and regeneration. Additionally, sharks and rays can offer crucial insights into the characters of the dentition in the ancestor of all jawed vertebrates. Despite this, tooth development and regeneration in chondrichthyans is poorly understood and remains virtually uncharacterized from a developmental genetic standpoint. Using the emerging chondrichthyan model, the catshark (Scyliorhinus spp.), we characterized the expression of genes homologous to those known to be expressed during stages of early dental competence, tooth initiation, morphogenesis, and regeneration in bony vertebrates. We have found that expression patterns of several genes from Hh, Wnt/β-catenin, Bmp and Fgf signalling pathways indicate deep conservation over ~450 million years of tooth development and regeneration. We describe how these genes participate in the initial emergence of the shark dentition and how they are redeployed during regeneration of successive tooth generations. We suggest that at the dawn of the vertebrate lineage, teeth (i) were most likely continuously regenerative structures, and (ii) utilised a core set of genes from members of key developmental signalling pathways that were instrumental in creating a dental legacy redeployed throughout vertebrate evolution. These data lay the foundation for further experimental investigations utilizing the unique regenerative capacity of chondrichthyan models to answer evolutionary, developmental, and regenerative biological questions that are impossible to explore in classical models.
Collapse
Affiliation(s)
- Liam J Rasch
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Kyle J Martin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Rory L Cooper
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Brian D Metscher
- Department of Theoretical Biology, University of Vienna, Vienna A-1090, Austria
| | - Charlie J Underwood
- Department of Earth and Planetary Sciences, Birkbeck, University of London, London WC1E 7HX, United Kingdom
| | - Gareth J Fraser
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.
| |
Collapse
|
34
|
Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc Natl Acad Sci U S A 2015; 112:15940-5. [PMID: 26644578 DOI: 10.1073/pnas.1521818112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Extreme novelties in the shape and size of paired fins are exemplified by extinct and extant cartilaginous and bony fishes. Pectoral fins of skates and rays, such as the little skate (Batoid, Leucoraja erinacea), show a strikingly unique morphology where the pectoral fin extends anteriorly to ultimately fuse with the head. This results in a morphology that essentially surrounds the body and is associated with the evolution of novel swimming mechanisms in the group. In an approach that extends from RNA sequencing to in situ hybridization to functional assays, we show that anterior and posterior portions of the pectoral fin have different genetic underpinnings: canonical genes of appendage development control posterior fin development via an apical ectodermal ridge (AER), whereas an alternative Homeobox (Hox)-Fibroblast growth factor (Fgf)-Wingless type MMTV integration site family (Wnt) genetic module in the anterior region creates an AER-like structure that drives anterior fin expansion. Finally, we show that GLI family zinc finger 3 (Gli3), which is an anterior repressor of tetrapod digits, is expressed in the posterior half of the pectoral fin of skate, shark, and zebrafish but in the anterior side of the pelvic fin. Taken together, these data point to both highly derived and deeply ancestral patterns of gene expression in skate pectoral fins, shedding light on the molecular mechanisms behind the evolution of novel fin morphologies.
Collapse
|
35
|
Zuniga A. Next generation limb development and evolution: old questions, new perspectives. Development 2015; 142:3810-20. [DOI: 10.1242/dev.125757] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The molecular analysis of limb bud development in vertebrates continues to fuel our understanding of the gene regulatory networks that orchestrate the patterning, proliferation and differentiation of embryonic progenitor cells. In recent years, systems biology approaches have moved our understanding of the molecular control of limb organogenesis to the next level by incorporating next generation ‘omics’ approaches, analyses of chromatin architecture, enhancer-promoter interactions and gene network simulations based on quantitative datasets into experimental analyses. This Review focuses on the insights these studies have given into the gene regulatory networks that govern limb development and into the fin-to-limb transition and digit reductions that occurred during the evolutionary diversification of tetrapod limbs.
Collapse
Affiliation(s)
- Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
| |
Collapse
|
36
|
The phantoms of a high-seven - or - why do our thumbs stick out? Front Zool 2015; 12:23. [PMID: 26379756 PMCID: PMC4570229 DOI: 10.1186/s12983-015-0117-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/05/2015] [Indexed: 11/30/2022] Open
Abstract
The earliest tetrapods had hands and feet with up to eight digits but this number was subsequently reduced during evolution. It was assumed that lineages with more than five digits no longer exist but investigations of clawed-frogs now indicate that they posses a rudimentary or atavistic sixth digit in their hindlimb. A recent reevaluation of the stem tetrapod Ichthyostega predicts that its seven digits evolved from two different types of ancestral fin radials, pre-axial and post-axial. In this context we now ask the question, should we consider a pre-axial origin of the thumb as reason for its unique genetic signature?
Collapse
|