1
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Shaping Hox gene activity to generate morphological diversity across vertebrate phylogeny. Essays Biochem 2022; 66:717-726. [PMID: 35924372 DOI: 10.1042/ebc20220050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 02/07/2023]
Abstract
The importance of Hox genes for the development and evolution of the vertebrate axial skeleton and paired appendages has been recognized for already several decades. The steady growth of genomic sequence data from an increasing number of vertebrate species, together with the improvement of methods to analyze genomic structure and interactions, as well as to control gene activity in various species has refined our understanding of Hox gene activity in development and evolution. Here, I will review recent data addressing the influence of Hox regulatory processes in the evolution of the fins and the emergence of the tetrapod limb. In addition, I will discuss the involvement of posterior Hox genes in the control of vertebrate axial extension, focusing on an apparently divergent activity that Hox13 paralog group genes have on the regulation of tail bud development in mouse and zebrafish embryos.
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2
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Neel DV, Basu H, Gunner G, Chiu IM. Catching a killer: Mechanisms of programmed cell death and immune activation in Amyotrophic Lateral Sclerosis. Immunol Rev 2022; 311:130-150. [PMID: 35524757 PMCID: PMC9489610 DOI: 10.1111/imr.13083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 12/13/2022]
Abstract
In the central nervous system (CNS), execution of programmed cell death (PCD) is crucial for proper neurodevelopment. However, aberrant activation of these pathways in adult CNS leads to neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). How a cell dies is critical, as it can drive local immune activation and tissue damage. Classical apoptosis engages several mechanisms to evoke "immunologically silent" responses, whereas other forms of programmed death such as pyroptosis, necroptosis, and ferroptosis release molecules that can potentiate immune responses and inflammation. In ALS, a fatal neuromuscular disorder marked by progressive death of lower and upper motor neurons, several cell types in the CNS express machinery for multiple PCD pathways. The specific cell types engaging PCD, and ultimate mechanisms by which neuronal death occurs in ALS are not well defined. Here, we provide an overview of different PCD pathways implicated in ALS. We also examine immune activation in ALS and differentiate apoptosis from necrotic mechanisms based on downstream immunological consequences. Lastly, we highlight therapeutic strategies that target cell death pathways in the treatment of neurodegeneration and inflammation in ALS.
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Affiliation(s)
- Dylan V Neel
- Harvard Medical School, Department of Immunology, Blavatnik Institute, Boston, MA, USA
| | - Himanish Basu
- Harvard Medical School, Department of Immunology, Blavatnik Institute, Boston, MA, USA
| | - Georgia Gunner
- Harvard Medical School, Department of Immunology, Blavatnik Institute, Boston, MA, USA
| | - Isaac M Chiu
- Harvard Medical School, Department of Immunology, Blavatnik Institute, Boston, MA, USA
- Lead contact
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3
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Evans KM, Buser TJ, Larouche O, Kolmann MA. Untangling the relationship between developmental and evolutionary integration. Semin Cell Dev Biol 2022; 145:22-27. [PMID: 35659472 DOI: 10.1016/j.semcdb.2022.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/29/2022] [Accepted: 05/25/2022] [Indexed: 11/15/2022]
Abstract
Patterns of integration and modularity among organismal traits are prevalent across the tree of life, and at multiple scales of biological organization. Over the past several decades, researchers have studied these patterns at the developmental, and evolutionary levels. While their work has identified the potential drivers of these patterns at different scales, there appears to be a lack of consensus on the relationship between developmental and evolutionary integration. Here, we review and summarize key studies and build a framework to describe the conceptual relationship between these patterns across organismal scales and illustrate how, and why some of these studies may have yielded seemingly conflicting outcomes. We find that among studies that analyze patterns of integration and modularity using morphological data, the lack of consensus may stem in part from the difficulty of fully disentangling the developmental and functional causes of integration. Nonetheless, in some empirical systems, patterns of evolutionary modularity have been found to coincide with expectations based on developmental processes, suggesting that in some circumstances, developmental modularity may translate to evolutionary modularity. We also advance an extension to Hallgrímsson et al.'s palimpsest model to describe how patterns of trait modularity may shift across different evolutionary scales. Finally, we also propose some directions for future research which will hopefully be useful for investigators interested in these issues.
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Affiliation(s)
- Kory M Evans
- Rice University, Biosciences Department, 6100 Main St, Houston, TX 77005, USA.
| | - Thaddaeus J Buser
- Rice University, Biosciences Department, 6100 Main St, Houston, TX 77005, USA
| | - Olivier Larouche
- Rice University, Biosciences Department, 6100 Main St, Houston, TX 77005, USA
| | - Matthew A Kolmann
- Rice University, Biosciences Department, 6100 Main St, Houston, TX 77005, USA
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4
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Stainton H, Towers M. Retinoic acid influences the timing and scaling of avian wing development. Cell Rep 2022; 38:110288. [PMID: 35081337 PMCID: PMC8810399 DOI: 10.1016/j.celrep.2021.110288] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/08/2021] [Accepted: 12/29/2021] [Indexed: 12/23/2022] Open
Abstract
A fundamental question in biology is how embryonic development is timed between different species. To address this problem, we compared wing development in the quail and the larger chick. We reveal that pattern formation is faster in the quail as determined by the earlier activation of 5′Hox genes, termination of developmental organizers (Shh and Fgf8), and the laying down of the skeleton (Sox9). Using interspecies tissue grafts, we show that developmental timing can be reset during a critical window of retinoic acid signaling. Accordingly, extending the duration of retinoic acid signaling switches developmental timing between the quail and the chick and the chick and the larger turkey. However, the incremental growth rate is comparable between all three species, suggesting that the pace of development primarily governs differences in the expansion of the skeletal pattern. The widespread distribution of retinoic acid could coordinate developmental timing throughout the embryo. Quail wings develop faster than chick and turkey wings Retinoic acid can set the species timing of wing development Developmental timing is independent of growth and scales the skeletal pattern
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Affiliation(s)
- Holly Stainton
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Matthew Towers
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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5
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de Bakker MAG, van der Vos W, de Jager K, Chung WY, Fowler DA, Dondorp E, Spiekman SNF, Chew KY, Xie B, Jiménez R, Bickelmann C, Kuratani S, Blazek R, Kondrashov P, Renfree MB, Richardson MK. Selection on phalanx development in the evolution of the bird wing. Mol Biol Evol 2021; 38:4222-4237. [PMID: 34164688 PMCID: PMC8476175 DOI: 10.1093/molbev/msab150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 05/03/2021] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- Merijn A G de Bakker
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Wessel van der Vos
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72.,Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstrasse 43, 10115 Berlin, Germany
| | - Kaylah de Jager
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Wing Yu Chung
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Donald A Fowler
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Esther Dondorp
- Naturalis Biodiversity Center, 2300 RA Leiden, PO Box 9517, The Netherlands
| | - Stephan N F Spiekman
- Paläontologisches Institut und Museum, Universität Zürich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland
| | - Keng Yih Chew
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Bing Xie
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
| | - Rafael Jiménez
- Departamento de Genética, Universidad de Granada, Lab 127 Centro de Investigación Biomédica, Avenida del Conocimiento S/N, 1810018016 Armilla, Granada, Spain
| | - Constanze Bickelmann
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstrasse 43, 10115 Berlin, Germany
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,RIKEN Cluster for Pioneering Research, Kobe, Japan
| | - Radim Blazek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna, 603 65, Czech Republic 8, Brno
| | - Peter Kondrashov
- Kirksville College of Osteopathic Medicine, A. T. Still University of Health Sciences, Kirksville, 63501, MO USA)
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Michael K Richardson
- Animal Science & Health, Institute of Biology Leiden (IBL), Leiden University, 2333BE Leiden, the Netherlands Sylviusweg 72
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6
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Ishikawa S, Nishida N, Fujino S, Ogino T, Takahashi H, Miyoshi N, Uemura M, Satoh T, Yamamoto H, Mizushima T, Doki Y, Eguchi H. Comprehensive profiling of novel epithelial-mesenchymal transition mediators and their clinical significance in colorectal cancer. Sci Rep 2021; 11:11759. [PMID: 34083586 PMCID: PMC8175715 DOI: 10.1038/s41598-021-91102-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 05/21/2021] [Indexed: 12/27/2022] Open
Abstract
Epithelial–mesenchymal transition (EMT) is a drastic phenotypic change during cancer metastasis and is one of the most important hallmarks of aggressive cancer. Although the overexpression of some specific transcription factors explains the functional alteration of EMT-induced cells, a complete picture of this biological process is yet to be elucidated. To comprehensively profile EMT-related genes in colorectal cancer, we quantified the EMT induction ability of each gene according to its similarity to the cancer stromal gene signature and termed it “mesenchymal score.” This bioinformatic approach successfully identified 90 candidate EMT mediators, which are strongly predictive of survival in clinical samples. Among these candidates, we discovered that the neuronal gene ARC, possibly originating from the retrotransposon, unexpectedly plays a crucial role in EMT induction. Profiling of novel EMT mediators we demonstrated here may help understand the complexity of the EMT program and open up new avenues for therapeutic intervention in colorectal cancer.
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Affiliation(s)
- Satoshi Ishikawa
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Naohiro Nishida
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Department of Frontier Science for Cancer and Chemotherapy, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Shiki Fujino
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takayuki Ogino
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Norikatsu Miyoshi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Taroh Satoh
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Frontier Science for Cancer and Chemotherapy, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hirofumi Yamamoto
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tsunekazu Mizushima
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
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7
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Abstract
The HOXC10 gene, a member of the HOX genes family, plays crucial roles in mammalian physiological processes, such as limb morphological development, limb regeneration, and lumbar motor neuron differentiation. HOXC10 is also associated with angiogenesis, fat metabolism, and sex regulation. Additional evidence suggests that HOXC10 dysregulation is closely associated with various tumors. HOXC10 is an important transcription factor that can activate several oncogenic pathways by regulating various target molecules such as ERK, AKT, p65, and epithelial mesenchymal transition-related genes. HOXC10 also induces drug resistance in cancers by promoting the DNA repair pathway. In this review, we summarize HOXC10 gene structure and expression as well as the role of HOXC10 in different human cancer processes. This review will provide insight into the status of HOXC10 research and help identify novel targets for cancer therapy.
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Affiliation(s)
- Jinyong Fang
- Department of Science and Education, Jinhua Guangfu Oncology Hospital, Jinhua, China
| | - Jianjun Wang
- Department of Gastroenterological Surgery, Jinhua Guangfu Oncology Hospital, Jinhua, China
| | - Liangliang Yu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Wenxia Xu
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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8
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Castro J, Beviano V, Paço A, Leitão-Castro J, Cadete F, Francisco M, Freitas R. Hoxd13/Bmp2-mediated mechanism involved in zebrafish finfold design. Sci Rep 2021; 11:7165. [PMID: 33785799 PMCID: PMC8009906 DOI: 10.1038/s41598-021-86621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The overexpression of hoxd13a during zebrafish fin development causes distal endochondral expansion and simultaneous reduction of the finfold, mimicking the major events thought to have happened during the fin-to-limb transition in Vertebrates. We investigated the effect of hoxd13a overexpression on putative downstream targets and found it to cause downregulation of proximal fin identity markers (meis1 and emx2) and upregulation of genes involved in skeletogenesis/patterning (fbn1, dacha) and AER/Finfold maintenance (bmps). We then show that bmp2b overexpression leads to finfold reduction, recapitulating the phenotype observed in hoxd13a-overexpressing fins. In addition, we show that during the development of the long finfold in leot1/lofdt1 mutants, hoxd13a and bmp2b are downregulated. Our results suggest that modulation of the transcription factor Hoxd13 during evolution may have been involved in finfold reduction through regulation of the Bmp signalling that then activated apoptotic mechanisms impairing finfold elongation.
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Affiliation(s)
- João Castro
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Vanessa Beviano
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Ana Paço
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Joana Leitão-Castro
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Francisco Cadete
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Miguel Francisco
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Renata Freitas
- grid.5808.50000 0001 1503 7226I3S, Institute for Innovation and Health Research, University of Porto, Porto, Portugal ,Cell Growth and Differentiation Group, IBMC/I3S, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
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9
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Hawkins MB, Henke K, Harris MP. Latent developmental potential to form limb-like skeletal structures in zebrafish. Cell 2021; 184:899-911.e13. [PMID: 33545089 DOI: 10.1016/j.cell.2021.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 10/28/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Changes in appendage structure underlie key transitions in vertebrate evolution. Addition of skeletal elements along the proximal-distal axis facilitated critical transformations, including the fin-to-limb transition that permitted generation of diverse modes of locomotion. Here, we identify zebrafish mutants that form supernumerary long bones in their pectoral fins. These new bones integrate into musculature, form joints, and articulate with neighboring elements. This phenotype is caused by activating mutations in previously unrecognized regulators of appendage patterning, vav2 and waslb, that function in a common pathway. This pathway is required for appendage development across vertebrates, and loss of Wasl in mice causes defects similar to those seen in murine Hox mutants. Concordantly, formation of supernumerary bones requires Hox11 function, and mutations in the vav2/wasl pathway drive enhanced expression of hoxa11b, indicating developmental homology with the forearm. Our findings reveal a latent, limb-like pattern ability in fins that is activated by simple genetic perturbation.
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Affiliation(s)
- M Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA; Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Katrin Henke
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA.
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10
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Newton AH, Smith CA. Regulation of vertebrate forelimb development and wing reduction in the flightless emu. Dev Dyn 2021; 250:1248-1263. [PMID: 33368781 DOI: 10.1002/dvdy.288] [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: 10/01/2020] [Revised: 12/01/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
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.
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Affiliation(s)
- Axel H Newton
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Craig A Smith
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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11
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Lin GH, Zhang L. Apical ectodermal ridge regulates three principal axes of the developing limb. J Zhejiang Univ Sci B 2020; 21:757-766. [PMID: 33043642 PMCID: PMC7606201 DOI: 10.1631/jzus.b2000285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/06/2020] [Indexed: 11/11/2022]
Abstract
Understanding limb development not only gives insights into the outgrowth and differentiation of the limb, but also has clinical relevance. Limb development begins with two paired limb buds (forelimb and hindlimb buds), which are initially undifferentiated mesenchymal cells tipped with a thickening of the ectoderm, termed the apical ectodermal ridge (AER). As a transitional embryonic structure, the AER undergoes four stages and contributes to multiple axes of limb development through the coordination of signalling centres, feedback loops, and other cell activities by secretory signalling and the activation of gene expression. Within the scope of proximodistal patterning, it is understood that while fibroblast growth factors (FGFs) function sequentially over time as primary components of the AER signalling process, there is still no consensus on models that would explain proximodistal patterning itself. In anteroposterior patterning, the AER has a dual-direction regulation by which it promotes the sonic hedgehog (Shh) gene expression in the zone of polarizing activity (ZPA) for proliferation, and inhibits Shh expression in the anterior mesenchyme. In dorsoventral patterning, the AER activates Engrailed-1 (En1) expression, and thus represses Wnt family member 7a (Wnt7a) expression in the ventral ectoderm by the expression of Fgfs, Sp6/8, and bone morphogenetic protein (Bmp) genes. The AER also plays a vital role in shaping the individual digits, since levels of Fgf4/8 and Bmps expressed in the AER affect digit patterning by controlling apoptosis. In summary, the knowledge of crosstalk within AER among the three main axes is essential to understand limb growth and pattern formation, as the development of its areas proceeds simultaneously.
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Affiliation(s)
- Guo-hao Lin
- Centre for Anatomy and Human Identification, University of Dundee, Dundee DD1 5EH, UK
- Collaborative Innovation Center for Sports Health Promotion, Shandong Sport University, Jinan 250102, China
| | - Lan Zhang
- Collaborative Innovation Center for Sports Health Promotion, Shandong Sport University, Jinan 250102, China
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12
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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: 23] [Impact Index Per Article: 5.8] [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.
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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
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13
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Harsanyi S, Zamborsky R, Kokavec M, Danisovic L. Genetics of developmental dysplasia of the hip. Eur J Med Genet 2020; 63:103990. [PMID: 32540376 DOI: 10.1016/j.ejmg.2020.103990] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022]
Abstract
In the last decade, the advances in the molecular analyses and sequencing techniques allowed researchers to study developmental dysplasia of the hip (DDH) more thoroughly. Certain chromosomes, genes, loci and polymorphisms are being associated with variable severity of this disorder. The wide range of signs and symptoms is dependent either on isolated or systemic manifestation. Phenotypes of isolated cases range from only a mild ligamental laxity, through subluxation, to a complete dislocation of the femoral head. Systemic manifestation is connected to various forms of skeletal dysplasia and other malformations characterized by significant genetic aberrations. To reveal the background of DDH heredity, multiple studies focused on large sample sizes with an emphasis on the correlation between genotype, phenotype and continuous clinical examination. Etiological risk factors that have been observed and documented in patients include genetic, environmental, and mechanical factors, which significantly contribute to the familial or nonfamilial occurrence and phenotypic variability of this disorder. Still, the multifactorial etiology and pathogenesis of DDH are not yet sufficiently clarified, explained, or understood. Formation of connective tissue, osteogenesis, chondrogenesis, and all other affected pathways and variations in the function of their individual elements contribute to the creation of the pathology in a developing human body. This review article presents an up-to-date list of known DDH associated genes, their products, and functional characteristics.
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Affiliation(s)
- Stefan Harsanyi
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08, Bratislava, Slovakia.
| | - Radoslav Zamborsky
- Department of Orthopedics, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Limbova 1, 833 40, Bratislava, Slovakia.
| | - Milan Kokavec
- Department of Orthopedics, Faculty of Medicine, Comenius University and National Institute of Children's Diseases, Limbova 1, 833 40, Bratislava, Slovakia.
| | - Lubos Danisovic
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08, Bratislava, Slovakia.
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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.
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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.
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15
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Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Mungall CJ, Vision TJ. A Logical Model of Homology for Comparative Biology. Syst Biol 2020; 69:345-362. [PMID: 31596473 PMCID: PMC7672696 DOI: 10.1093/sysbio/syz067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/20/2019] [Accepted: 09/26/2019] [Indexed: 01/09/2023] Open
Abstract
There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery. [Homology; ontology; anatomy; morphology; evolution; knowledgebase; phenoscape.].
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Affiliation(s)
- Paula M Mabee
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - James P Balhoff
- Renaissance Computing Institute, University of North Carolina, 100 Europa Drive, Suite 540, Chapel Hill, NC 27517, USA
| | - Wasila M Dahdul
- Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA
| | - Hilmar Lapp
- Center for Genomic and Computational Biology, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - Christopher J Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Todd J Vision
- Department of Biology and School of Information and Library Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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Andrews TGR, Gattoni G, Busby L, Schwimmer MA, Benito-Gutiérrez È. Hybridization Chain Reaction for Quantitative and Multiplex Imaging of Gene Expression in Amphioxus Embryos and Adult Tissues. Methods Mol Biol 2020; 2148:179-194. [PMID: 32394382 PMCID: PMC7612682 DOI: 10.1007/978-1-0716-0623-0_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In situ hybridization (ISH) methods remain the most popular approach for profiling the expression of a gene at high spatial resolution and have been broadly used to address many biological questions. One compelling application is in the field of evo-devo, where comparing gene expression patterns has offered insight into how vertebrate development has evolved. Gene expression profiling in the invertebrate chordate amphioxus (cephalochordate) has been particularly instrumental in this context: its key phylogenetic position as sister group to all other chordates makes it an ideal model system to compare with vertebrates and for reconstructing the ancestral condition of our phylum. However, while ISH methods have been developed extensively in vertebrate model systems to fluorescently detect the expression of multiple genes simultaneously at a cellular and subcellular resolution, amphioxus gene expression profiling is still based on single-gene nonfluorescent chromogenic methods, whose spatial resolution is often compromised by diffusion of the chromogenic product. This represents a serious limitation for reconciling gene expression dynamics between amphioxus and vertebrates and for molecularly identifying cell types, defined by their combinatorial code of gene expression, that may have played pivotal roles in evolutionary innovation. Herein we overcome these problems by describing a new protocol for application of the third-generation hybridization chain reaction (HCR) to the amphioxus, which permits fluorescent, multiplex, and quantitative detection of gene expression in situ, within the changing morphology of the developing embryo, and in adult tissues. A detailed protocol is herein provided for whole-mount preparations of embryos and vibratome sections of adult tissues.
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Affiliation(s)
| | - Giacomo Gattoni
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Lara Busby
- Department of Zoology, University of Cambridge, Cambridge, UK
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Woltering JM, Holzem M, Meyer A. Lissamphibian limbs and the origins of tetrapod hox domains. Dev Biol 2019; 456:138-144. [DOI: 10.1016/j.ydbio.2019.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 12/30/2022]
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Hilton EJ, Warth P, Konstantinidis P. The morphology, development, and evolution of the head of fishes: Foundational studies for a renaissance of comparative morphology. ACTA ZOOL-STOCKHOLM 2019. [DOI: 10.1111/azo.12299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eric J. Hilton
- Virginia Institute of Marine Science William & Mary Gloucester Point Virginia
| | - Peter Warth
- Institut für Zoologie und Evolutionsforschung Friedrich‐Schiller‐Universität Jena Jena Germany
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Song JY, Pineault KM, Wellik DM. Development, repair, and regeneration of the limb musculoskeletal system. Curr Top Dev Biol 2019; 132:451-486. [PMID: 30797517 DOI: 10.1016/bs.ctdb.2018.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The limb musculoskeletal system provides a primary means for locomotion, manipulation of objects and protection for most vertebrate organisms. Intricate integration of the bone, tendon and muscle tissues are required for function. These three tissues arise largely independent of one another, but the connections formed during later development are maintained throughout life and are re-established following injury. Each of these tissues also have mesenchymal stem/progenitor cells that function in maintenance and repair. Here in, we will review the major events in the development of limb skeleton, tendon, and muscle tissues, their response to injury, and discuss current knowledge regarding resident progenitor/stem cells within each tissue that participate in development, repair, and regeneration in vivo.
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Affiliation(s)
- Jane Y Song
- Program in Cell and Molecular Biology Program, University of Michigan, Ann Arbor, MI, United States
| | - Kyriel M Pineault
- Department of Cell & Regenerative Biology, University of Wisconsin, Madison, WI, United States
| | - Deneen M Wellik
- Department of Cell & Regenerative Biology, University of Wisconsin, Madison, WI, United States.
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20
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Yakushiji-Kaminatsui N, Lopez-Delisle L, Bolt CC, Andrey G, Beccari L, Duboule D. Similarities and differences in the regulation of HoxD genes during chick and mouse limb development. PLoS Biol 2018; 16:e3000004. [PMID: 30475793 PMCID: PMC6283595 DOI: 10.1371/journal.pbio.3000004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 12/06/2018] [Accepted: 11/09/2018] [Indexed: 12/22/2022] Open
Abstract
In all tetrapods examined thus far, the development and patterning of limbs require the activation of gene members of the HoxD cluster. In mammals, they are regulated by a complex bimodal process that controls first the proximal patterning and then the distal structure. During the shift from the former to the latter regulation, this bimodal regulatory mechanism allows the production of a domain with low Hoxd gene expression, at which both telomeric (T-DOM) and centromeric regulatory domains (C-DOM) are silent. These cells generate the future wrist and ankle articulations. We analyzed the implementation of this regulatory mechanism in chicken, i.e., in an animal for which large morphological differences exist between fore- and hindlimbs. We report that although this bimodal regulation is globally conserved between the mouse and the chick, some important modifications evolved at least between these two model systems, in particular regarding the activity of specific enhancers, the width of the TAD boundary separating the two regulations, and the comparison between the forelimb versus hindlimb regulatory controls. At least one aspect of these regulations seems to be more conserved between chick and bats than with mouse, which may relate to the extent to which forelimbs and hindlimbs of these various animals differ in their morphologies. A comparison of Hox gene regulation during the development of limbs in birds and mammals reveals that whereas the characteristic bimodal regulatory system, based on large chromatin domains, is largely conserved between these morphologically distinct structures, some differences are revealed in the way this is implemented in various vertebrates. The shapes of limbs vary greatly among tetrapod species, even between the forelimbs and hindlimbs of the same animal. Hox genes regulate the proper growth and patterning of tetrapod limbs. In order to evaluate whether variations in the complex regulation of a cluster of Hox genes—the Hoxd genes—during limb development contribute to the differences in limb shape, we compared their transcriptional control during limb bud development in the forelimbs and hindlimbs of mouse and chicken embryos. We found that the regulatory mechanism underlying Hoxd gene expression is highly conserved, but some clear differences exist. For instance, we observed a variation in the topologically associating domain (TAD; a self-interacting genomic region) boundary interval between the mouse and the chick, as well as differences in the activity of a conserved enhancer element situated within the telomeric regulatory domain. In contrast to the mouse, the chicken enhancer has a stronger activity in the forelimb buds than in the hindlimb buds, which is correlated with the striking differences in the mRNA levels of the genes. We conclude that differences in both the timing and duration of TAD activities and in the width of their boundary may parallel the important decrease in Hoxd gene transcription in chick hindlimb buds versus forelimb buds. These differences may also account for the slightly distinct regulatory strategies implemented by mammals and birds at this locus.
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Affiliation(s)
| | - Lucille Lopez-Delisle
- School of Life Sciences, Federal Institute of Technology, Lausanne, Lausanne, Switzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Federal Institute of Technology, Lausanne, Lausanne, Switzerland
| | - Guillaume Andrey
- School of Life Sciences, Federal Institute of Technology, Lausanne, Lausanne, Switzerland
| | - Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, Geneva 4, Switzerland
| | - Denis Duboule
- School of Life Sciences, Federal Institute of Technology, Lausanne, Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva 4, Switzerland
- * E-mail:
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21
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Márquez-Flórez KM, Monaghan JR, Shefelbine SJ, Ramirez-Martínez A, Garzón-Alvarado DA. A computational model for the joint onset and development. J Theor Biol 2018; 454:345-356. [DOI: 10.1016/j.jtbi.2018.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 11/28/2022]
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Godfrey TC, Wildman BJ, Beloti MM, Kemper AG, Ferraz EP, Roy B, Rehan M, Afreen LH, Kim E, Lengner CJ, Hassan Q. The microRNA-23a cluster regulates the developmental HoxA cluster function during osteoblast differentiation. J Biol Chem 2018; 293:17646-17660. [PMID: 30242124 DOI: 10.1074/jbc.ra118.003052] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/22/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRs) and Hox transcription factors have decisive roles in postnatal bone formation and homeostasis. In silico analysis identified extensive interaction between HOXA cluster mRNA and microRNAs from the miR-23a cluster. However, Hox regulation by the miR-23a cluster during osteoblast differentiation remains undefined. We examined this regulation in preosteoblasts and in a novel miR-23a cluster knockdown mouse model. Overexpression and knockdown of the miR-23a cluster in preosteoblasts decreased and increased, respectively, the expression of the proteins HOXA5, HOXA10, and HOXA11; these proteins' mRNAs exhibited significant binding with the miR-23a cluster miRNAs, and miRNA 3'-UTR reporter assays confirmed repression. Importantly, during periods correlating with development and differentiation of bone cells, we found an inverse pattern of expression between HoxA factors and members of the miR-23a cluster. HOXA5 and HOXA11 bound to bone-specific promoters, physically interacted with transcription factor RUNX2, and regulated bone-specific genes. Depletion of HOXA5 or HOXA11 in preosteoblasts also decreased cellular differentiation. Additionally, stable overexpression of the miR-23a cluster in osteoblasts decreased the recruitment of HOXA5 and HOXA11 to osteoblast gene promoters, significantly inhibiting histone H3 acetylation. Heterozygous miR-23a cluster knockdown female mice (miR-23a ClWT/ZIP) had significantly increased trabecular bone mass when compared with WT mice. Furthermore, miR-23a cluster knockdown in calvarial osteoblasts of these mice increased the recruitment of HOXA5 and HOXA11, with a substantial enrichment of promoter histone H3 acetylation. Taken together, these findings demonstrate that the miR-23a cluster is required for maintaining stage-specific HoxA factor expression during osteogenesis.
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Affiliation(s)
- Tanner C Godfrey
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Benjamin J Wildman
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Marcio M Beloti
- the School of Dentistry of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP 14040-904, Brazil, and
| | - Austin G Kemper
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Emanuela P Ferraz
- the School of Dentistry of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP 14040-904, Brazil, and
| | - Bhaskar Roy
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Mohammad Rehan
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Lubana H Afreen
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Eddy Kim
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Christopher J Lengner
- the Department of Biomedical Sciences, School of Veterinary Medicine, and Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Quamarul Hassan
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294,
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Fabre PJ, Leleu M, Mascrez B, Lo Giudice Q, Cobb J, Duboule D. Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development. BMC Biol 2018; 16:101. [PMID: 30223853 PMCID: PMC6142630 DOI: 10.1186/s12915-018-0570-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Global analyses of gene expression during development reveal specific transcription patterns associated with the emergence of various cell types, tissues, and organs. These heterogeneous patterns are instrumental to ensure the proper formation of the different parts of our body, as shown by the phenotypic effects generated by functional genetic approaches. However, variations at the cellular level can be observed within each structure or organ. In the developing mammalian limbs, expression of Hox genes from the HoxD cluster is differentially controlled in space and time, in cells that will pattern the digits and the forearms. While the Hoxd genes broadly share a common regulatory landscape and large-scale analyses have suggested a homogenous Hox gene transcriptional program, it has not previously been clear whether Hoxd genes are expressed together at the same levels in the same cells. RESULTS We report a high degree of heterogeneity in the expression of the Hoxd11 and Hoxd13 genes. We analyzed single-limb bud cell transcriptomes and show that Hox genes are expressed in specific combinations that appear to match particular cell types. In cells giving rise to digits, we find that the expression of the five relevant Hoxd genes (Hoxd9 to Hoxd13) is unbalanced, despite their control by known global enhancers. We also report that specific combinatorial expression follows a pseudo-time sequence, which is established based on the transcriptional diversity of limb progenitors. CONCLUSIONS Our observations reveal the existence of distinct combinations of Hoxd genes at the single-cell level during limb development. In addition, we document that the increasing combinatorial expression of Hoxd genes in this developing structure is associated with specific transcriptional signatures and that these signatures illustrate a temporal progression in the differentiation of these cells.
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Affiliation(s)
- P J Fabre
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015, Lausanne, Switzerland. .,Department of Basic Neurosciences, University of Geneva, 1211, Geneva, Switzerland.
| | - M Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015, Lausanne, Switzerland
| | - B Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland
| | - Q Lo Giudice
- Department of Basic Neurosciences, University of Geneva, 1211, Geneva, Switzerland
| | - J Cobb
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - D Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015, Lausanne, Switzerland. .,Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland.
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Expression of meis and hoxa11 in dipnoan and teleost fins provides new insights into the evolution of vertebrate appendages. EvoDevo 2018; 9:11. [PMID: 29719716 PMCID: PMC5924435 DOI: 10.1186/s13227-018-0099-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/20/2018] [Indexed: 11/22/2022] Open
Abstract
Background The concerted activity of Meis and Hoxa11 transcription factors is essential for the subdivision of tetrapod limbs into proximo-distal (PD) domains; however, little is know about the evolution of this patterning mechanism. Here, we aim to study the expression of meis and hoxa11 orthologues in the median and paired rayed fins of zebrafish and in the lobed fins of the Australian lungfish. Results First, a late phase of expression of meis1.1 and hoxa11b in zebrafish dorsal and anal fins relates with segmentation of endochondral elements in proximal and distal radials. Second, our zebrafish in situ hybridization results reveal spatial and temporal changes between pectoral and pelvic fins. Third, in situ analysis of meis1, meis3 and hoxa11 genes in Neoceratodus pectoral fins identifies decoupled domains of expression along the PD axis. Conclusions Our data raise the possibility that the origin of stylopod and zeugopod lies much deeper in gnathostome evolution and that variation in meis and hoxa11 expression has played a substantial role in the transformation of appendage anatomy. Moreover, these observations provide evidence that the Meis/Hoxa11 profile considered a hallmark of stylopod/zeugopod patterning is present in Neoceratodus. Electronic supplementary material The online version of this article (10.1186/s13227-018-0099-9) contains supplementary material, which is available to authorized users.
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Kondo M, Sekine T, Miyakoshi T, Kitajima K, Egawa S, Seki R, Abe G, Tamura K. Flight feather development: its early specialization during embryogenesis. ZOOLOGICAL LETTERS 2018; 4:2. [PMID: 29372073 PMCID: PMC5771061 DOI: 10.1186/s40851-017-0085-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/29/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Flight feathers, a type of feather that is unique to extant/extinct birds and some non-avian dinosaurs, are the most evolutionally advanced type of feather. In general, feather types are formed in the second or later generation of feathers at the first and following molting, and the first molting begins at around two weeks post hatching in chicken. However, it has been stated in some previous reports that the first molting from the natal down feathers to the flight feathers is much earlier than that for other feather types, suggesting that flight feather formation starts as an embryonic event. The aim of this study was to determine the inception of flight feather morphogenesis and to identify embryological processes specific to flight feathers in contrast to those of down feathers. RESULTS We found that the second generation of feather that shows a flight feather-type arrangement has already started developing by chick embryonic day 18, deep in the skin of the flight feather-forming region. This was confirmed by shh gene expression that shows barb pattern, and the expression pattern revealed that the second generation of feather development in the flight feather-forming region seems to start by embryonic day 14. The first stage at which we detected a specific morphology of the feather bud in the flight feather-forming region was embryonic day 11, when internal invagination of the feather bud starts, while the external morphology of the feather bud is radial down-type. CONCLUSION The morphogenesis for the flight feather, the most advanced type of feather, has been drastically modified from the beginning of feather morphogenesis, suggesting that early modification of the embryonic morphogenetic process may have played a crucial role in the morphological evolution of this key innovation. Co-optation of molecular cues for axial morphogenesis in limb skeletal development may be able to modify morphogenesis of the feather bud, giving rise to flight feather-specific morphogenesis of traits.
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Affiliation(s)
- Mao Kondo
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Tomoe Sekine
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Taku Miyakoshi
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Keiichi Kitajima
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Shiro Egawa
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Ryohei Seki
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
- Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Gembu Abe
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Koji Tamura
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
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Barry SN, Crow KD. The role of HoxA11 and HoxA13 in the evolution of novel fin morphologies in a representative batoid ( Leucoraja erinacea). EvoDevo 2017; 8:24. [PMID: 29214009 PMCID: PMC5709974 DOI: 10.1186/s13227-017-0088-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/21/2017] [Indexed: 01/13/2023] Open
Abstract
Background Batoids exhibit unique body plans with derived fin morphologies, such as the anteriorly expanded pectoral fins that fuse to the head, or distally extended anterior pelvic fin lobes used for a modified swimming technique utilized by skates (Rajidae). The little skate (Leucoraja erinacea), exhibits both of these unique fin morphologies. These fin modifications are not present in a typical shark body plan, and little is known regarding the mechanisms underlying their development. A recent study identified a novel apical ectodermal ridge (AER) associated with the development of the anterior pectoral fin in the little skate, but the role of the posterior HoxA genes was not featured during skate fin development. Results We present the first evidence for HoxA expression (HoxA11 and HoxA13) in novel AER domains associated with the development of three novel fin morphologies in a representative batoid, L. erinacea. We found HoxA13 expression associated with the recently described novel AER in the anterior pectoral fin, and HoxA11 expression in a novel AER domain in the anterior pelvic fin that we describe here. We find that both HoxA11 and HoxA13 are expressed in claspers, and while HoxA11 is expressed in pelvic fins and claspers, HoxA13 is expressed exclusively in developing claspers of males. Finally, HoxA11 expression is associated with the developing fin rays in paired fins. Conclusion Overall, these results indicate that the posterior HoxA genes play an important role in the morphological evolution of paired fins in a representative batoid. These data suggest that the batoids utilize a unique Hox code, where the posterior HoxA genes exhibit distinct expression patterns that are likely associated with specification of novel fin morphologies. Electronic supplementary material The online version of this article (10.1186/s13227-017-0088-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shannon N Barry
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94127 USA
| | - Karen D Crow
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94127 USA
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27
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Abstract
Collinear regulation of Hox genes in space and time has been an outstanding question ever since the initial work of Ed Lewis in 1978. Here we discuss recent advances in our understanding of this phenomenon in relation to novel concepts associated with large-scale regulation and chromatin structure during the development of both axial and limb patterns. We further discuss how this sequential transcriptional activation marks embryonic stem cell-like axial progenitors in mammals and, consequently, how a temporal genetic system is further translated into spatial coordinates via the fate of these progenitors. In this context, we argue the benefit and necessity of implementing this unique mechanism as well as the difficulty in evolving an alternative strategy to deliver this critical positional information.
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Affiliation(s)
- Jacqueline Deschamps
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015 Lausanne, Switzerland.,Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
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28
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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.
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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
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29
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Enokizono T, Ohto T, Tanaka R, Tanaka M, Suzuki H, Sakai A, Imagawa K, Fukushima H, Iwabuti A, Fukushima T, Sumazaki R, Uehara T, Takenouchi T, Kosaki K. Preaxial polydactyly in an individual with Wiedemann-Steiner syndrome caused by a novel nonsense mutation in KMT2A. Am J Med Genet A 2017; 173:2821-2825. [PMID: 28815892 DOI: 10.1002/ajmg.a.38405] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/12/2022]
Abstract
Wiedemann-Steiner syndrome (WDSTS) is an autosomal dominant disorder characterized by hypertrichosis, intellectual disability, and dysmorphic facial appearances (down-slanted vertically narrow palpebral fissures, wide nasal bridge, broad nasal tip, and thick eyebrows). In 2012, Jones and co-workers identified heterozygous mutations in KMT2A (lysine methyltransferase 2A) as the molecular cause of WDSTS. Although the phenotype of this syndrome continues to expand, the associated features are not fully understood. Here, we report WDSTS in a 12-year-old Japanese boy with a novel nonsense mutation in KMT2A. He had right preaxial polydactyly, which has not been previously reported in WDSTS. We could not identify a causal relationship between the KMT2A mutation and preaxial polydactyly, and cannot exclude the preaxial polydactyly is a simple coincidence. We summarized the clinical features of WDSTS associated with KMT2A mutation and discussed the cardinal symptoms in detail.
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Affiliation(s)
- Takashi Enokizono
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki, Japan
| | - Tatsuyuki Ohto
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Ryuta Tanaka
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Mai Tanaka
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki, Japan
| | - Hisato Suzuki
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki, Japan
| | - Aiko Sakai
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki, Japan
| | - Kazuo Imagawa
- Department of Pediatrics, University of Tsukuba Hospital, Ibaraki, Japan
| | - Hiroko Fukushima
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Atsushi Iwabuti
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Takashi Fukushima
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Ryo Sumazaki
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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30
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Nemec S, Luxey M, Jain D, Huang Sung A, Pastinen T, Drouin J. Pitx1 directly modulates the core limb development program to implement hindlimb identity. Development 2017; 144:3325-3335. [PMID: 28807899 DOI: 10.1242/dev.154864] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/04/2017] [Indexed: 01/24/2023]
Abstract
Forelimbs (FLs) and hindlimbs (HLs) develop complex musculoskeletal structures that rely on the deployment of a conserved developmental program. Pitx1, a transcription factor gene with expression restricted to HL and absent from FL, plays an important role in generating HL features. The genomic mechanisms by which Pitx1 effects HL identity remain poorly understood. Here, we use expression profiling and analysis of direct Pitx1 targets to characterize the HL- and FL-restricted genetic programs in mouse and situate the Pitx1-dependent gene network within the context of limb-specific gene regulation. We show that Pitx1 is a crucial component of a narrow network of HL-restricted regulators, acting on a developmental program that is shared between FL and HL. Pitx1 targets sites that are in a similar chromatin state in FL and HL and controls expression of patterning genes as well as the chondrogenic program, consistent with impaired chondrogenesis in Pitx1-/- HL. These findings support a model in which multifactorial actions of a limited number of HL regulators redirect the generic limb development program in order to generate the unique structural features of the limb.
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Affiliation(s)
- Stephen Nemec
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada
| | - Maëva Luxey
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Deepak Jain
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
| | - Aurélie Huang Sung
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1 Canada
| | - Jacques Drouin
- Institut de Recherches Cliniques de Montréal, Montréal, QC, H2W 1R7 Canada .,Department of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1 Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6 Canada
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31
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Hiscock TW, Tschopp P, Tabin CJ. On the Formation of Digits and Joints during Limb Development. Dev Cell 2017; 41:459-465. [PMID: 28586643 PMCID: PMC5546220 DOI: 10.1016/j.devcel.2017.04.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 02/27/2017] [Accepted: 04/24/2017] [Indexed: 01/30/2023]
Abstract
Critical steps in forming the vertebrate limb include the positioning of digits and the positioning of joints within each digit. Recent studies have proposed that the iterative series of digits is established by a Turing-like mechanism generating stripes of chondrogenic domains. However, re-examination of available data suggest that digits are actually patterned as evenly spaced spots, not stripes, which then elongate into rod-shaped digit rays by incorporating new cells at their tips. Moreover, extension of the digit rays and the patterning of the joints occur simultaneously at the distal tip, implying that an integrated model is required to fully understand these processes.
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Affiliation(s)
- Tom W Hiscock
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Tschopp
- Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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32
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Dobbs MB, Gurnett CA. The 2017 ABJS Nicolas Andry Award: Advancing Personalized Medicine for Clubfoot Through Translational Research. Clin Orthop Relat Res 2017; 475:1716-1725. [PMID: 28236079 PMCID: PMC5406347 DOI: 10.1007/s11999-017-5290-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/16/2017] [Indexed: 01/31/2023]
Abstract
BACKGROUND Clubfoot is one of the most common pediatric orthopaedic disorders. While the Ponseti method has revolutionized clubfoot treatment, it is not effective for all patients. When the Ponseti method does not correct the foot, patients are at risk for lifelong disability and may require more-extensive surgery. QUESTIONS/PURPOSES (1) What genetic and morphologic abnormalities contribute to the development of clubfoot? (2) How can this information be used to devise personalized treatment paradigms for patients with clubfoot? METHODS Human gene sequencing, molecular genetic engineering of mouse models of clubfoot, MRI of clubfoot, and development of new treatment methods all have been used by our group to understand the biological basis and improve therapy for this group of disorders. RESULTS We gained new insight into clubfoot pathogenesis from our discovery that mutations in the PITX1-TBX4-HOXC transcriptional pathway cause familial clubfoot and vertical talus in a small number of families, with the unique lower limb expression of these genes providing an explanation for the lack of upper extremity involvement in these disorders. MRI studies revealed corresponding morphologic abnormalities, including hypomorphic muscle, bone, and vasculature, that are not only associated with these gene mutations, but also are biomarkers for treatment-resistant clubfoot. CONCLUSIONS Based on an understanding of the underlying biology, we improved treatment methods for neglected and syndromic clubfoot, developed new treatment for congenital vertical talus based on the principles of the Ponseti method, and designed a new dynamic clubfoot brace to improve strength and compliance.
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Affiliation(s)
- Matthew B. Dobbs
- 0000 0000 9953 7617grid.416775.6Department of Orthopaedics, St. Louis Children’s Hospital, 1 Children’s Place, Suite 4S-60, St. Louis, MO 63110 USA
| | - Christina A. Gurnett
- 0000 0001 2355 7002grid.4367.6Department of Neurology, Washington University School of Medicine in St Louis, St. Louis, MO USA
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33
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Chen J, Liu X, Yao X, Gao F, Bao B. Dorsal fin development in flounder, Paralichthys olivaceus: Bud formation and its cellular origin. Gene Expr Patterns 2017; 25-26:22-28. [PMID: 28442438 DOI: 10.1016/j.gep.2017.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 04/15/2017] [Accepted: 04/19/2017] [Indexed: 01/25/2023]
Abstract
The development of the median fin has not been investigated extensively in teleosts, although in other fishes it has been proposed that it involves the same genetic programs operating in the paired appendages. Adult median fins develop from the larval bud; therefore an investigation of fin bud formation and its cellular origin is essential to understanding the maturation mechanisms. In Paralichthys olivaceus, skeletogenesis proceeds from an anterior to posterior direction providing a good opportunity to study the formation of dorsal fin bud. An apical ectodermal ridge appeared at the basal stratum of the presumptive dorsal fin was first observed at 3 days post hatching. Then the apical ectodermal fold formed as the bud outgrew in 6 days post-hatch larvae. The bud continued to grow, breaking through the dorsal fin fold in 9 days post-hatch larvae. At 13 days post-hatch, the bud grew beyond the edge of the fin fold and formed into the four future rays. Molecular markers of cell type showed the existence of neural crest cells, scleroblasts and sclerotomes in the dorsal fin bud. The earliest gene expression in the dorsal fin bud was Hoxd10 at 3 days post-hatch larvae, then Hoxd9, Hoxd11 and Hoxd12. This indicates Hoxd10 might be a candidate molecular marker of the bud formation site. Some key molecular markers for paired appendage development, such as FGF8, Wnt7, and Shh were expressed at the apical ectodermal ridge and later the apical ectodermal fold. Moreover, the form of the dorsal fin bud could be inhibited by Hh pathway inhibitor, further indicating that common basic molecular mechanisms might be utilized by median fins.
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Affiliation(s)
- Jie Chen
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xiaoyu Liu
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Xiaohua Yao
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Fei Gao
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Baolong Bao
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China.
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34
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Matsubara H, Saito D, Abe G, Yokoyama H, Suzuki T, Tamura K. Upstream regulation for initiation of restricted Shh expression in the chick limb bud. Dev Dyn 2017; 246:417-430. [PMID: 28205287 DOI: 10.1002/dvdy.24493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/06/2017] [Accepted: 02/10/2017] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND The organizing center, which serves as a morphogen source, has crucial functions in morphogenesis in animal development. The center is necessarily located in a certain restricted area in the morphogenetic field, and there are several ways in which an organizing center can be restricted. The organizing center for limb morphogenesis, the ZPA (zone of polarizing activity), specifically expresses the Shh gene and is restricted to the posterior region of the developing limb bud. RESULTS The pre-pattern along the limb anteroposterior axis, provided by anterior Gli3 expression and posterior Hand2 expression, seems insufficient for the initiation of Shh expression restricted to a narrow, small spot in the posterior limb field. Comparison of the spatiotemporal patterns of gene expression between Shh and some candidate genes (Fgf8, Hoxd10, Hoxd11, Tbx2, and Alx4) upstream of Shh expression suggested that a combination of these genes' expression provides the restricted initiation of Shh expression. CONCLUSIONS Taken together with results of functional assays, we propose a model in which positive and negative transcriptional regulatory networks accumulate their functions in the intersection area of their expression regions to provide a restricted spot for the ZPA, the source of morphogen, Shh. Developmental Dynamics 246:417-430, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Haruka Matsubara
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
| | - Daisuke Saito
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
| | - Gembu Abe
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
| | - Hitoshi Yokoyama
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, 036-8561, Japan
| | - Takayuki Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-Cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Koji Tamura
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai, 980-8578, Japan
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35
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Integration of Shh and Fgf signaling in controlling Hox gene expression in cultured limb cells. Proc Natl Acad Sci U S A 2017; 114:3139-3144. [PMID: 28270602 DOI: 10.1073/pnas.1620767114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
During embryonic development, fields of progenitor cells form complex structures through dynamic interactions with external signaling molecules. How complex signaling inputs are integrated to yield appropriate gene expression responses is poorly understood. In the early limb bud, for instance, Sonic hedgehog (Shh) is expressed in the distal posterior mesenchyme, where it acts as a mediator of anterior to posterior (AP) patterning, whereas fibroblast growth factor 8 (Fgf8) is produced by the apical ectodermal ridge (AER) at the distal tip of the limb bud to direct outgrowth along the proximal to distal (PD) axis. Here we use cultured limb mesenchyme cells to assess the response of the target Hoxd genes to these two factors. We find that they act synergistically and that both factors are required to activate Hoxd13 in limb mesenchymal cells. However, the analysis of the enhancer landscapes flanking the HoxD cluster reveals that the bimodal regulatory switch observed in vivo is only partially achieved under these in vitro conditions, suggesting an additional requirement for other factors.
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36
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Tickle C, Towers M. Sonic Hedgehog Signaling in Limb Development. Front Cell Dev Biol 2017; 5:14. [PMID: 28293554 PMCID: PMC5328949 DOI: 10.3389/fcell.2017.00014] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/08/2017] [Indexed: 02/04/2023] Open
Abstract
The gene encoding the secreted protein Sonic hedgehog (Shh) is expressed in the polarizing region (or zone of polarizing activity), a small group of mesenchyme cells at the posterior margin of the vertebrate limb bud. Detailed analyses have revealed that Shh has the properties of the long sought after polarizing region morphogen that specifies positional values across the antero-posterior axis (e.g., thumb to little finger axis) of the limb. Shh has also been shown to control the width of the limb bud by stimulating mesenchyme cell proliferation and by regulating the antero-posterior length of the apical ectodermal ridge, the signaling region required for limb bud outgrowth and the laying down of structures along the proximo-distal axis (e.g., shoulder to digits axis) of the limb. It has been shown that Shh signaling can specify antero-posterior positional values in limb buds in both a concentration- (paracrine) and time-dependent (autocrine) fashion. Currently there are several models for how Shh specifies positional values over time in the limb buds of chick and mouse embryos and how this is integrated with growth. Extensive work has elucidated downstream transcriptional targets of Shh signaling. Nevertheless, it remains unclear how antero-posterior positional values are encoded and then interpreted to give the particular structure appropriate to that position, for example, the type of digit. A distant cis-regulatory enhancer controls limb-bud-specific expression of Shh and the discovery of increasing numbers of interacting transcription factors indicate complex spatiotemporal regulation. Altered Shh signaling is implicated in clinical conditions with congenital limb defects and in the evolution of the morphological diversity of vertebrate limbs.
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Affiliation(s)
- Cheryll Tickle
- Department of Biology and Biochemistry, University of BathBath, UK,*Correspondence: Cheryll Tickle
| | - Matthew Towers
- Department of Biomedical Science, The Bateson Centre, University of SheffieldWestern Bank, Sheffield, UK,Matthew Towers
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37
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Saxena A, Towers M, Cooper KL. The origins, scaling and loss of tetrapod digits. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0482. [PMID: 27994123 PMCID: PMC5182414 DOI: 10.1098/rstb.2015.0482] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/19/2022] Open
Abstract
Many of the great morphologists of the nineteenth century marvelled at similarities between the limbs of diverse species, and Charles Darwin noted these homologies as significant supporting evidence for descent with modification from a common ancestor. Sir Richard Owen also took great care to highlight each of the elements of the forelimb and hindlimb in a multitude of species with focused attention on the homology between the hoof of the horse and the middle digit of man. The ensuing decades brought about a convergence of palaeontology, experimental embryology and molecular biology to lend further support to the homologies of tetrapod limbs and their developmental origins. However, for all that we now understand about the conserved mechanisms of limb development and the development of gross morphological disturbances, little of what is presented in the experimental or medical literature reflects the remarkable diversity resulting from the 450 million year experiment of natural selection. An understanding of conserved and divergent limb morphologies in this new age of genomics and genome engineering promises to reveal more of the developmental potential residing in all limbs and to unravel the mechanisms of evolutionary variation in limb size and shape. In this review, we present the current state of our rapidly advancing understanding of the evolutionary origin of hands and feet and highlight what is known about the mechanisms that shape diverse limbs.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Aditya Saxena
- Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Matthew Towers
- Bateson Centre, Department of Biomedical Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Kimberly L. Cooper
- Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,e-mail:
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38
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Saiz-Lopez P, Chinnaiya K, Towers M, Ros MA. Intrinsic properties of limb bud cells can be differentially reset. Development 2017; 144:479-486. [PMID: 28087638 PMCID: PMC5341798 DOI: 10.1242/dev.137661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 12/15/2016] [Indexed: 02/04/2023]
Abstract
An intrinsic timing mechanism specifies the positional values of the zeugopod (i.e. radius/ulna) and then autopod (i.e. wrist/digits) segments during limb development. Here, we have addressed whether this timing mechanism ensures that patterning events occur only once by grafting GFP-expressing autopod progenitor cells to the earlier host signalling environment of zeugopod progenitor cells. We show by detecting Hoxa13 expression that early and late autopod progenitors fated for the wrist and phalanges, respectively, both contribute to the entire host autopod, indicating that the autopod positional value is irreversibly determined. We provide evidence that Hoxa13 provides an autopod-specific positional value that correctly allocates cells into the autopod, most likely through the control of cell-surface properties as shown by cell-cell sorting analyses. However, we demonstrate that only the earlier autopod cells can adopt the host proliferation rate to permit normal morphogenesis. Therefore, our findings reveal that the ability of embryonic cells to differentially reset their intrinsic behaviours confers robustness to limb morphogenesis. We speculate that this plasticity could be maintained beyond embryogenesis in limbs with regenerative capacity.
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Affiliation(s)
- Patricia Saiz-Lopez
- Departamento de Señalización Celular y Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria), Santander 39011, Spain
| | - Kavitha Chinnaiya
- Bateson Centre, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Matthew Towers
- Bateson Centre, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Maria A Ros
- Departamento de Señalización Celular y Molecular, Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria), Santander 39011, Spain
- Departamento de Anatomía y Biología Celular, Facultad de Medicina, Universidad de Cantabria, Santander 39011, Spain
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Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF. PLoS Genet 2017; 13:e1006567. [PMID: 28103242 PMCID: PMC5289628 DOI: 10.1371/journal.pgen.1006567] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/02/2017] [Accepted: 01/04/2017] [Indexed: 11/29/2022] Open
Abstract
Homeotic genes code for key transcription factors (HOX-TFs) that pattern the animal body plan. During embryonic development, Hox genes are expressed in overlapping patterns and function in a partially redundant manner. In vitro biochemical screens probing the HOX-TF sequence specificity revealed largely overlapping sequence preferences, indicating that co-factors might modulate the biological function of HOX-TFs. However, due to their overlapping expression pattern, high protein homology, and insufficiently specific antibodies, little is known about their genome-wide binding preferences. In order to overcome this problem, we virally expressed tagged versions of limb-expressed posterior HOX genes (HOXA9-13, and HOXD9-13) in primary chicken mesenchymal limb progenitor cells (micromass). We determined the effect of each HOX-TF on cellular differentiation (chondrogenesis) and gene expression and found that groups of HOX-TFs induce distinct regulatory programs. We used ChIP-seq to determine their individual genome-wide binding profiles and identified between 12,721 and 28,572 binding sites for each of the nine HOX-TFs. Principal Component Analysis (PCA) of binding profiles revealed that the HOX-TFs are clustered in two subgroups (Group 1: HOXA/D9, HOXA/D10, HOXD12, and HOXA13 and Group 2: HOXA/D11 and HOXD13), which are characterized by differences in their sequence specificity and by the presence of cofactor motifs. Specifically, we identified CTCF binding sites in Group 1, indicating that this subgroup of HOX-proteins cooperates with CTCF. We confirmed this interaction by an independent biological assay (Proximity Ligation Assay) and demonstrated that CTCF is a novel HOX cofactor that specifically associates with Group 1 HOX-TFs, pointing towards a possible interplay between HOX-TFs and chromatin architecture. Hox genes encode transcription factors that determine the vertebrate body plan and pattern structures and organs in the developing embryo. Despite decades of effort and research on Hox genes, little is known about the HOX-DNA binding properties in vivo. This lack of knowledge is mainly due to the absence of appropriate antibodies to distinguish between different HOX transcription factors. Here, we adapt a cell culture system that allows us to investigate HOX-DNA binding on a genome-wide scale. With this approach, we define and directly compare the genome-wide binding sites of nine posterior HOXA and HOXD transcription factors. We report that the in vivo HOX binding specificity differs from the in vitro specificity and find that HOX-TFs largely rely on co-factor binding and not only on direct HOX-DNA binding. Finally, we identify a novel HOX co-factor, a genome architecture protein, CTCF suggesting a possible interplay between HOX-TF function and chromatin architecture.
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Matsubara Y, Nakano M, Kawamura K, Tsudzuki M, Funahashi JI, Agata K, Matsuda Y, Kuroiwa A, Suzuki T. Inactivation of Sonic Hedgehog Signaling and Polydactyly in Limbs of Hereditary Multiple Malformation, a Novel Type of Talpid Mutant. Front Cell Dev Biol 2016; 4:149. [PMID: 28083533 PMCID: PMC5187386 DOI: 10.3389/fcell.2016.00149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/13/2016] [Indexed: 12/26/2022] Open
Abstract
Hereditary Multiple Malformation (HMM) is a naturally occurring, autosomal recessive, homozygous lethal mutation found in Japanese quail. Homozygote embryos (hmm−/−) show polydactyly similar to talpid2 and talpid3 mutants. Here we characterize the molecular profile of the hmm−/− limb bud and identify the cellular mechanisms that cause its polydactyly. The hmm−/− limb bud shows a severe lack of sonic hedgehog (SHH) signaling, and the autopod has 4 to 11 unidentifiable digits with syn-, poly-, and brachydactyly. The Zone of Polarizing Activity (ZPA) of the hmm−/− limb bud does not show polarizing activity regardless of the presence of SHH protein, indicating that either the secretion pathway of SHH is defective or the SHH protein is dysfunctional. Furthermore, mesenchymal cells in the hmm−/− limb bud do not respond to ZPA transplanted from the normal limb bud, suggesting that signal transduction downstream of SHH is also defective. Since primary cilia are present in the hmm−/− limb bud, the causal gene must be different from talpid2 and talpid3. In the hmm−/− limb bud, a high amount of GLI3A protein is expressed and GLI3 protein is localized to the nucleus. Our results suggest that the regulatory mechanism of GLI3 is disorganized in the hmm−/− limb bud.
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Affiliation(s)
- Yoshiyuki Matsubara
- Division of Biological Science, Graduate School of Science, Nagoya University Nagoya, Japan
| | - Mikiharu Nakano
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University Nagoya, Japan
| | - Kazuki Kawamura
- Division of Biological Science, Graduate School of Science, Nagoya University Nagoya, Japan
| | - Masaoki Tsudzuki
- Laboratory of Animal Breeding and Genetics, Graduate School of Biosphere Science, Hiroshima University Hiroshima, Japan
| | - Jun-Ichi Funahashi
- Institute of Development, Aging and Cancer, Tohoku University Sendai, Japan
| | - Kiyokazu Agata
- Department of Biophysics, Graduate School of Science, Kyoto University Kyoto, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya UniversityNagoya, Japan; Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya UniversityNagoya, Japan
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University Nagoya, Japan
| | - Takayuki Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University Nagoya, Japan
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Young JJ, Tabin CJ. Saunders's framework for understanding limb development as a platform for investigating limb evolution. Dev Biol 2016; 429:401-408. [PMID: 27840200 DOI: 10.1016/j.ydbio.2016.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/02/2016] [Accepted: 11/05/2016] [Indexed: 11/16/2022]
Abstract
John W. Saunders, Jr. made seminal discoveries unveiling how chick embryos develop their limbs. He discovered the apical ectodermal ridge (AER), the zone of polarizing activity (ZPA), and the domains of interdigital cell death within the developing limb and determined their function through experimental analysis. These discoveries provided the basis for subsequent molecular understanding of how vertebrate limbs are induced, patterned, and differentiated. These mechanisms are strongly conserved among the vast diversity of tetrapod limbs suggesting that relatively minor changes and tweaks to the molecular cascades are responsible for the diversity observed in nature. Analysis of the pathway systems first identified by Saunders in the context of animals displaying limb reduction show how alterations in these pathways have resulted in multiple mechanisms of limb and digit loss. Other classes of modification to these same patterning systems are seen at the root of other, novel limb morphological alterations and elaborations.
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Affiliation(s)
- John J Young
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Leal F, Cohn M. Loss and Re-emergence of Legs in Snakes by Modular Evolution of Sonic hedgehog and HOXD Enhancers. Curr Biol 2016; 26:2966-2973. [DOI: 10.1016/j.cub.2016.09.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/29/2016] [Accepted: 09/12/2016] [Indexed: 01/19/2023]
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Reno PL, Kjosness KM, Hines JE. The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:303-21. [DOI: 10.1002/jez.b.22688] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 06/13/2016] [Accepted: 06/28/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Philip L. Reno
- Department of Anthropology; The Pennsylvania State University; University Park Pennsylvania
| | - Kelsey M. Kjosness
- Department of Anthropology; The Pennsylvania State University; University Park Pennsylvania
| | - Jasmine E. Hines
- Department of Anthropology; The Pennsylvania State University; University Park Pennsylvania
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Tufcea DE, François P. Critical Timing without a Timer for Embryonic Development. Biophys J 2016; 109:1724-34. [PMID: 26488664 DOI: 10.1016/j.bpj.2015.08.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 07/12/2015] [Accepted: 08/10/2015] [Indexed: 10/22/2022] Open
Abstract
Timing of embryonic development is precisely controlled, but the mechanisms underlying biological timers are still unclear. Here, a validated model for timing under control of Sonic Hedgehog is revisited and generalized to an arbitrary number of genes. The developmental dynamics where a temporal sequence of gene expression recapitulates a steady-state spatial pattern can be realized through a simple network close to criticality, controlled by the duration of exposure to a morphogen. Criticality simultaneously accounts for many observed biological properties, such as timing, multistability, and canalization of genetic expression. This process can be parsimoniously generalized in many dimensions with a minimum number of genes, all repressing each other with asymmetrical strengths, which also explains sequential activation of different fates. Separation of timescales allows for a simple analytical interpretation. Finally, it is shown that even in the presence of noise, coupling between cells preserves criticality and robust patterning. The model offers a simple theoretical framework for the study of emergent developmental timers.
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Affiliation(s)
- Daniel E Tufcea
- Ernest Rutherford Physics Building, McGill University, Montreal, Quebec, Canada
| | - Paul François
- Ernest Rutherford Physics Building, McGill University, Montreal, Quebec, Canada.
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Beaupeux M, François P. Positional information from oscillatory phase shifts : insights from in silico evolution. Phys Biol 2016; 13:036009. [PMID: 27346171 DOI: 10.1088/1478-3975/13/3/036009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Complex cellular decisions are based on temporal dynamics of pathways, including genetic oscillators. In development, recent works on vertebrae formation have suggested that relative phase of genetic oscillators encode positional information, including differentiation front defining vertebrae positions. Precise mechanisms for this are still unknown. Here, we use computational evolution to find gene network topologies that can compute the phase difference between oscillators and convert it into a decoder morphogen concentration. Two types of networks are discovered, based on symmetry properties of the decoder gene. So called asymmetric networks are studied, and two submodules are identified converting phase information into an amplitude variable. Those networks naturally display a 'shock' for a well defined phase difference, that can be used to define a wavefront of differentiation. We show how implementation of these ideas reproduce experimental features of vertebrate segmentation.
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Affiliation(s)
- M Beaupeux
- Ernest Rutherford Physics Building, McGill University, H3A2T8 Montreal QC, Canada
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Beccari L, Yakushiji-Kaminatsui N, Woltering JM, Necsulea A, Lonfat N, Rodríguez-Carballo E, Mascrez B, Yamamoto S, Kuroiwa A, Duboule D. A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus. Genes Dev 2016; 30:1172-86. [PMID: 27198226 PMCID: PMC4888838 DOI: 10.1101/gad.281055.116] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/22/2016] [Indexed: 11/24/2022]
Abstract
During vertebrate limb development, Hoxd genes are regulated following a bimodal strategy involving two topologically associating domains (TADs) located on either side of the gene cluster. These regulatory landscapes alternatively control different subsets of Hoxd targets, first into the arm and subsequently into the digits. We studied the transition between these two global regulations, a switch that correlates with the positioning of the wrist, which articulates these two main limb segments. We show that the HOX13 proteins themselves help switch off the telomeric TAD, likely through a global repressive mechanism. At the same time, they directly interact with distal enhancers to sustain the activity of the centromeric TAD, thus explaining both the sequential and exclusive operating processes of these two regulatory domains. We propose a model in which the activation of Hox13 gene expression in distal limb cells both interrupts the proximal Hox gene regulation and re-enforces the distal regulation. In the absence of HOX13 proteins, a proximal limb structure grows without any sign of wrist articulation, likely related to an ancestral fish-like condition.
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Affiliation(s)
- Leonardo Beccari
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
| | | | - Joost M Woltering
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
| | - Anamaria Necsulea
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Lonfat
- School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
| | | | - Benedicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
| | - Shiori Yamamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Atsushi Kuroiwa
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland; School of Life Sciences, Federal Institute of Technology, Lausanne, 1015 Lausanne, Switzerland
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Developmental Mechanism of Limb Field Specification along the Anterior-Posterior Axis during Vertebrate Evolution. J Dev Biol 2016; 4:jdb4020018. [PMID: 29615584 PMCID: PMC5831784 DOI: 10.3390/jdb4020018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/19/2022] Open
Abstract
In gnathostomes, limb buds arise from the lateral plate mesoderm at discrete positions along the body axis. Specification of these limb-forming fields can be subdivided into several steps. The lateral plate mesoderm is regionalized into the anterior lateral plate mesoderm (ALPM; cardiac mesoderm) and the posterior lateral plate mesoderm (PLPM). Subsequently, Hox genes appear in a nested fashion in the PLPM and provide positional information along the body axis. The lateral plate mesoderm then splits into the somatic and splanchnic layers. In the somatic layer of the PLPM, the expression of limb initiation genes appears in the limb-forming region, leading to limb bud initiation. Furthermore, past and current work in limbless amphioxus and lampreys suggests that evolutionary changes in developmental programs occurred during the acquisition of paired fins during vertebrate evolution. This review presents these recent advances and discusses the mechanisms of limb field specification during development and evolution, with a focus on the role of Hox genes in this process.
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Tanaka M. Fins into limbs: Autopod acquisition and anterior elements reduction by modifying gene networks involving 5’Hox , Gli3 , and Shh. Dev Biol 2016; 413:1-7. [DOI: 10.1016/j.ydbio.2016.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 11/25/2022]
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HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution. Sci Rep 2016; 6:22720. [PMID: 26940624 PMCID: PMC4778128 DOI: 10.1038/srep22720] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 02/18/2016] [Indexed: 11/24/2022] Open
Abstract
The role of Homeobox transcription factors during fin and limb development have been the focus of recent work investigating the evolutionary origin of limb-specific morphologies. Here we characterize the expression of HoxD genes, as well as the cluster-associated genes Evx2 and LNP, in the paddlefish Polyodon spathula, a basal ray-finned fish. Our results demonstrate a collinear pattern of nesting in early fin buds that includes HoxD14, a gene previously thought to be isolated from global Hox regulation. We also show that in both Polyodon and the catshark Scyliorhinus canicula (a representative chondrichthyan) late phase HoxD transcripts are present in cells of the fin-fold and co-localize with And1, a component of the dermal skeleton. These new data support an ancestral role for HoxD genes in patterning the fin-folds of jawed vertebrates, and fuel new hypotheses about the evolution of cluster regulation and the potential downstream differentiation outcomes of distinct HoxD-regulated compartments.
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