1
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Mary L, Leclerc D, Gilot D, Belaud-Rotureau MA, Jaillard S. The TALE never ends: A comprehensive overview of the role of PBX1, a TALE transcription factor, in human developmental defects. Hum Mutat 2022; 43:1125-1148. [PMID: 35451537 DOI: 10.1002/humu.24388] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/25/2022] [Accepted: 04/20/2022] [Indexed: 11/07/2022]
Abstract
PBX1 is a highly conserved atypical homeodomain transcription factor (TF) belonging to the TALE (three amino acid loop extension) family. Dimerized with other TALE proteins, it can interact with numerous partners and reach dozens of regulating sequences, suggesting its role as a pioneer factor. PBX1 is expressed throughout the embryonic stages (as early as the blastula stage) in vertebrates. In human, PBX1 germline variations are linked to syndromic renal anomalies (CAKUTHED). In this review, we summarized available data on PBX1 functions, PBX1-deficient animal models, and PBX1 germline variations in humans. Two types of genetic alterations were identified in PBX1 gene. PBX1 missense variations generate a severe phenotype including lung hypoplasia, cardiac malformations, and sexual development defects (DSDs). Conversely, truncating variants generate milder phenotypes (mainly cryptorchidism and deafness). We suggest that defects in PBX1 interactions with various partners, including proteins from the HOX (HOXA7, HOXA10, etc.), WNT (WNT9B, WNT3), and Polycomb (BMI1, EED) families are responsible for abnormal proliferation and differentiation of the embryonic mesenchyme. These alterations could explain most of the defects observed in humans. However, some phenotype variability (especially DSDs) remains poorly understood. Further studies are needed to explore the TALE family in greater depth.
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Affiliation(s)
- Laura Mary
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Delphine Leclerc
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - David Gilot
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- Inserm U1242, Centre de lutte contre le cancer Eugène Marquis, Université de Rennes, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET (Institut de recherche en santé, environnement et travail)- UMR_S 1085, Université Rennes 1, Rennes, France
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2
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Fuglerud BM, Drissler S, Lotto J, Stephan TL, Thakur A, Cullum R, Hoodless PA. SOX9 reprograms endothelial cells by altering the chromatin landscape. Nucleic Acids Res 2022; 50:8547-8565. [PMID: 35904801 PMCID: PMC9410909 DOI: 10.1093/nar/gkac652] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 01/08/2023] Open
Abstract
The transcription factor SOX9 is activated at the onset of endothelial-to-mesenchymal transition (EndMT) during embryonic development and in pathological conditions. Its roles in regulating these processes, however, are not clear. Using human umbilical vein endothelial cells (HUVECs) as an EndMT model, we show that SOX9 expression alone is sufficient to activate mesenchymal genes and steer endothelial cells towards a mesenchymal fate. By genome-wide mapping of the chromatin landscape, we show that SOX9 displays features of a pioneer transcription factor, such as opening of chromatin and leading to deposition of active histone modifications at silent chromatin regions, guided by SOX dimer motifs and H2A.Z enrichment. We further observe highly transient and dynamic SOX9 binding, possibly promoted through its eviction by histone phosphorylation. However, while SOX9 binding is dynamic, changes in the chromatin landscape and cell fate induced by SOX9 are persistent. Finally, our analysis of single-cell chromatin accessibility indicates that SOX9 opens chromatin to drive EndMT in atherosclerotic lesions in vivo. This study provides new insight into key molecular functions of SOX9 and mechanisms of EndMT and highlights the crucial developmental role of SOX9 and relevance to human disease.
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Affiliation(s)
- Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada
| | - Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Cell and Developmental Biology Program, University of British Columbia V6T 1Z3, Vancouver, British Columbia, Canada.,School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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3
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Delgado I, Giovinazzo G, Temiño S, Gauthier Y, Balsalobre A, Drouin J, Torres M. Control of mouse limb initiation and antero-posterior patterning by Meis transcription factors. Nat Commun 2021; 12:3086. [PMID: 34035267 PMCID: PMC8149412 DOI: 10.1038/s41467-021-23373-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 04/21/2021] [Indexed: 12/31/2022] Open
Abstract
Meis1 and Meis2 are homeodomain transcription factors that regulate organogenesis through cooperation with Hox proteins. Elimination of Meis genes after limb induction has shown their role in limb proximo-distal patterning; however, limb development in the complete absence of Meis function has not been studied. Here, we report that Meis1/2 inactivation in the lateral plate mesoderm of mouse embryos leads to limb agenesis. Meis and Tbx factors converge in this function, extensively co-binding with Tbx to genomic sites and co-regulating enhancers of Fgf10, a critical factor in limb initiation. Limbs with three deleted Meis alleles show proximal-specific skeletal hypoplasia and agenesis of posterior skeletal elements. This failure in posterior specification results from an early role of Meis factors in establishing the limb antero-posterior prepattern required for Shh activation. Our results demonstrate roles for Meis transcription factors in early limb development and identify their involvement in previously undescribed interaction networks that regulate organogenesis.
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Affiliation(s)
- Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Giovanna Giovinazzo
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Susana Temiño
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Yves Gauthier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Aurelio Balsalobre
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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4
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Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, Dalton S, Zaugg JB, Snyder M. Landscape of cohesin-mediated chromatin loops in the human genome. Nature 2020; 583:737-743. [PMID: 32728247 PMCID: PMC7410831 DOI: 10.1038/s41586-020-2151-x] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/11/2019] [Indexed: 01/14/2023]
Abstract
Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear. Here, to address these questions as part of phase III of the Encyclopedia of DNA Elements (ENCODE), we mapped cohesin-mediated chromatin loops, using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene expression in 24 diverse human cell types, including core ENCODE cell lines. Twenty-eight per cent of all chromatin loops vary across cell types; these variations modestly correlate with changes in gene expression and are effective at grouping cell types according to their tissue of origin. The connectivity of genes corresponds to different functional classes, with housekeeping genes having few contacts, and dosage-sensitive genes being more connected to enhancer elements. This atlas of chromatin loops complements the diverse maps of regulatory architecture that comprise the ENCODE Encyclopedia, and will help to support emerging analyses of genome structure and function.
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Affiliation(s)
- Fabian Grubert
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Rohith Srivas
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Damek V Spacek
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Maya Kasowski
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Mariana Ruiz-Velasco
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Peyton Greenside
- Biomedical Informatics Graduate Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Anil Narasimha
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Qing Liu
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Benjamin Geller
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Akshay Sanghi
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Michael Kulik
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Silin Sa
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Marlene Rabinovitch
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Stephen Dalton
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Judith B Zaugg
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA.
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5
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PKNOX2 expression and regulation in the bone marrow mesenchymal stem cells of Fanconi anemia patients and healthy donors. Mol Biol Rep 2018; 46:669-678. [DOI: 10.1007/s11033-018-4522-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/22/2018] [Indexed: 12/30/2022]
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6
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Gezelius H, Moreno-Juan V, Mezzera C, Thakurela S, Rodríguez-Malmierca LM, Pistolic J, Benes V, Tiwari VK, López-Bendito G. Genetic Labeling of Nuclei-Specific Thalamocortical Neurons Reveals Putative Sensory-Modality Specific Genes. Cereb Cortex 2018; 27:5054-5069. [PMID: 27655933 DOI: 10.1093/cercor/bhw290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/22/2016] [Indexed: 11/14/2022] Open
Abstract
The thalamus is a central brain structure with topographically ordered long-range axonal projections that convey sensory information to the cortex via distinct nuclei. Although there is an increasing knowledge about genes important for thalamocortical (TC) development, the identification of genetic landmarks of the distinct thalamic nuclei during the embryonic development has not been addressed systematically. Indeed, a more comprehensive understanding of how the axons from the individual nuclei find their way and connect to their corresponding cortical area is called for. Here, we used a genetic dual labeling strategy in mice to purify distinct principal sensory thalamic neurons. Subsequent genome-wide transcriptome profiling revealed genes specifically expressed in each nucleus during embryonic development. Analysis of regulatory regions of the identified genes revealed key transcription factors and networks that likely underlie the specification of individual sensory-modality TC connections. Finally, the importance of correct axon targeting for the specific sensory-modality population transcriptome was evidenced in a Sema6A mutant, in which visual TC axons are derailed at embryonic life. In sum, our data determined the developmental transcriptional profile of the TC neurons that will eventually support sensory processing.
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Affiliation(s)
- Henrik Gezelius
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Spain
| | - Verónica Moreno-Juan
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Spain
| | - Cecilia Mezzera
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Spain.,Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal
| | - Sudhir Thakurela
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128 Mainz, Germany
| | - Luis Miguel Rodríguez-Malmierca
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Spain
| | | | - Vladimir Benes
- EMBL, GeneCore, Meyerhofstr. 1, D-69117 Heidelberg, Germany
| | - Vijay K Tiwari
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128 Mainz, Germany
| | - Guillermina López-Bendito
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550 Sant Joan d'Alacant, Spain
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7
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Kimura T, Hino K, Kono T, Takano A, Nitta N, Ushio N, Hino S, Takase R, Kudo M, Daigo Y, Morita W, Nakao M, Nakatsukasa M, Tamagawa T, Rafiq AM, Matsumoto A, Otani H, Udagawa J. Maternal undernutrition during early pregnancy inhibits postnatal growth of the tibia in the female offspring of rats by alteration of chondrogenesis. Gen Comp Endocrinol 2018; 260:58-66. [PMID: 29277418 DOI: 10.1016/j.ygcen.2017.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 11/30/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022]
Abstract
Epidemiological research has suggested that birth weights are correlated with adult leg lengths. However, the relationship between prenatal undernutrition (UN) and postnatal leg growth remains controversial. We investigated the effects of UN during early pregnancy on postnatal hindlimb growth and determined whether early embryonic malnutrition affects the functions of postnatal chondrocytes in rats. Undernourished Wistar dams were fed 40% of the daily intake of rats in the control groups from gestational days 5.5-11.5, and femurs, tibias, and trunks or spinal columns were morphologically measured at birth and at 16 weeks of age in control and undernourished offspring of both sexes. We evaluated cell proliferation and differentiation of cultured chondrocytes derived from neonatal tibias of female offspring and determined chondrocyte-related gene expression levels in neonatal epiphysis and embryonic limb buds. Tibial lengths of undernourished female, but not male, offspring were longer at birth and shorter at 16 weeks of age (p < .05) compared with those of control rats. In chondrocyte culture studies, stimulating effects of IGF-1 on cell proliferation (p < .01) were significantly decreased and levels of type II collagen were lower in female undernourished offspring (p < .05). These phenomena were accompanied by decreased expression levels of Col2a1 and Igf1r and increased expression levels of Fgfr3 (p < .05), which might be attributable to the decreased expression of specificity protein 1 (p < .05), a key transactivator of Col2a1 and Igf1r. In conclusion, UN stress during early pregnancy reduces postnatal tibial growth in female offspring by altering the function of chondrocytes, likely reflecting altered expression of gene transactivators.
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Affiliation(s)
- Tomoko Kimura
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Kodai Hino
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Tadaaki Kono
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Atsushi Takano
- Department of Medical Oncology, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Norihisa Nitta
- Department of Radiology, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Noritoshi Ushio
- Department of Radiology, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-8555, Japan
| | - Ryuta Takase
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-8555, Japan
| | - Motoi Kudo
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Yataro Daigo
- Department of Medical Oncology, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Wataru Morita
- Department of Oral Functional Anatomy, Faculty of Dental Medicine, Hokkaido University, Hokkaido 060-8586, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-8555, Japan
| | - Masato Nakatsukasa
- Laboratory of Physical Anthropology, Kyoto University Graduate School of Science, Kyoto 606-8502, Japan
| | - Toshihiro Tamagawa
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan
| | - Ashiq Mahmood Rafiq
- Department of Anatomy, Faculty of Medicine, Shimane University, Shimane 693-8501, Japan
| | - Akihiro Matsumoto
- Department of Anatomy, Faculty of Medicine, Shimane University, Shimane 693-8501, Japan
| | - Hiroki Otani
- Department of Anatomy, Faculty of Medicine, Shimane University, Shimane 693-8501, Japan
| | - Jun Udagawa
- Department of Anatomy, Shiga University of Medical Science, Shiga 520-2192, Japan.
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8
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Tulenko FJ, Massey JL, Holmquist E, Kigundu G, Thomas S, Smith SME, Mazan S, Davis MC. Fin-fold development in paddlefish and catshark and implications for the evolution of the autopod. Proc Biol Sci 2018; 284:rspb.2016.2780. [PMID: 28539509 DOI: 10.1098/rspb.2016.2780] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/24/2017] [Indexed: 01/04/2023] Open
Abstract
The evolutionary origin of the autopod involved a loss of the fin-fold and associated dermal skeleton with a concomitant elaboration of the distal endoskeleton to form a wrist and digits. Developmental studies, primarily from teleosts and amniotes, suggest a model for appendage evolution in which a delay in the AER-to-fin-fold conversion fuelled endoskeletal expansion by prolonging the function of AER-mediated regulatory networks. Here, we characterize aspects of paired fin development in the paddlefish Polyodon spathula (a non-teleost actinopterygian) and catshark Scyliorhinus canicula (chondrichthyan) to explore aspects of this model in a broader phylogenetic context. Our data demonstrate that in basal gnathostomes, the autopod marker HoxA13 co-localizes with the dermoskeleton component And1 to mark the position of the fin-fold, supporting recent work demonstrating a role for HoxA13 in zebrafish fin ray development. Additionally, we show that in paddlefish, the proximal fin and fin-fold mesenchyme share a common mesodermal origin, and that components of the Shh/LIM/Gremlin/Fgf transcriptional network critical to limb bud outgrowth and patterning are expressed in the fin-fold with a profile similar to that of tetrapods. Together these data draw contrast with hypotheses of AER heterochrony and suggest that limb-specific morphologies arose through evolutionary changes in the differentiation outcome of conserved early distal patterning compartments.
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Affiliation(s)
- Frank J Tulenko
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA.,Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - James L Massey
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309, USA
| | - Elishka Holmquist
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Gabriel Kigundu
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sarah Thomas
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sylvie Mazan
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, UMR7232, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marcus C Davis
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
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9
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Raines AM, Magella B, Adam M, Potter SS. Key pathways regulated by HoxA9,10,11/HoxD9,10,11 during limb development. BMC DEVELOPMENTAL BIOLOGY 2015; 15:28. [PMID: 26186931 PMCID: PMC4506574 DOI: 10.1186/s12861-015-0078-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/07/2015] [Indexed: 11/17/2022]
Abstract
Background The 39 mammalian Hox genes show problematic patterns of functional overlap. In order to more fully define the developmental roles of Hox genes it is necessary to remove multiple combinations of paralogous and flanking genes. In addition, the downstream molecular pathways regulated by Hox genes during limb development remain incompletely delineated. Results In this report we examine limb development in mice with frameshift mutations in six Hox genes, Hoxa9,10,11 and Hoxd9,10,11. The mice were made with a novel recombineering method that allows the simultaneous targeting of frameshift mutations into multiple flanking genes. The Hoxa9,10,11−/−/Hoxd9,10,11−/− mutant mice show a reduced ulna and radius that is more severe than seen in Hoxa11−/−/Hoxd11−/− mice, indicating a minor role for the flanking Hox9,10 genes in zeugopod development, as well as their primary function in stylopod development. The mutant mice also show severe reduction of Shh expression in the zone of polarizing activity, and decreased Fgf8 expression in the apical ectodermal ridge, thereby better defining the roles of these specific Hox genes in the regulation of critical signaling centers during limb development. Importantly, we also used laser capture microdissection coupled with RNA-Seq to characterize the gene expression programs in wild type and mutant limbs. Resting, proliferative and hypertrophic compartments of E15.5 forelimb zeugopods were examined. The results provide an RNA-Seq characterization of the progression of gene expression patterns during normal endochondral bone formation. In addition of the Hox mutants showed strongly altered expression of Pknox2, Zfp467, Gdf5, Bmpr1b, Dkk3, Igf1, Hand2, Shox2, Runx3, Bmp7 and Lef1, all of which have been previously shown to play important roles in bone formation. Conclusions The recombineering based frameshift mutation of the six flanking and paralogous Hoxa9,10,11 and Hoxd9,10,11 genes provides a resource for the analysis of their overlapping functions. Analysis of the Hoxa9,10,11−/−/Hoxd9,10,11−/− mutant limbs confirms and extends the results of previous studies using mice with Hox mutations in single paralogous groups or with entire Hox cluster deletions. The RNA-Seq analysis of specific compartments of the normal and mutant limbs defines the multiple key perturbed pathways downstream of these Hox genes. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0078-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna M Raines
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
| | - Bliss Magella
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
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10
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Anguria P, Kitinya J, Ntuli S, Carmichael T. The role of heredity in pterygium development. Int J Ophthalmol 2014; 7:563-73. [PMID: 24967209 DOI: 10.3980/j.issn.2222-3959.2014.03.31] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 03/01/2014] [Indexed: 11/02/2022] Open
Abstract
Several risk factors, which include heredity, ultra-violet (UV) light and chronic inflammation, contribute to pterygium development. However, there is no report integrating these factors in the pathogenesis of pterygium. The aim of this review is to describe the connection between heredity, UV, and inflammation in pterygium development. Existing reports indicate that sunlight exposure is the main factor in pterygium occurrence by inducing growth factor production or chronic inflammation or DNA damage. Heredity may be a factor. Our studies on factors in pterygium occurrence and recurrence identify that heredity is crucial for pterygium to develop, and that sunlight is only a trigger, and that chronic inflammation promotes pterygium enlargement. We propose that genetic factors may interfere with the control of fibrovascular proliferation while UV light or (sunlight) most likely only triggers pterygium development by inducing growth factors which promote vibrant fibrovascular proliferation in predisposed individuals. It also just triggers inflammation and collagenolysis, which may be promoters of the enlargement of the fibrovascular mass. Pterygium probably occurs in the presence of exuberant collagen production and profuse neovascularisation.
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Affiliation(s)
- Peter Anguria
- Department of Neurosciences, Division of Ophthalmology, University of the Witwatersrand Johannesburg, 7 York Road, Park Town 2193, South Africa
| | - James Kitinya
- Department of Anatomic Pathology, University of Limpopo Polokwane Campus, Private Bag X9316 Polokwane 0700, South Africa
| | - Sam Ntuli
- Department of Public Health Medicine, University of Limpopo Polokwane Campus, Private Bag X9316 Polokwane 0700, South Africa
| | - Trevor Carmichael
- Department of Neurosciences, Division of Ophthalmology, University of the Witwatersrand Johannesburg, 7 York Road, Park Town 2193, South Africa
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