1
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Ghermezian B, Namavari M, Abdi-Hachesoo B, Mohammadi A, Hayati M, Bootorabi Z, Khabazan Z, Dabiri F, Rajablou H. Growth and replication of infectious bursal disease virus in the fish cell line as an experimental vaccine. Res Vet Sci 2024; 174:105293. [PMID: 38754221 DOI: 10.1016/j.rvsc.2024.105293] [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: 03/05/2024] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Recently, several attempts have been made to replace egg-based with cell-based vaccines to prevent and control Infectious Bursal Disease Virus (IBDV). This study aimed to evaluate a new fish cell line (M99) for culturing and replicating IBDV. After observing complete cytopathic effects (CPE) on the M99 cell line, virus titers were determined using the TCID50 test, and the presence of the virus was confirmed using an RT-PCR test. Subsequently, 135 broiler chickens (14 days old) were randomly divided into three equal groups for immune response measurements: G1: immunized with a commercial vaccine, G2: immunized with an experimental vaccine, and G3: control. Antibody responses, bursal index, and histopathological evaluations were examined on different days after immunization. Based on the results, CPE of the virus was noticeable from the first passage, becoming complete by the third passage. The infectious titer of the virus was log106.9. Antibody titer measured 21 days after immunization in both vaccinated groups were significantly differed from the control group (p < 0.05). The results obtained from examining the bursal index and histopathological evaluations showed no significant difference between the studied groups at different times. Overall, this research is the first report on the successful cultivation of infectious bursal virus on a permanent cell line of fish origin, with the advantages of tolerance to a wide temperature range (26-40 degrees Celsius). Therefore, this cell line has potential for use to attenuate, cultivate, and adapt other pathogens to cold temperatures in future studies.
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Affiliation(s)
- Babak Ghermezian
- Avian Diseases Research Center, Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Mehdi Namavari
- Razi Serum and Vaccine Research Institute, Agricultural Research, Education and Extension Organization, Shiraz, Iran.
| | - Bahman Abdi-Hachesoo
- Avian Diseases Research Center, Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Ali Mohammadi
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Masoumeh Hayati
- Razi Serum and Vaccine Research Institute, Agricultural Research, Education and Extension Organization, Shiraz, Iran
| | - Zahra Bootorabi
- Razi Serum and Vaccine Research Institute, Agricultural Research, Education and Extension Organization, Shiraz, Iran
| | - Zahra Khabazan
- Razi Serum and Vaccine Research Institute, Agricultural Research, Education and Extension Organization, Shiraz, Iran
| | - Fatemeh Dabiri
- Razi Serum and Vaccine Research Institute, Agricultural Research, Education and Extension Organization, Shiraz, Iran
| | - Hadi Rajablou
- Avian Diseases Research Center, Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
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2
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Cooper F, Souilhol C, Haston S, Gray S, Boswell K, Gogolou A, Frith TJR, Stavish D, James BM, Bose D, Kim Dale J, Tsakiridis A. Notch signalling influences cell fate decisions and HOX gene induction in axial progenitors. Development 2024; 151:dev202098. [PMID: 38223992 PMCID: PMC10911136 DOI: 10.1242/dev.202098] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
The generation of the post-cranial embryonic body relies on the coordinated production of spinal cord neurectoderm and presomitic mesoderm cells from neuromesodermal progenitors (NMPs). This process is orchestrated by pro-neural and pro-mesodermal transcription factors that are co-expressed in NMPs together with Hox genes, which are essential for axial allocation of NMP derivatives. NMPs reside in a posterior growth region, which is marked by the expression of Wnt, FGF and Notch signalling components. Although the importance of Wnt and FGF in influencing the induction and differentiation of NMPs is well established, the precise role of Notch remains unclear. Here, we show that the Wnt/FGF-driven induction of NMPs from human embryonic stem cells (hESCs) relies on Notch signalling. Using hESC-derived NMPs and chick embryo grafting, we demonstrate that Notch directs a pro-mesodermal character at the expense of neural fate. We show that Notch also contributes to activation of HOX gene expression in human NMPs, partly in a non-cell-autonomous manner. Finally, we provide evidence that Notch exerts its effects via the establishment of a negative-feedback loop with FGF signalling.
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Affiliation(s)
- Fay Cooper
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Celine Souilhol
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield S1 1WB, UK
| | - Scott Haston
- Developmental Biology and Cancer, Birth Defects Research Centre, UCL GOS Institute of Child Health, London WC1N 1EH, UK
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
| | - Shona Gray
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
| | - Katy Boswell
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Antigoni Gogolou
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Thomas J. R. Frith
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Dylan Stavish
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Bethany M. James
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Daniel Bose
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Jacqueline Kim Dale
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
| | - Anestis Tsakiridis
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
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3
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Filippopoulou K, Konstantinides N. Evolution of patterning. FEBS J 2024; 291:663-671. [PMID: 37943156 DOI: 10.1111/febs.16995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/28/2023] [Accepted: 11/07/2023] [Indexed: 11/10/2023]
Abstract
Developing tissues are patterned in space and time; this enables them to differentiate their cell types and form complex structures to support different body plans. Although space and time are two independent entities, there are many examples of spatial patterns that originate from temporal ones. The most prominent example is the expression of the genes hunchback, Krüppel, pdm, and castor, which are expressed temporally in the neural stem cells of the Drosophila ventral nerve cord and spatially along the anteroposterior axis of the blastoderm stage embryo. In this Viewpoint, we investigate the relationship between space and time in specific examples of spatial and temporal patterns with the aim of gaining insight into the evolutionary history of patterning.
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4
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Abstract
Hox genes encode evolutionarily conserved transcription factors that are essential for the proper development of bilaterian organisms. Hox genes are unique because they are spatially and temporally regulated during development in a manner that is dictated by their tightly linked genomic organization. Although their genetic function during embryonic development has been interrogated, less is known about how these transcription factors regulate downstream genes to direct morphogenetic events. Moreover, the continued expression and function of Hox genes at postnatal and adult stages highlights crucial roles for these genes throughout the life of an organism. Here, we provide an overview of Hox genes, highlighting their evolutionary history, their unique genomic organization and how this impacts the regulation of their expression, what is known about their protein structure, and their deployment in development and beyond.
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Affiliation(s)
- Katharine A. Hubert
- Program in Genetics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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5
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Chang YC, Manent J, Schroeder J, Wong SFL, Hauswirth GM, Shylo NA, Moore EL, Achilleos A, Garside V, Polo JM, Trainor P, McGlinn E. Nr6a1 controls Hox expression dynamics and is a master regulator of vertebrate trunk development. Nat Commun 2022; 13:7766. [PMID: 36522318 PMCID: PMC9755267 DOI: 10.1038/s41467-022-35303-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
The vertebrate main-body axis is laid down during embryonic stages in an anterior-to-posterior (head-to-tail) direction, driven and supplied by posteriorly located progenitors. Whilst posterior expansion and segmentation appears broadly uniform along the axis, there is developmental and evolutionary support for at least two discrete modules controlling processes within different axial regions: a trunk and a tail module. Here, we identify Nuclear receptor subfamily 6 group A member 1 (Nr6a1) as a master regulator of trunk development in the mouse. Specifically, Nr6a1 was found to control vertebral number and segmentation of the trunk region, autonomously from other axial regions. Moreover, Nr6a1 was essential for the timely progression of Hox signatures, and neural versus mesodermal cell fate choice, within axial progenitors. Collectively, Nr6a1 has an axially-restricted role in all major cellular and tissue-level events required for vertebral column formation, supporting the view that changes in Nr6a1 levels may underlie evolutionary changes in axial formulae.
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Affiliation(s)
- Yi-Cheng Chang
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Jan Manent
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Jan Schroeder
- grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC Australia
| | - Siew Fen Lisa Wong
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Gabriel M. Hauswirth
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Natalia A. Shylo
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, Missouri USA
| | - Emma L. Moore
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, Missouri USA
| | - Annita Achilleos
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, Missouri USA ,grid.413056.50000 0004 0383 4764University of Nicosia, Nicosia, Cyprus
| | - Victoria Garside
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Jose M. Polo
- grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC Australia
| | - Paul Trainor
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, Missouri USA ,grid.412016.00000 0001 2177 6375Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas USA
| | - Edwina McGlinn
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
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6
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Hintermann A, Guerreiro I, Lopez-Delisle L, Bolt CC, Gitto S, Duboule D, Beccari L. Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken. Development 2022; 149:275867. [PMID: 35770682 PMCID: PMC9307994 DOI: 10.1242/dev.200594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022]
Abstract
Modifications in gene regulation are driving forces in the evolution of organisms. Part of these changes involve cis-regulatory elements (CREs), which contact their target genes through higher-order chromatin structures. However, how such architectures and variations in CREs contribute to transcriptional evolvability remains elusive. We use Hoxd genes as a paradigm for the emergence of regulatory innovations, as many relevant enhancers are located in a regulatory landscape highly conserved in amniotes. Here, we analysed their regulation in murine vibrissae and chicken feather primordia, two skin appendages expressing different Hoxd gene subsets, and compared the regulation of these genes in these appendages with that in the elongation of the posterior trunk. In the two former structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, probably as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the gene regulation that occurs in the mouse and chicken embryonic trunk partially relies on conserved CREs. A high proportion of these non-coding sequences active in the trunk have functionally diverged between species, suggesting that transcriptional robustness is maintained, despite considerable divergence in enhancer sequences. Summary: Analyses of the relationships between chromatin architecture and regulatory activities at the HoxD locus show that ancestral transcription patterns can be maintained while new regulations evolve.
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Affiliation(s)
- Aurélie Hintermann
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Isabel Guerreiro
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Lucille Lopez-Delisle
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Christopher Chase Bolt
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
| | - Sandra Gitto
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
| | - Denis Duboule
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
- Swiss Institute for Experimental Cancer Research (EPFL ISREC), School of Life Sciences, Federal School of Technology (EPFL) 2 , 1015 Lausanne , Switzerland
- Collège de France 3 , 11 Place Marcelin Berthelot, 75005 Paris , France
| | - Leonardo Beccari
- University of Geneva 1 Department of Genetics and Evolution , , 30 quai Ernest-Ansermet, 1211 Geneva , Switzerland
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7
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Essay the (unusual) heuristic value of Hox gene clusters; a matter of time? Dev Biol 2022; 484:75-87. [PMID: 35182536 DOI: 10.1016/j.ydbio.2022.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/22/2022]
Abstract
Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.
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8
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Pourquié O. A brief history of the segmentation clock. Dev Biol 2022; 485:24-36. [DOI: 10.1016/j.ydbio.2022.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022]
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9
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Diaz-Cuadros M, Pourquié O, El-Sherif E. Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans. PLoS Genet 2021; 17:e1009812. [PMID: 34648490 PMCID: PMC8516289 DOI: 10.1371/journal.pgen.1009812] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Oscillatory and sequential processes have been implicated in the spatial patterning of many embryonic tissues. For example, molecular clocks delimit segmental boundaries in vertebrates and insects and mediate lateral root formation in plants, whereas sequential gene activities are involved in the specification of regional identities of insect neuroblasts, vertebrate neural tube, vertebrate limb, and insect and vertebrate body axes. These processes take place in various tissues and organisms, and, hence, raise the question of what common themes and strategies they share. In this article, we review 2 processes that rely on the spatial regulation of periodic and sequential gene activities: segmentation and regionalization of the anterior-posterior (AP) axis of animal body plans. We study these processes in species that belong to 2 different phyla: vertebrates and insects. By contrasting 2 different processes (segmentation and regionalization) in species that belong to 2 distantly related phyla (arthropods and vertebrates), we elucidate the deep logic of patterning by oscillatory and sequential gene activities. Furthermore, in some of these organisms (e.g., the fruit fly Drosophila), a mode of AP patterning has evolved that seems not to overtly rely on oscillations or sequential gene activities, providing an opportunity to study the evolution of pattern formation mechanisms.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ezzat El-Sherif
- Division of Developmental Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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10
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Allais-Bonnet A, Hintermann A, Deloche MC, Cornette R, Bardou P, Naval-Sanchez M, Pinton A, Haruda A, Grohs C, Zakany J, Bigi D, Medugorac I, Putelat O, Greyvenstein O, Hadfield T, Jemaa SB, Bunevski G, Menzi F, Hirter N, Paris JM, Hedges J, Palhiere I, Rupp R, Lenstra JA, Gidney L, Lesur J, Schafberg R, Stache M, Wandhammer MD, Arbogast RM, Guintard C, Blin A, Boukadiri A, Rivière J, Esquerré D, Donnadieu C, Danchin-Burge C, Reich CM, Riley DG, Marle-Koster EV, Cockett N, Hayes BJ, Drögemüller C, Kijas J, Pailhoux E, Tosser-Klopp G, Duboule D, Capitan A. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae. Mol Biol Evol 2021; 38:2260-2272. [PMID: 33528505 PMCID: PMC8136503 DOI: 10.1093/molbev/msab021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In the course of evolution, pecorans (i.e., higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as “headgear,” which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.
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Affiliation(s)
- Aurélie Allais-Bonnet
- ALLICE, Paris, France.,Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Aurélie Hintermann
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Marie-Christine Deloche
- ALLICE, Paris, France.,Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Raphaël Cornette
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France.,INRAE, Sigenae, Castanet-Tolosan, France
| | | | - Alain Pinton
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Ashleigh Haruda
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Cécile Grohs
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Jozsef Zakany
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Daniele Bigi
- Dipartimento di Scienza e Tecnologie Agro-Alimentari, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Olivier Putelat
- Archéologie Alsace, Sélestat, France.,UMR 7044, ARCHIMEDE, MISHA, Strasbourg, France
| | - Ockert Greyvenstein
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Tracy Hadfield
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Slim Ben Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, Ariana, Tunisia
| | - Gjoko Bunevski
- Livestock Department, Faculty of Agricultural Sciences and Food Institute of Animal Biotechnology, University Ss. Cyril and Methodius, Skopje, North Macedonia
| | - Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nathalie Hirter
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Julia M Paris
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - John Hedges
- Manx Loaghtan Sheep Breeders' Group, Bassingbourn, Cambridgeshire, United Kingdom
| | - Isabelle Palhiere
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Louisa Gidney
- Rent a Peasant, Tow Law, Bishop Auckland, Durham County, United Kingdom
| | - Joséphine Lesur
- Unité Archéozoologie, Archéobotanique, Sociétés Pratiques et Environnements (AASPE), CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Renate Schafberg
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Stache
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | | | - Claude Guintard
- Unité d'Anatomie Comparée, Ecole Nationale Vétérinaire de l'Agroalimentaire et de l'Alimentation, Nantes Atlantique-ONIRIS, Nantes, France.,Groupe d'Études Remodelage Osseux et bioMatériaux (GEROM), Université d'Angers, Unité INSERM 922, LHEA/IRIS-IBS, CHU d'Angers, Angers, France
| | - Amandine Blin
- Muséum National d'Histoire Naturelle, CNRS, UMS 2700 2AD, Paris, France
| | - Abdelhak Boukadiri
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Julie Rivière
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,INRAE, Micalis Institute, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Diane Esquerré
- INRAE, US, 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | | | | | - Coralie M Reich
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - David G Riley
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | | | - Noelle Cockett
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Benjamin J Hayes
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Animal Science, University of Queensland, St. Lucia, QLD, Australia
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - James Kijas
- CSIRO Agriculture & Food, St. Lucia, QLD, Australia
| | - Eric Pailhoux
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France.,Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | | | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Swiss Cancer Research Institute, EPFL, Lausanne, Switzerland.,Collège de France, Paris, France
| | - Aurélien Capitan
- ALLICE, Paris, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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11
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Yamada K, Maeno A, Araki S, Kikuchi M, Suzuki M, Ishizaka M, Satoh K, Akama K, Kawabe Y, Suzuki K, Kobayashi D, Hamano N, Kawamura A. An atlas of seven zebrafish hox cluster mutants provides insights into sub/neofunctionalization of vertebrate Hox clusters. Development 2021; 148:269044. [PMID: 34096572 DOI: 10.1242/dev.198325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Vertebrate Hox clusters are comprised of multiple Hox genes that control morphology and developmental timing along multiple body axes. Although results of genetic analyses using Hox-knockout mice have been accumulating, genetic studies in other vertebrates have not been sufficient for functional comparisons of vertebrate Hox genes. In this study, we isolated all of the seven hox cluster loss-of-function alleles in zebrafish using the CRISPR-Cas9 system. Comprehensive analysis of the embryonic phenotype and X-ray micro-computed tomography scan analysis of adult fish revealed several species-specific functional contributions of homologous Hox clusters along the appendicular axis, whereas important shared general principles were also confirmed, as exemplified by serial anterior vertebral transformations along the main body axis, observed in fish for the first time. Our results provide insights into discrete sub/neofunctionalization of vertebrate Hox clusters after quadruplication of the ancient Hox cluster. This set of seven complete hox cluster loss-of-function alleles provide a formidable resource for future developmental genetic analysis of the Hox patterning system in zebrafish.
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Affiliation(s)
- Kazuya Yamada
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Akiteru Maeno
- Plant Resource Development, Division of Genetic Resource Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Soh Araki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Morimichi Kikuchi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Masato Suzuki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Mizuki Ishizaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Koumi Satoh
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kagari Akama
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Yuki Kawabe
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Kenya Suzuki
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Daiki Kobayashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Nanami Hamano
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
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12
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Abstract
In this review, we consider transformations of axial symmetry in metazoan evolution and development, the genetic basis, and phenotypic expressions of different axial body plans. In addition to the main symmetry types in metazoan body plans, such as rotation (radial symmetry), reflection (mirror and glide reflection symmetry), and translation (metamerism), many biological objects show scale (fractal) symmetry as well as some symmetry-type combinations. Some genetic mechanisms of axial pattern establishment, creating a coordinate system of a metazoan body plan, bilaterian segmentation, and left–right symmetry/asymmetry, are analysed. Data on the crucial contribution of coupled functions of the Wnt, BMP, Notch, and Hedgehog signaling pathways (all pathways are designated according to the abbreviated or full names of genes or their protein products; for details, see below) and the axial Hox-code in the formation and maintenance of metazoan body plans are necessary for an understanding of the evolutionary diversification and phenotypic expression of various types of axial symmetry. The lost body plans of some extinct Ediacaran and early Cambrian metazoans are also considered in comparison with axial body plans and posterior growth in living animals.
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13
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Durston AJ. Some Questions and Answers About the Role of Hox Temporal Collinearity in Vertebrate Axial Patterning. Front Cell Dev Biol 2019; 7:257. [PMID: 31850338 PMCID: PMC6895010 DOI: 10.3389/fcell.2019.00257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/16/2019] [Indexed: 01/02/2023] Open
Abstract
The vertebrate anterior-posterior (A-P = craniocaudal) axis is evidently made by a timing mechanism. Evidence has accumulated that tentatively identifies the A-P timer as being or involving Hox temporal collinearity (TC). Here, I focus on the two current competing models based on this premise. Common features and points of dissent are examined and a common model is distilled from what remains. This is an attempt to make sense of the literature.
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14
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Billing AM, Dib SS, Bhagwat AM, da Silva IT, Drummond RD, Hayat S, Al-Mismar R, Ben-Hamidane H, Goswami N, Engholm-Keller K, Larsen MR, Suhre K, Rafii A, Graumann J. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells. Mol Cell Proteomics 2019; 18:1950-1966. [PMID: 31332097 PMCID: PMC6773553 DOI: 10.1074/mcp.ra119.001356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) are self-renewing multipotent cells with regenerative, secretory and immunomodulatory capabilities that are beneficial for the treatment of various diseases. To avoid the issues that come with using tissue-derived MSCs in therapy, MSCs may be generated by the differentiation of human embryonic stems cells (hESCs) in culture. However, the changes that occur during the differentiation process have not been comprehensively characterized. Here, we combined transcriptome, proteome and phosphoproteome profiling to perform an in-depth, multi-omics study of the hESCs-to-MSCs differentiation process. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation. Among the earliest and strongest induced proteins with extensive differential phosphorylation was AHNAK, which we hypothesized to be a defining factor in MSC biology. We observed two distinct expression waves of developmental HOX genes and an AGO2-to-AGO3 switch in gene silencing. Exploring the kinetic of noncoding ORFs during differentiation, we mapped new functions to well annotated long noncoding RNAs (CARMN, MALAT, NEAT1, LINC00152) as well as new candidates which we identified to be important to the differentiation process. Phosphoproteome analysis revealed ESC and MSC-specific phosphorylation motifs with PAK2 and RAF1 as top predicted upstream kinases in MSCs. Our data represent a rich systems-level resource on ESC-to-MSC differentiation that will be useful for the study of stem cell biology.
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Affiliation(s)
- Anja M Billing
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar.
| | - Shaima S Dib
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Aditya M Bhagwat
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Israel T da Silva
- Laboratory of Bioinformatics and Computational Biology, A. C., Camargo Cancer Center, São Paulo 01508-010, Brazil; Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065
| | - Rodrigo D Drummond
- Laboratory of Bioinformatics and Computational Biology, A. C., Camargo Cancer Center, São Paulo 01508-010, Brazil
| | - Shahina Hayat
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Rasha Al-Mismar
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Hisham Ben-Hamidane
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Neha Goswami
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Kasper Engholm-Keller
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark; Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Karsten Suhre
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Arash Rafii
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar; Department of Gynecology and Obstetrics, Hôpital Foch, 92100 Suresnes, France
| | - Johannes Graumann
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar.
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15
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Durston AJ. What are the roles of retinoids, other morphogens, and Hox genes in setting up the vertebrate body axis? Genesis 2019; 57:e23296. [PMID: 31021058 PMCID: PMC6767176 DOI: 10.1002/dvg.23296] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/24/2019] [Accepted: 03/29/2019] [Indexed: 01/09/2023]
Abstract
This article is concerned with the roles of retinoids and other known anterior-posterior morphogens in setting up the embryonic vertebrate anterior-posterior axis. The discussion is restricted to the very earliest events in setting up the anterior-posterior axis (from blastula to tailbud stages in Xenopus embryos). In these earliest developmental stages, morphogen concentration gradients are not relevant for setting up this axis. It emerges that at these stages, the core patterning mechanism is timing: BMP-anti BMP mediated time space translation that regulates Hox temporal and spatial collinearities and Hox-Hox auto- and cross- regulation. The known anterior-posterior morphogens and signaling pathways--retinoids, FGF's, Cdx, Wnts, Gdf11 and others--interact with this core mechanism at and after space-time defined "decision points," leading to the separation of distinct axial domains. There are also other roles for signaling pathways. Besides the Hox regulated hindbrain/trunk part of the axis, there is a rostral part (including the anterior part of the head and the extreme anterior domain [EAD]) that appears to be regulated by additional mechanisms. Key aspects of anterior-posterior axial patterning, including: the nature of different phases in early patterning and in the whole process; the specificities of Hox action and of intercellular signaling; and the mechanisms of Hox temporal and spatial collinearities, are discussed in relation to the facts and hypotheses proposed above.
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16
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Galis F, Metz JA, van Alphen JJ. Development and Evolutionary Constraints in Animals. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062339] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We review the evolutionary importance of developmental mechanisms in constraining evolutionary changes in animals—in other words, developmental constraints. We focus on hard constraints that can act on macroevolutionary timescales. In particular, we discuss the causes and evolutionary consequences of the ancient metazoan constraint that differentiated cells cannot divide and constraints against changes of phylotypic stages in vertebrates and other higher taxa. We conclude that in all cases these constraints are caused by complex and highly controlled global interactivity of development, the disturbance of which has grave consequences. Mutations that affect such global interactivity almost unavoidably have many deleterious pleiotropic effects, which will be strongly selected against and will lead to long-term evolutionary stasis. The discussed developmental constraints have pervasive consequences for evolution and critically restrict regeneration capacity and body plan evolution.
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Affiliation(s)
- Frietson Galis
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Johan A.J. Metz
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
- International Institute for Applied Systems Analysis, A-2361 Laxenburg, Austria
- Mathematical Institute, University of Leiden; 2333 CA Leiden, The Netherlands
| | - Jacques J.M. van Alphen
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
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17
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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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18
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Abstract
During embryonic development, Hox genes participate in the building of a functional digestive system in metazoans, and genetic conditions involving these genes lead to important, sometimes lethal, growth retardation. Recently, this phenotype was obtained after deletion of Haglr, the Hoxd antisense growth-associated long noncoding RNA (lncRNA) located between Hoxd1 and Hoxd3 In this study, we have analyzed the function of Hoxd genes in delayed growth trajectories by looking at several nested targeted deficiencies of the mouse HoxD cluster. Mutant pups were severely stunted during the suckling period, but many recovered after weaning. After comparing seven distinct HoxD alleles, including CRISPR/Cas9 deletions involving Haglr, we identified Hoxd3 as the critical component for the gut to maintain milk-digestive competence. This essential function could be abrogated by the dominant-negative effect of HOXD10 as shown by a genetic rescue approach, thus further illustrating the importance of posterior prevalence in Hox gene function. A role for the lncRNA Haglr in the control of postnatal growth could not be corroborated.
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19
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Soul LC, Benson RBJ. Developmental mechanisms of macroevolutionary change in the tetrapod axis: A case study of Sauropterygia. Evolution 2017; 71:1164-1177. [PMID: 28240769 PMCID: PMC5485078 DOI: 10.1111/evo.13217] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 02/05/2017] [Accepted: 02/19/2017] [Indexed: 01/29/2023]
Abstract
Understanding how developmental processes change on macroevolutionary timescales to generate body plan disparity is fundamental to the study of vertebrate evolution. Adult morphology of the vertebral column directly reflects the mechanisms that generate vertebral counts (somitogenesis) and their regionalisation (homeotic effects) during embryonic development. Sauropterygians were a group of Mesozoic marine reptiles that exhibited an extremely high disparity of presacral vertebral/somite counts. Using phylogenetic comparative methods, we demonstrate that somitogenesis and homeotic effects evolved in a co-ordinated way among sauropterygians, contrasting with the wider pattern in tetrapods, in which somitogenetic and homeotic shifts are uncorrelated. Changes in sauropterygian body proportions were primarily enabled by homeotic shifts, with a lesser, but important, contribution from differences in postpatterning growth among somites. High body plan plasticity was present in Triassic sauropterygians and was maintained among their Jurassic and Cretaceous descendants. The extreme disparity in the body plan of plesiosaurian sauropterygians did not result from accelerated rates of evolutionary change in neck length, but instead reflect this ancestral versatility of sauropterygian axial development. Our results highlight variation in modes of axial development among tetrapods, and show that heterogeneous statistical models can uncover novel macroevolutionary patterns for animal body plans and the developmental mechanisms that control them.
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Affiliation(s)
- Laura C. Soul
- Department of Paleobiology, National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia20013
- Department of Earth SciencesUniversity of Oxford,OX1 3ANUnited Kingdom
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20
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Warrier S, Nuwayhid S, Sabatino JA, Sugrue KF, Zohn IE. Supt20 is required for development of the axial skeleton. Dev Biol 2016; 421:245-257. [PMID: 27894818 DOI: 10.1016/j.ydbio.2016.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 09/08/2016] [Accepted: 11/11/2016] [Indexed: 10/20/2022]
Abstract
Somitogenesis and subsequent axial skeletal development is regulated by the interaction of pathways that determine the periodicity of somite formation, rostrocaudal somite polarity and segment identity. Here we use a hypomorphic mutant mouse line to demonstrate that Supt20 (Suppressor of Ty20) is required for development of the axial skeleton. Supt20 hypomorphs display fusions of the ribs and vertebrae at lower thoracic levels along with anterior homeotic transformation of L1 to T14. These defects are preceded by reduction of the rostral somite and posterior shifts in Hox gene expression. While cycling of Notch target genes in the posterior presomitic mesoderm (PSM) appeared normal, expression of Lfng was reduced. In the anterior PSM, Mesp2 expression levels and cycling were unaffected; yet, expression of downstream targets such as Lfng, Ripply2, Mesp1 and Dll3 in the prospective rostral somite was reduced accompanied by expansion of caudal somite markers such as EphrinB2 and Hes7. Supt20 interacts with the Gcn5-containing SAGA histone acetylation complex. Gcn5 hypomorphic mutant embryos show similar defects in axial skeletal development preceded by posterior shift of Hoxc8 and Hoxc9 gene expression. We demonstrate that Gcn5 and Supt20 hypomorphs show similar defects in rostral-caudal somite patterning potentially suggesting shared mechanisms.
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Affiliation(s)
- Sunita Warrier
- Center for Neuroscience Research, Children's Research Institute, Children's National Medical Center, Washington, DC 20010, USA
| | - Samer Nuwayhid
- Center for Neuroscience Research, Children's Research Institute, Children's National Medical Center, Washington, DC 20010, USA
| | - Julia A Sabatino
- Center for Neuroscience Research, Children's Research Institute, Children's National Medical Center, Washington, DC 20010, USA
| | - Kelsey F Sugrue
- Center for Neuroscience Research, Children's Research Institute, Children's National Medical Center, Washington, DC 20010, USA; Institute for Biomedical Sciences, The George Washington University, Washington, DC 20052, USA
| | - Irene E Zohn
- Center for Neuroscience Research, Children's Research Institute, Children's National Medical Center, Washington, DC 20010, USA.
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21
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Guerreiro I, Gitto S, Novoa A, Codourey J, Nguyen Huynh TH, Gonzalez F, Milinkovitch MC, Mallo M, Duboule D. Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan. eLife 2016; 5. [PMID: 27476854 PMCID: PMC4969037 DOI: 10.7554/elife.16087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/10/2016] [Indexed: 12/15/2022] Open
Abstract
Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated with changes in the function or regulation of Hox genes. Here, we use an interspecies comparative approach to investigate different regulatory aspects at the snake HoxD locus. We report that, unlike in other vertebrates, snake mesoderm-specific enhancers are mostly located within the HoxD cluster itself rather than outside. In addition, despite both the absence of limbs and an altered Hoxd gene regulation in external genitalia, the limb-associated bimodal HoxD chromatin structure is maintained at the snake locus. Finally, we show that snake and mouse orthologous enhancer sequences can display distinct expression specificities. These results show that vertebrate morphological evolution likely involved extensive reorganisation at Hox loci, yet within a generally conserved regulatory framework.
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Affiliation(s)
- Isabel Guerreiro
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Ana Novoa
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Julien Codourey
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Federico Gonzalez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Moises Mallo
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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22
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Kappen C. Developmental Patterning as a Quantitative Trait: Genetic Modulation of the Hoxb6 Mutant Skeletal Phenotype. PLoS One 2016; 11:e0146019. [PMID: 26800342 PMCID: PMC4723086 DOI: 10.1371/journal.pone.0146019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 12/12/2015] [Indexed: 11/24/2022] Open
Abstract
The process of patterning along the anterior-posterior axis in vertebrates is highly conserved. The function of Hox genes in the axis patterning process is particularly well documented for bone development in the vertebral column and the limbs. We here show that Hoxb6, in skeletal elements at the cervico-thoracic junction, controls multiple independent aspects of skeletal pattern, implicating discrete developmental pathways as substrates for this transcription factor. In addition, we demonstrate that Hoxb6 function is subject to modulation by genetic factors. These results establish Hox-controlled skeletal pattern as a quantitative trait modulated by gene-gene interactions, and provide evidence that distinct modifiers influence the function of conserved developmental genes in fundamental patterning processes.
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Affiliation(s)
- Claudia Kappen
- Department of Developmental Biology, Pennington Biomedical Research Center/Louisiana State University System, 6400 Perkins Road, Baton Rouge, Louisiana, 70808, United States of America
- * E-mail:
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23
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Visualizing the HoxD Gene Cluster at the Nanoscale Level. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:9-16. [PMID: 26767994 DOI: 10.1101/sqb.2015.80.027177] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Transcription of HoxD cluster genes in limbs is coordinated by two topologically associating domains (TADs), neighboring the cluster and containing various enhancers. Here, we use a combination of microscopy approaches and chromosome conformation capture to assess the structural changes occurring in this global architecture in various functional states. We observed that despite their spatial juxtaposition, the TADs are consistently kept as distinct three-dimensional units. Hox genes located at their boundary can show significant spatial segregation over long distances, suggesting that physical elongation of the HoxD cluster occurs. The use of superresolution imaging (STORM [stochastic optical reconstruction microscopy]) revealed that the gene cluster can be in an either compact or elongated shape. The latter configuration is observed in transcriptionally active tissue and in embryonic stem cells, consistent with chromosome conformation capture results. Such morphological changes at HoxD in developing digits seem to be associated with its position at the boundary between two TADs and support the idea that chromatin dynamics is important in the establishment of transcriptional activity.
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24
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Abstract
In development, cells organize into biological tissues through cell growth, migration, and differentiation. Globally, this process is dictated by a genetically encoded program in which secreted morphogens and cell-cell interactions prompt the adoption of unique cell fates. Yet, at its lowest level, development is achieved through the modification of cell-cell adhesion and actomyosin-based contractility, which set the level of tension within cells and dictate how they pack together into tissues. The regulation of tension within individual cells and across large groups of cells is a major driving force of tissue organization and the basis of all cell shape change and cell movement in development.
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Affiliation(s)
- Evan Heller
- Howard Hughes Medical Institute, Robin Neustein Chemers Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Neustein Chemers Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY 10065
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25
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Hayward AG, Joshi P, Skromne I. Spatiotemporal analysis of zebrafishhoxgene regulation by Cdx4. Dev Dyn 2015; 244:1564-73. [DOI: 10.1002/dvdy.24343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 08/07/2015] [Accepted: 08/24/2015] [Indexed: 12/16/2022] Open
Affiliation(s)
| | - Piyush Joshi
- Department of Biology; University of Miami; Coral Gables Florida
| | - Isaac Skromne
- Department of Biology; University of Miami; Coral Gables Florida
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26
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Gouveia A, Marcelino HM, Gonçalves L, Palmeirim I, Andrade RP. Patterning in time and space: HoxB cluster gene expression in the developing chick embryo. Cell Cycle 2015; 14:135-45. [PMID: 25602523 DOI: 10.4161/15384101.2014.972868] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The developing embryo is a paradigmatic model to study molecular mechanisms of time control in Biology. Hox genes are key players in the specification of tissue identity during embryo development and their expression is under strict temporal regulation. However, the molecular mechanisms underlying timely Hox activation in the early embryo remain unknown. This is hindered by the lack of a rigorous temporal framework of sequential Hox expression within a single cluster. Herein, a thorough characterization of HoxB cluster gene expression was performed over time and space in the early chick embryo. Clear temporal collinearity of HoxB cluster gene expression activation was observed. Spatial collinearity of HoxB expression was evidenced in different stages of development and in multiple tissues. Using embryo explant cultures we showed that HoxB2 is cyclically expressed in the rostral presomitic mesoderm with the same periodicity as somite formation, suggesting a link between timely tissue specification and somite formation. We foresee that the molecular framework herein provided will facilitate experimental approaches aimed at identifying the regulatory mechanisms underlying Hox expression in Time and Space.
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Affiliation(s)
- Analuce Gouveia
- a Life and Health Sciences Research Institute (ICVS); School of Health Sciences , University of Minho ; Braga , Portugal
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27
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Woltering JM, Duboule D. Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model. Mech Dev 2015; 138 Pt 2:64-72. [PMID: 26238020 PMCID: PMC4678112 DOI: 10.1016/j.mod.2015.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 02/05/2023]
Abstract
The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. A transgenic mouse line expressing fish Hox genes has anterior homeotic transformations. Fish Hox genes are capable of inducing tetrapod specific vertebral characters. A sacral Hox-code influences adult hindlimb position, yet not the position of limb budding.
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Affiliation(s)
- Joost M Woltering
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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Abstract
How vertebrates generate their anterior-posterior axis is a >90-year-old unsolved probem. This mechanism clearly works very differently in vertebrates than in Drosophila. Here, we present evidence from the Amphibian Xenopus that a time space translation mechanism underlies initial axial patterning in the trunk part of the axis. We show that a timer in the gastrula's non organiser mesoderm (NOM) undergoes sequential timed interactions with the Spemann organiser (SO) during gastrulation to generate the spatial axial pattern. Evidence is also presented that this mechanism works via Hox collinearity and that it requires Hox functionality. The NOM timer is putatively Hox temporal collinearity. This generates a spatially collinear axial Hox pattern in the emerging dorsal central nervous system and dorsal paraxial mesoderm. The interactions with the organiser are mediated by a BMP-anti BMP dependent mechanism. Hox functionality is implicated because knocking out the Hox1 paralogue group not only disrupts expression of Hox1 genes but also of the whole spatially collinear axial Hox sequence in the early embryo's A-P axis. This mechanism and its nature are discussed. The evidence supporting this hypothesis is presented and critically assessed. Strengths and weaknesses, questions, uncertainties and holes in the evidence are identified. Future directions are indicated.
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29
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Abstract
Anterior-posterior (A-P) patterning of the vertebrate main body axis regulated by timing. Anterior structures are specified early, posterior late. (1) Timing involves timed decision points as emphasised by the Wnt studies of Sokol and colleagues. It also involves complex timers, where large parts of the axis are patterned sequentially by a common upstream mechanism (articles by Durston et al., Mullins et al., Oates et al.,). (2) A gastrula BMP-anti BMP dependent time-space translation (TST) mechanism was demonstrated for the trunk section of the axis (Durston). (3) Thisses' studies emphasise the importance of BMP-anti BMP and the organiser inducing factor nodal for A-P patterning. (4) Meinhardt's interesting studies on the organiser and A-P patterning are reviewed in relation to TST. (5) Mullins' investigations show that anti-BMP dependent TST starts earlier (at the blastula stage) and extends further anteriorly (to the anterior head). Sive's studies imply it may extend further still to the "extreme anterior domain" (EAD). (6) The somitogenesis timer (clock) is presented. Stern's and Oates' findings are discussed. (7) Relations between somitogenesis and axial TST are discussed. (8) Relations of classical axial patterning pathways to TST decision points and somitogenesis are inventarised. In conclusion, all of these findings point to an integral BMP-anti BMP dependent A-P TST mechanism, running from cement gland in the EAD, Six3 and the anterior tip of the forebrain at blastula stages to Hox13 and the tip of the tail by the mid neurula stage. TST acts via sequential timed transitions between ventral (unstable, timed) and dorsal (stabilised) states. In the trunk-tail, the timer is thought to be Hox temporal collinearity and TST depends on Hox function. In the head, TST is under investigation. The somitogenesis clock is upstream of the TST timer, providing precision in the posterior part of the axis at least. Classical A-P signalling pathways: retinoids, FGFs and Wnts, change behaviour at functional decision points on the axis.
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Musumeci G, Castrogiovanni P, Coleman R, Szychlinska MA, Salvatorelli L, Parenti R, Magro G, Imbesi R. Somitogenesis: From somite to skeletal muscle. Acta Histochem 2015; 117:313-28. [PMID: 25850375 DOI: 10.1016/j.acthis.2015.02.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/31/2015] [Accepted: 02/08/2015] [Indexed: 12/21/2022]
Abstract
Myogenesis is controlled by an elaborate system of extrinsic and intrinsic regulatory mechanisms in all development stages. The aim of this review is to provide an overview of the different stages of myogenesis and muscle differentiation in mammals, starting from somitogenesis and analysis of the different portions that constitute the mature somite. Particular attention was paid to regulatory genes, in addition to mesodermal stem cells, which represent the earliest elements of myogenesis. Finally, the crucial role of growth factors, molecules of vital importance in contractile regulation, hormones and their function in skeletal muscle differentiation, growth and metabolism, and the role played by central nervous system, are discussed.
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Affiliation(s)
- Giuseppe Musumeci
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy.
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Raymond Coleman
- Department of Anatomy and Cell Biology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Marta Anna Szychlinska
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
| | - Lucia Salvatorelli
- Department of Anatomy and Cell Biology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Rosalba Parenti
- Department of Biomedical and Biotechnological Sciences, Section of Physiology, School of Medicine, University of Catania, Catania, Italy
| | - Gaetano Magro
- Department of Medical and Surgical Sciences and Advanced Technologies, G.F. Ingrassia, Azienda Ospedaliero-Universitaria "Policlinico-Vittorio Emanuele", Anatomic Pathology Section, University of Catania, Catania, Italy
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Human Anatomy and Histology Section, School of Medicine, University of Catania, Catania, Italy
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31
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Arya R, Sarkissian T, Tan Y, White K. Neural stem cell progeny regulate stem cell death in a Notch and Hox dependent manner. Cell Death Differ 2015; 22:1378-87. [PMID: 25633198 DOI: 10.1038/cdd.2014.235] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/02/2014] [Accepted: 12/12/2014] [Indexed: 01/05/2023] Open
Abstract
Cell death is a prevalent, well-controlled and fundamental aspect of development, particularly in the nervous system. In Drosophila, specific neural stem cells are eliminated by apoptosis during embryogenesis. In the absence of apoptosis, these stem cells continue to divide, resulting in a dramatically hyperplastic central nervous system and adult lethality. Although core cell death pathways have been well described, the spatial, temporal and cell identity cues that activate the cell death machinery in specific cells are largely unknown. We identified a cis-regulatory region that controls the transcription of the cell death activators reaper, grim and sickle exclusively in neural stem cells. Using a reporter generated from this regulatory region, we found that Notch activity is required for neural stem cell death. Notch regulates the expression of the abdominalA homeobox protein, which provides important spatial cues for death. Importantly, we show that pro-apoptotic Notch signaling is activated by the Delta ligand expressed on the neighboring progeny of the stem cell. Thus we identify a previously undescribed role for progeny in regulating the proper developmental death of their parental stem cells.
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Affiliation(s)
- R Arya
- CBRC, Massachusetts General Hospital/Harvard Medical School, Boston, MA 02129, USA
| | - T Sarkissian
- CBRC, Massachusetts General Hospital/Harvard Medical School, Boston, MA 02129, USA
| | - Y Tan
- CBRC, Massachusetts General Hospital/Harvard Medical School, Boston, MA 02129, USA
| | - K White
- CBRC, Massachusetts General Hospital/Harvard Medical School, Boston, MA 02129, USA
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32
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Casaca A, Nóvoa A, Mallo M. Hoxb6 can interfere with somitogenesis in the posterior embryo through a mechanism independent of its rib-promoting activity. Development 2015; 143:437-48. [DOI: 10.1242/dev.133074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 12/18/2015] [Indexed: 01/19/2023]
Abstract
Formation of the vertebrate axial skeleton requires coordinated Hox gene activity. Hox group 6 genes are involved in the formation of the thoracic area due to their unique rib-promoting properties. We show here that the linker region (LR) connecting the homeodomain and the hexapeptide is essential for Hoxb6 rib-promoting activity. The LR-defective Hoxb6 protein was still able to bind a target enhancer together with Pax3 producing a dominant negative effect, indicating that the LR brings additional regulatory factors to target DNA elements. We also found an unexpected association between Hoxb6 and segmentation in the paraxial mesoderm. In particular, Hoxb6 can disturb somitogenesis and anterior-posterior somite patterning by deregulating Lfng expression. Interestingly, this interaction occurred differently in thoracic and more caudal embryonic areas, indicating functional differences in somitogenesis before and after the trunk to tail transition. Our results suggest the requirement of precisely regulated Hoxb6 expression for proper segmentation at tailbud stages.
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Affiliation(s)
- Ana Casaca
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Ana Nóvoa
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Moisés Mallo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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33
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Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA, Ponting CP. Considerations when investigating lncRNA function in vivo. eLife 2014; 3:e03058. [PMID: 25124674 PMCID: PMC4132285 DOI: 10.7554/elife.03058] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although a small number of the vast array of animal long non-coding RNAs (lncRNAs) have known effects on cellular processes examined in vitro, the extent of their contributions to normal cell processes throughout development, differentiation and disease for the most part remains less clear. Phenotypes arising from deletion of an entire genomic locus cannot be unequivocally attributed either to the loss of the lncRNA per se or to the associated loss of other overlapping DNA regulatory elements. The distinction between cis- or trans-effects is also often problematic. We discuss the advantages and challenges associated with the current techniques for studying the in vivo function of lncRNAs in the light of different models of lncRNA molecular mechanism, and reflect on the design of experiments to mutate lncRNA loci. These considerations should assist in the further investigation of these transcriptional products of the genome. DOI:http://dx.doi.org/10.7554/eLife.03058.001
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Affiliation(s)
- Andrew R Bassett
- Andrew R Bassett is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
| | - Asifa Akhtar
- Asifa Akhtar is in the Department of Chromatin Regulation, Max-Planck-Institut für Immunbiologie und Epigenetik, Freiburg im Breisgau, Germany
| | - Denise P Barlow
- Denise P Barlow is in the CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Adrian P Bird
- Adrian P Bird is in the Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil Brockdorff
- Neil Brockdorff is in the Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Denis Duboule
- Denis Duboule is in the School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland; Department of Genetics and Evolution, Université de Genève, Geneva, Switzerland
| | - Anne Ephrussi
- Anne Ephrussi is in the Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anne C Ferguson-Smith
- Anne C Ferguson-Smith is in the Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Thomas R Gingeras
- Thomas R Gingeras is in the Functional Genomics Group, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Wilfried Haerty
- Wilfried Haerty is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Douglas R Higgs
- Douglas R Higgs is in the MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom
| | - Eric A Miska
- Eric A Miska is in the Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chris P Ponting
- Chris P Ponting is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom; Wellcome Trust Sanger Institute, Cambridge, United Kingdom
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34
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Abstract
eLife has introduced a new type of article-the Research Advance-that allows the authors of an eLife paper to publish results that build on their original research paper.
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35
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Hox gene regulation and timing in embryogenesis. Semin Cell Dev Biol 2014; 34:76-84. [PMID: 24930771 DOI: 10.1016/j.semcdb.2014.06.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/15/2014] [Accepted: 06/05/2014] [Indexed: 11/22/2022]
Abstract
Hox genes are critical regulators of embryonic development in bilaterian animals. They exhibit a unique mode of transcriptional regulation where the position of the genes along the chromosome corresponds to the time and place of their expression during development. The sequential temporal activation of these genes in the primitive streak helps determining their subsequent pattern of expression along the anterior-posterior axis of the embryo, yet the precise correspondence between these two collinear processes is not fully understood. In addition, vertebrate Hox genes evolved similar modes of regulation along secondary body axes, such as the developing limbs. We review the current understanding of the mechanisms operating during activation, maintenance and silencing of Hox gene expression in these various contexts, and discuss the evolutionary significance of their genomic organization.
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36
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Noordermeer D, Leleu M, Schorderet P, Joye E, Chabaud F, Duboule D. Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci. eLife 2014; 3:e02557. [PMID: 24843030 PMCID: PMC4017647 DOI: 10.7554/elife.02557] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hox genes are essential regulators of embryonic development. Their step-wise transcriptional activation follows their genomic topology and the various states of activation are subsequently memorized into domains of progressively overlapping gene products. We have analyzed the 3D chromatin organization of Hox clusters during their early activation in vivo, using high-resolution circular chromosome conformation capture. Initially, Hox clusters are organized as single chromatin compartments containing all genes and bivalent chromatin marks. Transcriptional activation is associated with a dynamic bi-modal 3D organization, whereby the genes switch autonomously from an inactive to an active compartment. These local 3D dynamics occur within a framework of constitutive interactions within the surrounding Topological Associated Domains, indicating that this regulation process is mostly cluster intrinsic. The step-wise progression in time is fixed at various body levels and thus can account for the chromatin architectures previously described at a later stage for different anterior to posterior levels.DOI: http://dx.doi.org/10.7554/eLife.02557.001.
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Affiliation(s)
- Daan Noordermeer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marion Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Patrick Schorderet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Department of Molecular Biology, Harvard University, Boston, United States
| | - Elisabeth Joye
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Fabienne Chabaud
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
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37
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Tschopp P, Duboule D. The genetics of murine Hox loci: TAMERE, STRING, and PANTHERE to engineer chromosome variants. Methods Mol Biol 2014; 1196:89-102. [PMID: 25151159 DOI: 10.1007/978-1-4939-1242-1_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Following their duplications at the base of the vertebrate clade, Hox gene clusters underwent remarkable sub- and neo-functionalization events. Many of these evolutionary innovations can be associated with changes in the transcriptional regulation of their genes, where an intricate relationship between the structure of the gene cluster and the architecture of the surrounding genomic landscape is at play. Here, we report on a portfolio of in vivo genome engineering strategies in mice, which have been used to probe and decipher the genetic and molecular underpinnings of the complex regulatory mechanisms implemented at these loci.
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Affiliation(s)
- Patrick Tschopp
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
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38
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Nolte C, Jinks T, Wang X, Martinez Pastor MT, Krumlauf R. Shadow enhancers flanking the HoxB cluster direct dynamic Hox expression in early heart and endoderm development. Dev Biol 2013; 383:158-73. [PMID: 24055171 DOI: 10.1016/j.ydbio.2013.09.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 09/03/2013] [Accepted: 09/11/2013] [Indexed: 11/29/2022]
Abstract
The products of Hox genes function in assigning positional identity along the anterior-posterior body axis during animal development. In mouse embryos, Hox genes located at the 3' end of HoxA and HoxB complexes are expressed in nested patterns in the progenitors of the secondary heart field during early cardiogenesis and the combined activities of both of these clusters are required for proper looping of the heart. Using Hox bacterial artificial chromosomes (BACs), transposon reporters, and transgenic analyses in mice, we present the identification of several novel enhancers flanking the HoxB complex which can work over a long range to mediate dynamic reporter expression in the endoderm and embryonic heart during development. These enhancers respond to exogenously added retinoic acid and we have identified two retinoic acid response elements (RAREs) within these control modules that play a role in potentiating their regulatory activity. Deletion analysis in HoxB BAC reporters reveals that these control modules, spread throughout the flanking intergenic region, have regulatory activities that overlap with other local enhancers. This suggests that they function as shadow enhancers to modulate the expression of genes from the HoxB complex during cardiac development. Regulatory analysis of the HoxA complex reveals that it also has enhancers in the 3' flanking region which contain RAREs and have the potential to modulate expression in endoderm and heart tissues. Together, the similarities in their location, enhancer output, and dependence on retinoid signaling suggest that a conserved cis-regulatory cassette located in the 3' proximal regions adjacent to the HoxA and HoxB complexes evolved to modulate Hox gene expression during mammalian cardiac and endoderm development. This suggests a common regulatory mechanism, whereby the conserved control modules act over a long range on multiple Hox genes to generate nested patterns of HoxA and HoxB expression during cardiogenesis.
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Affiliation(s)
- Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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39
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Franzosa JA, Bugel SM, Tal TL, La Du JK, Tilton SC, Waters KM, Tanguay RL. Retinoic acid-dependent regulation of miR-19 expression elicits vertebrate axis defects. FASEB J 2013; 27:4866-76. [PMID: 23975936 DOI: 10.1096/fj.12-225524] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Retinoic acid (RA) is involved in multifarious and complex functions necessary for vertebrate development. RA signaling is reliant on strict enzymatic regulation of RA synthesis and metabolism. Improper spatiotemporal expression of RA during development can result in vertebrate axis defects. microRNAs (miRNAs) are also pivotal in orchestrating developmental processes. While mechanistic links between miRNAs and axial development are established, the role of miRNAs in regulating metabolic enzymes responsible for RA abundance during axis formation has yet to be elucidated. Our results uncovered a role of miR-19 family members in controlling RA metabolism through the regulation of CYP26A1 during vertebrate axis formation. Global miRNA expression profiling showed that developmental RA exposure suppressed the expression of miR-19 family members during zebrafish somitogenesis. A reporter assay confirmed that cyp26a1 is a bona fide target of miR-19 in vivo. Transient knockdown of miR-19 phenocopied axis defects caused by RA exposure. Exogenous miR-19 rescued the axis defects induced by RA exposure. Taken together, these results indicate that the teratogenic effects of RA exposure result, in part, from repression of miR-19 expression and subsequent misregulation of cyp26a1. This highlights a previously unidentified role of miR-19 in facilitating vertebrate axis development via regulation of RA signaling.
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Affiliation(s)
- Jill A Franzosa
- 3Department of Environmental and Molecular Toxicology, Oregon State University, 28645 East HWY 34. Corvallis, OR 97333, USA.
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40
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Kusumi K, May CM, Eckalbar WL. A large-scale view of the evolution of amniote development: insights from somitogenesis in reptiles. Curr Opin Genet Dev 2013; 23:491-7. [DOI: 10.1016/j.gde.2013.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/18/2013] [Accepted: 02/19/2013] [Indexed: 11/30/2022]
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41
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Ten Tusscher KHWJ. Mechanisms and constraints shaping the evolution of body plan segmentation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:54. [PMID: 23708840 DOI: 10.1140/epje/i2013-13054-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 05/07/2013] [Indexed: 06/02/2023]
Abstract
Segmentation of the major body axis into repeating units is arguably one of the major inventions in the evolution of animal body plan pattering. It is found in current day vertebrates, annelids and arthropods. Most segmented animals seem to use a clock-and-wavefront type mechanism in which oscillations emanating from a posterior growth zone become transformed into an anterior posterior sequence of segments. In contrast, few animals such as Drosophila use a complex gene regulatory hierarchy to simultaneously subdivide their entire body axis into segments. Here I discuss how in silico models simulating the evolution of developmental patterning can be used to investigate the forces and constraints that helped shape these two developmental modes. I perform an analysis of a series of previous simulation studies, exploiting the similarities and differences in their outcomes in relation to model characteristics to elucidate the circumstances and constraints likely to have been important for the evolution of sequential and simultaneous segmentation modes. The analysis suggests that constraints arising from the involved growth process and spatial patterning signal--posterior elongation producing a propagating wavefront versus a tissue wide morphogen gradient--and the evolutionary history--ancestral versus derived segmentation mode--strongly shaped both segmentation mechanisms. Furthermore, this implies that these patterning types are to be expected rather than random evolutionary outcomes and supports the likelihood of multiple parallel evolutionary origins.
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Affiliation(s)
- K H W J Ten Tusscher
- Theoretical Biology and Bioinformactics Group, Utrecht University, Padualaan 8, 3584, CH Utrecht, The Netherlands.
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42
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Harima Y, Takashima Y, Ueda Y, Ohtsuka T, Kageyama R. Accelerating the tempo of the segmentation clock by reducing the number of introns in the Hes7 gene. Cell Rep 2012; 3:1-7. [PMID: 23219549 DOI: 10.1016/j.celrep.2012.11.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/26/2012] [Accepted: 11/15/2012] [Indexed: 01/04/2023] Open
Abstract
Periodic somite segmentation is controlled by the cyclic gene Hes7, whose oscillatory expression depends upon negative feedback with a delayed timing. The mechanism that regulates the pace of segmentation remains to be determined, but mathematical modeling has predicted that negative feedback with shorter delays would give rise to dampened but more rapid oscillations. Here, we show that reducing the number of introns within the Hes7 gene shortens the delay and results in a more rapid tempo of both Hes7 oscillation and somite segmentation, increasing the number of somites and vertebrae in the cervical and upper thoracic region. These results suggest that the number of introns is important for the appropriate tempo of oscillatory expression and that Hes7 is a key regulator of the pace of the segmentation clock.
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Affiliation(s)
- Yukiko Harima
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
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43
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Abstract
The vertebrate A-P axis is a time axis. The head is made first and more and more posterior levels are made at later and later stages. This is different to the situation in most other animals, for example, in Drosophila. Central to this timing is Hox temporal collinearity (see below). This occurs rarely in the animal kingdom but is characteristic of vertebrates and is used to generate the primary axial Hox pattern using time space translation and to integrate successive derived patterns (see below). This is thus a different situation than in Drosophila, where the primary pattern guiding Hox spatial collinearity is generated externally, by the gap and segmentation genes.
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Affiliation(s)
- Aj Durston
- Institute of Biology, University of Leiden, Sylvius Laboratory, Wassenaarseweg 72, 2333 BE, Leiden, Netherlands
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44
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Williams T, Blachuta B, Hegna TA, Nagy LM. Decoupling elongation and segmentation: notch involvement in anostracan crustacean segmentation. Evol Dev 2012; 14:372-82. [PMID: 22765208 DOI: 10.1111/j.1525-142x.2012.00555.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Repeated body segments are a key feature of arthropods. The formation of body segments occurs via distinct developmental pathways within different arthropod clades. Although some species form their segments simultaneously without any accompanying measurable growth, most arthropods add segments sequentially from the posterior of the growing embryo or larva. The use of Notch signaling is increasingly emerging as a common feature of sequential segmentation throughout the Bilateria, as inferred from both the expression of proteins required for Notch signaling and the genetic or pharmacological disruption of Notch signaling. In this study, we demonstrate that blocking Notch signaling by blocking γ-secretase activity causes a specific, repeatable effect on segmentation in two different anostracan crustaceans, Artemia franciscana and Thamnocephalus platyurus. We observe that segmentation posterior to the third or fourth trunk segment is arrested. Despite this marked effect on segment addition, other aspects of segmentation are unaffected. In the segments that develop, segment size and boundaries between segments appear normal, engrailed stripes are normal in size and alignment, and overall growth is unaffected. By demonstrating Notch involvement in crustacean segmentation, our findings expand the evidence that Notch plays a crucial role in sequential segmentation in arthropods. At the same time, our observations contribute to an emerging picture that loss-of-function Notch phenotypes differ significantly between arthropods suggesting variability in the role of Notch in the regulation of sequential segmentation. This variability in the function of Notch in arthropod segmentation confounds inferences of homology with vertebrates and lophotrochozoans.
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Affiliation(s)
- Terri Williams
- Department of Biology, Trinity College, Hartford, CT 06106, USA.
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Ten Broek CMA, Bakker AJ, Varela-Lasheras I, Bugiani M, Van Dongen S, Galis F. Evo-Devo of the Human Vertebral Column: On Homeotic Transformations, Pathologies and Prenatal Selection. Evol Biol 2012; 39:456-471. [PMID: 23226903 PMCID: PMC3514701 DOI: 10.1007/s11692-012-9196-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/11/2012] [Indexed: 12/21/2022]
Abstract
Homeotic transformations of vertebrae are particularly common in humans and tend to come associated with malformations in a wide variety of organ systems. In a dataset of 1,389 deceased human foetuses and infants a majority had cervical ribs and approximately half of these individuals also had missing twelfth ribs or lumbar ribs. In ~10 % of all cases there was an additional shift of the lumbo-sacral boundary and, hence, homeotic transformations resulted in shifts of at least three vertebral boundaries. We found a strong coupling between the abnormality of the vertebral patterns and the amount and strength of associated malformations, i.e., the longer the disturbance of the vertebral patterning has lasted, the more associated malformations have developed and the more organ systems are affected. The germ layer of origin of the malformations was not significantly associated with the frequency of vertebral patterns. In contrast, we find significant associations with the different developmental mechanisms that are involved in the causation of the malformations, that is, segmentation, neural crest development, left-right patterning, etc. Our results, thus, suggest that locally perceived developmental signals are more important for the developmental outcome than the origin of the cells. The low robustness of vertebral A-P patterning apparent from the large number of homeotic transformations is probably caused by the strong interactivity of developmental processes and the low redundancy of involved morphogens during early organogenesis. Additionally, the early irreversibility of the specification of the A-P identity of vertebrae probably adds to the vulnerability of the process by limiting the possibility for recovery from developmental disturbances. The low developmental robustness of vertebral A-P patterning contrasts with a high robustness of the A-P patterning of the vertebral regions. Not only the order is invariable, also the variation in the number of vertebrae per region is small. This robustness is in agreement with the evolutionary stability of vertebral regions in tetrapods. Finally, we propose a new hypothesis regarding the constancy of the presacral number of vertebrae in mammals.
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Affiliation(s)
- Clara M A Ten Broek
- Group of Evolutionary Ecology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium ; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
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Evolutionary concepts meet the neck of penguins (Aves: Sphenisciformes), towards a “survival strategy” for evo-devo. Theory Biosci 2012; 131:231-42. [DOI: 10.1007/s12064-012-0156-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 06/03/2012] [Indexed: 01/07/2023]
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Zakany J, Duboule D. A genetic basis for altered sexual behavior in mutant female mice. Curr Biol 2012; 22:1676-80. [PMID: 22863319 DOI: 10.1016/j.cub.2012.06.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 06/06/2012] [Accepted: 06/26/2012] [Indexed: 12/01/2022]
Abstract
Although neural substrates of mammalian female mating behavior have been described, the association between complex courtship activity and specific underlying mechanisms remains elusive. We have isolated a mouse line that unexpectedly shows altered female social behavior with increased investigation of males and increased genital biting. We investigated adult individuals by behavioral observation and genetic and molecular neuroanatomy methods. We report exacerbated inverse pursuits and incapacitating bites directed at the genitals of stud males. This extreme deviation from wild-type female courtship segregates with a deletion of the Hoxd1 to Hoxd9 genomic region. This dominant Atypical female courtship allele (HoxD(Afc)) induces ectopic Hoxd10 gene expression in several regions in newborn forebrain transitorily and stably in a sparse subpopulation of cells in the cornu ammonis fields of adult hippocampus, which may thus lead to an abnormal modulation in the sexual behavior of mutant females. The resulting compulsive sexual solicitation behavior displayed by the most affected individuals suggests new avenues to study the genetic and molecular bases of normal and pathological mammalian affect and raises the potential involvement of the hippocampus in the control of female courtship behavior. The potential relevance to human 2q.31.1 microdeletion syndrome is discussed.
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Affiliation(s)
- Jozsef Zakany
- National Research Centre Frontiers in Genetics, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland.
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Fisher RE, Smith HF, Kusumi K, Tassone EE, Rawls A, Wilson-Rawls J. Mutations in the Notch pathway alter the patterning of multifidus. Anat Rec (Hoboken) 2011; 295:32-9. [PMID: 22095884 DOI: 10.1002/ar.21488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 08/09/2011] [Indexed: 01/06/2023]
Abstract
Clinical studies have suggested that defects in the epaxial muscles, particularly multifidus, may contribute to the etiology of idiopathic scoliosis. While the epaxial muscles and the vertebrae derive from the same embryonic segmentation process, the mechanisms that pattern the multisegmental back muscles are still unclear. The process of segmentation is regulated by the Notch signaling pathway, and mutations in the modulators delta-like 3 (Dll3) and lunatic fringe (Lfng) are genetic models for spinal disorders such as scoliosis. Osteological defects have been characterized in these genetic models, but myological phenotypes have not previously been studied. We analyzed the multifidus muscle in the mouse (Mus musculus) and observed intriguing changes in the cranio-caudal borders of multifidus in Dll3 and Lfng models. Statistical analysis did not find a significant association between the majority of the multifidus anomalies and the vertebral defects, suggesting a previously unappreciated role for Notch signaling in patterning epaxial muscle groups. These findings indicate an additional mechanism by which DLL3 and LFNG may play a role in the etiology of human idiopathic scoliosis.
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Affiliation(s)
- Rebecca E Fisher
- Department of Basic Medical Sciences, The University of Arizona College of Medicine-Phoenix, USA.
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Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D. The Dynamic Architecture of Hox Gene Clusters. Science 2011; 334:222-5. [DOI: 10.1126/science.1207194] [Citation(s) in RCA: 330] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ten Tusscher KH, Hogeweg P. Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability. PLoS Comput Biol 2011; 7:e1002208. [PMID: 21998573 PMCID: PMC3188509 DOI: 10.1371/journal.pcbi.1002208] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 08/08/2011] [Indexed: 11/30/2022] Open
Abstract
A major goal of evolutionary developmental biology (evo-devo) is to understand how multicellular body plans of increasing complexity have evolved, and how the corresponding developmental programs are genetically encoded. It has been repeatedly argued that key to the evolution of increased body plan complexity is the modularity of the underlying developmental gene regulatory networks (GRNs). This modularity is considered essential for network robustness and evolvability. In our opinion, these ideas, appealing as they may sound, have not been sufficiently tested. Here we use computer simulations to study the evolution of GRNs' underlying body plan patterning. We select for body plan segmentation and differentiation, as these are considered to be major innovations in metazoan evolution. To allow modular networks to evolve, we independently select for segmentation and differentiation. We study both the occurrence and relation of robustness, evolvability and modularity of evolved networks. Interestingly, we observed two distinct evolutionary strategies to evolve a segmented, differentiated body plan. In the first strategy, first segments and then differentiation domains evolve (SF strategy). In the second scenario segments and domains evolve simultaneously (SS strategy). We demonstrate that under indirect selection for robustness the SF strategy becomes dominant. In addition, as a byproduct of this larger robustness, the SF strategy is also more evolvable. Finally, using a combined functional and architectural approach, we determine network modularity. We find that while SS networks generate segments and domains in an integrated manner, SF networks use largely independent modules to produce segments and domains. Surprisingly, we find that widely used, purely architectural methods for determining network modularity completely fail to establish this higher modularity of SF networks. Finally, we observe that, as a free side effect of evolving segmentation and differentiation in combination, we obtained in-silico developmental mechanisms resembling mechanisms used in vertebrate development.
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Affiliation(s)
- Kirsten H Ten Tusscher
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands.
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