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Sommer-Trembo C, Santos ME, Clark B, Werner M, Fages A, Matschiner M, Hornung S, Ronco F, Oliver C, Garcia C, Tschopp P, Malinsky M, Salzburger W. The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes. Science 2024; 384:470-475. [PMID: 38662824 DOI: 10.1126/science.adj9228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 03/12/2024] [Indexed: 05/03/2024]
Abstract
Behavior is critical for animal survival and reproduction, and possibly for diversification and evolutionary radiation. However, the genetics behind adaptive variation in behavior are poorly understood. In this work, we examined a fundamental and widespread behavioral trait, exploratory behavior, in one of the largest adaptive radiations on Earth, the cichlid fishes of Lake Tanganyika. By integrating quantitative behavioral data from 57 cichlid species (702 wild-caught individuals) with high-resolution ecomorphological and genomic information, we show that exploratory behavior is linked to macrohabitat niche adaptations in Tanganyikan cichlids. Furthermore, we uncovered a correlation between the genotypes at a single-nucleotide polymorphism upstream of the AMPA glutamate-receptor regulatory gene cacng5b and variation in exploratory tendency. We validated this association using behavioral predictions with a neural network approach and CRISPR-Cas9 genome editing.
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Affiliation(s)
- Carolin Sommer-Trembo
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Bethan Clark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Marco Werner
- Leibniz-Institute for Polymer Research Dresden, Dresden, Germany
| | - Antoine Fages
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | | | - Simon Hornung
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Fabrizia Ronco
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Chantal Oliver
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Cody Garcia
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Patrick Tschopp
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Milan Malinsky
- Department of Biology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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2
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Atsuta Y, Lee C, Rodrigues AR, Colle C, Tomizawa RR, Lujan EG, Tschopp P, Galan L, Zhu M, Gorham JM, Vannier JP, Seidman CE, Seidman JG, Ros MA, Pourquié O, Tabin CJ. Direct reprogramming of non-limb fibroblasts to cells with properties of limb progenitors. Dev Cell 2024; 59:415-430.e8. [PMID: 38320485 PMCID: PMC10932627 DOI: 10.1016/j.devcel.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 09/25/2022] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
Abstract
The early limb bud consists of mesenchymal limb progenitors derived from the lateral plate mesoderm (LPM). The LPM also gives rise to the mesodermal components of the flank and neck. However, the cells at these other levels cannot produce the variety of cell types found in the limb. Taking advantage of a direct reprogramming approach, we find a set of factors (Prdm16, Zbtb16, and Lin28a) normally expressed in the early limb bud and capable of imparting limb progenitor-like properties to mouse non-limb fibroblasts. The reprogrammed cells show similar gene expression profiles and can differentiate into similar cell types as endogenous limb progenitors. The further addition of Lin41 potentiates the proliferation of the reprogrammed cells. These results suggest that these same four factors may play pivotal roles in the specification of endogenous limb progenitors.
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Affiliation(s)
- Yuji Atsuta
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Department of Biology, Kyushu University, Fukuoka 819-0395, Japan
| | - ChangHee Lee
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Alan R Rodrigues
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Charlotte Colle
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Reiko R Tomizawa
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ernesto G Lujan
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA
| | - Patrick Tschopp
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Laura Galan
- Instituto de Biomedicina y Biotecnologia de Cantabria, CSIC, SODERCAN- Universidad de Cantabria, 39011 Santander, Spain
| | - Meng Zhu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Marian A Ros
- Instituto de Biomedicina y Biotecnologia de Cantabria, CSIC, SODERCAN- Universidad de Cantabria, 39011 Santander, Spain
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA.
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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3
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Grall E, Feregrino C, Fischer S, De Courten A, Sacher F, Hiscock TW, Tschopp P. Self-organized BMP signaling dynamics underlie the development and evolution of digit segmentation patterns in birds and mammals. Proc Natl Acad Sci U S A 2024; 121:e2304470121. [PMID: 38175868 PMCID: PMC10786279 DOI: 10.1073/pnas.2304470121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/03/2023] [Indexed: 01/06/2024] Open
Abstract
Repeating patterns of synovial joints are a highly conserved feature of articulated digits, with variations in joint number and location resulting in diverse digit morphologies and limb functions across the tetrapod clade. During the development of the amniote limb, joints form iteratively within the growing digit ray, as a population of distal progenitors alternately specifies joint and phalanx cell fates to segment the digit into distinct elements. While numerous molecular pathways have been implicated in this fate choice, it remains unclear how they give rise to a repeating pattern. Here, using single-cell RNA sequencing and spatial gene expression profiling, we investigate the transcriptional dynamics of interphalangeal joint specification in vivo. Combined with mathematical modeling, we predict that interactions within the BMP signaling pathway-between the ligand GDF5, the inhibitor NOGGIN, and the intracellular effector pSMAD-result in a self-organizing Turing system that forms periodic joint patterns. Our model is able to recapitulate the spatiotemporal gene expression dynamics observed in vivo, as well as phenocopy digit malformations caused by BMP pathway perturbations. By contrasting in silico simulations with in vivo morphometrics of two morphologically distinct digits, we show how changes in signaling parameters and growth dynamics can result in variations in the size and number of phalanges. Together, our results reveal a self-organizing mechanism that underpins amniote digit segmentation and its evolvability and, more broadly, illustrate how Turing systems based on a single molecular pathway may generate complex repetitive patterns in a wide variety of organisms.
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Affiliation(s)
- Emmanuelle Grall
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Christian Feregrino
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Sabrina Fischer
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Aline De Courten
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Fabio Sacher
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
| | - Tom W. Hiscock
- Institute of Medical Sciences, University of Aberdeen, AberdeenAB25 2ZD, Scotland, United Kingdom
| | - Patrick Tschopp
- Zoology, Department of Environmental Sciences, University of Basel, Basel4051, Switzerland
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4
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Luxey M, Stieger G, Berki B, Tschopp P. Distinct patterning responses of wing and leg neuromuscular systems to different preaxial polydactylies. Front Cell Dev Biol 2023; 11:1154205. [PMID: 37215090 PMCID: PMC10192688 DOI: 10.3389/fcell.2023.1154205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The tetrapod limb has long served as a paradigm to study vertebrate pattern formation and evolutionary diversification. The distal part of the limb, the so-called autopod, is of particular interest in this regard, given the numerous modifications in both its morphology and behavioral motor output. While the underlying alterations in skeletal form have received considerable attention, much less is known about the accompanying changes in the neuromuscular system. However, modifications in the skeleton need to be properly integrated with both muscle and nerve patterns, to result in a fully functional limb. This task is further complicated by the distinct embryonic origins of the three main tissue types involved-skeleton, muscles and nerves-and, accordingly, how they are patterned and connected with one another during development. To evaluate the degree of regulative crosstalk in this complex limb patterning process, here we analyze the developing limb neuromuscular system of Silkie breed chicken. These animals display a preaxial polydactyly, due to a polymorphism in the limb regulatory region of the Sonic Hedgehog gene. Using lightsheet microscopy and 3D-reconstructions, we investigate the neuromuscular patterns of extra digits in Silkie wings and legs, and compare our results to Retinoic Acid-induced polydactylies. Contrary to previous findings, Silkie autopod muscle patterns do not adjust to alterations in the underlying skeletal topology, while nerves show partial responsiveness. We discuss the implications of tissue-specific sensitivities to global limb patterning cues for our understanding of the evolution of novel forms and functions in the distal tetrapod limb.
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Affiliation(s)
- Maëva Luxey
- *Correspondence: Maëva Luxey, ; Patrick Tschopp,
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5
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Berki B, Sacher F, Fages A, Tschopp P, Luxey M. A method to investigate muscle target-specific transcriptional signatures of single motor neurons. Dev Dyn 2023; 252:208-219. [PMID: 35705847 PMCID: PMC10084336 DOI: 10.1002/dvdy.507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Motor neurons in the vertebrate spinal cord have long served as a paradigm to study the transcriptional logic of cell type specification and differentiation. At limb levels, pool-specific transcriptional signatures first restrict innervation to only one particular muscle in the periphery, and get refined, once muscle connection has been established. Accordingly, to study the transcriptional dynamics and specificity of the system, a method for establishing muscle target-specific motor neuron transcriptomes would be required. RESULTS To investigate target-specific transcriptional signatures of single motor neurons, here we combine ex-ovo retrograde axonal labeling in mid-gestation chicken embryos with manual isolation of individual fluorescent cells and Smart-seq2 single-cell RNA-sequencing. We validate our method by injecting the dorsal extensor metacarpi radialis and ventral flexor digiti quarti wing muscles and harvesting a total of 50 fluorescently labeled cells, in which we detect up to 12,000 transcribed genes. Additionally, we present visual cues and cDNA metrics predictive of sequencing success. CONCLUSIONS Our method provides a unique approach to study muscle target-specific motor neuron transcriptomes at a single-cell resolution. We anticipate that our method will provide key insights into the transcriptional logic underlying motor neuron pool specialization and proper neuromuscular circuit assembly and refinement.
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Affiliation(s)
- Bianka Berki
- DUW Zoology, University of Basel, Basel, Switzerland
| | - Fabio Sacher
- DUW Zoology, University of Basel, Basel, Switzerland
| | - Antoine Fages
- DUW Zoology, University of Basel, Basel, Switzerland
| | | | - Maëva Luxey
- DUW Zoology, University of Basel, Basel, Switzerland
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6
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Feregrino C, Tschopp P. Assessing evolutionary and developmental transcriptome dynamics in homologous cell types. Dev Dyn 2021; 251:1472-1489. [PMID: 34114716 PMCID: PMC9545966 DOI: 10.1002/dvdy.384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/19/2021] [Accepted: 06/04/2021] [Indexed: 12/03/2022] Open
Abstract
Background During development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built—largely—by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear. Results Here, we developed a user‐friendly bioinformatics workflow to detect gene co‐expression modules and test for their conservation across developmental stages and species boundaries. Using a paradigm of morphological diversification, the tetrapod limb, and single‐cell RNA‐sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. With mouse limb data as reference, we identified 19 gene co‐expression modules with varying tissue or cell type‐restricted activities. Testing for co‐expression conservation revealed modules with high evolutionary turnover, while others seemed maintained—to different degrees, in module make‐up, density or connectivity—over developmental and evolutionary timescales. Conclusions We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data. We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data.
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Affiliation(s)
- Christian Feregrino
- DUW Zoology, University of Basel, Basel, Switzerland.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany. Hannoversche Str. 28, Berlin, Germany
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7
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Sacher F, Feregrino C, Tschopp P, Ewald CY. Extracellular matrix gene expression signatures as cell type and cell state identifiers. Matrix Biol Plus 2021; 10:100069. [PMID: 34195598 PMCID: PMC8233473 DOI: 10.1016/j.mbplus.2021.100069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Transcriptomic signatures based on cellular mRNA expression profiles can be used to categorize cell types and states. Yet whether different functional groups of genes perform better or worse in this process remains largely unexplored. Here we test the core matrisome - that is, all genes coding for structural proteins of the extracellular matrix - for its ability to delineate distinct cell types in embryonic single-cell RNA-sequencing (scRNA-seq) data. We show that even though expressed core matrisome genes correspond to less than 2% of an entire cellular transcriptome, their RNA expression levels suffice to recapitulate essential aspects of cell type-specific clustering. Notably, using scRNA-seq data from the embryonic limb, we demonstrate that core matrisome gene expression outperforms random gene subsets of similar sizes and can match and exceed the predictive power of transcription factors. While transcription factor signatures generally perform better in predicting cell types at early stages of chicken and mouse limb development, i.e., when cells are less differentiated, the information content of the core matrisome signature increases in more differentiated cells. Moreover, using cross-species analyses, we show that these cell type-specific signatures are evolutionarily conserved. Our findings suggest that each cell type produces its own unique extracellular matrix, or matreotype, which becomes progressively more refined and cell type-specific as embryonic tissues mature.
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Affiliation(s)
- Fabio Sacher
- Laboratory of Regulatory Evolution, DUW Zoology, University of Basel, Basel CH-4051, Switzerland
| | - Christian Feregrino
- Laboratory of Regulatory Evolution, DUW Zoology, University of Basel, Basel CH-4051, Switzerland
| | - Patrick Tschopp
- Laboratory of Regulatory Evolution, DUW Zoology, University of Basel, Basel CH-4051, Switzerland
| | - Collin Y. Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach CH-8603, Switzerland
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8
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Luxey M, Berki B, Heusermann W, Fischer S, Tschopp P. Development of the chick wing and leg neuromuscular systems and their plasticity in response to changes in digit numbers. Dev Biol 2020; 458:133-140. [PMID: 31697937 DOI: 10.1016/j.ydbio.2019.10.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 01/28/2023]
Abstract
The tetrapod limb has long served as a paradigm to study vertebrate pattern formation. During limb morphogenesis, a number of distinct tissue types are patterned and subsequently must be integrated to form coherent functional units. For example, the musculoskeletal apparatus of the limb requires the coordinated development of the skeletal elements, connective tissues, muscles and nerves. Here, using light-sheet microscopy and 3D-reconstructions, we concomitantly follow the developmental emergence of nerve and muscle patterns in chicken wings and legs, two appendages with highly specialized locomotor outputs. Despite a comparable flexor/extensor-arrangement of their embryonic muscles, wings and legs show a rotated innervation pattern for their three main motor nerve branches. To test the functional implications of these distinct neuromuscular topologies, we challenge their ability to adapt and connect to an experimentally altered skeletal pattern in the distal limb, the autopod. Our results show that, unlike autopod muscle groups, motor nerves are unable to fully adjust to a changed peripheral organisation, potentially constrained by their original projection routes. As the autopod has undergone substantial morphological diversifications over the course of tetrapod evolution, our results have implications for the coordinated modification of the distal limb musculoskeletal apparatus, as well as for our understanding of the varying degrees of motor functionality associated with human hand and foot malformations.
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Affiliation(s)
- Maëva Luxey
- DUW Zoology, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Bianka Berki
- DUW Zoology, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | | | - Sabrina Fischer
- DUW Zoology, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Patrick Tschopp
- DUW Zoology, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland.
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9
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Grall E, Tschopp P. A sense of place, many times over ‐ pattern formation and evolution of repetitive morphological structures. Dev Dyn 2019; 249:313-327. [DOI: 10.1002/dvdy.131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/30/2019] [Accepted: 11/04/2019] [Indexed: 12/14/2022] Open
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10
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Abstract
BACKGROUND Through precise implementation of distinct cell type specification programs, differentially regulated in both space and time, complex patterns emerge during organogenesis. Thanks to its easy experimental accessibility, the developing chicken limb has long served as a paradigm to study vertebrate pattern formation. Through decades' worth of research, we now have a firm grasp on the molecular mechanisms driving limb formation at the tissue-level. However, to elucidate the dynamic interplay between transcriptional cell type specification programs and pattern formation at its relevant cellular scale, we lack appropriately resolved molecular data at the genome-wide level. Here, making use of droplet-based single-cell RNA-sequencing, we catalogue the developmental emergence of distinct tissue types and their transcriptome dynamics in the distal chicken limb, the so-called autopod, at cellular resolution. RESULTS Using single-cell RNA-sequencing technology, we sequenced a total of 17,628 cells coming from three key developmental stages of chicken autopod patterning. Overall, we identified 23 cell populations with distinct transcriptional profiles. Amongst them were small, albeit essential populations like the apical ectodermal ridge, demonstrating the ability to detect even rare cell types. Moreover, we uncovered the existence of molecularly distinct sub-populations within previously defined compartments of the developing limb, some of which have important signaling functions during autopod pattern formation. Finally, we inferred gene co-expression modules that coincide with distinct tissue types across developmental time, and used them to track patterning-relevant cell populations of the forming digits. CONCLUSIONS We provide a comprehensive functional genomics resource to study the molecular effectors of chicken limb patterning at cellular resolution. Our single-cell transcriptomic atlas captures all major cell populations of the developing autopod, and highlights the transcriptional complexity in many of its components. Finally, integrating our data-set with other single-cell transcriptomics resources will enable researchers to assess molecular similarities in orthologous cell types across the major tetrapod clades, and provide an extensive candidate gene list to functionally test cell-type-specific drivers of limb morphological diversification.
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Affiliation(s)
| | - Fabio Sacher
- DUW Zoology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Oren Parnas
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Present address: The Concern Foundation Laboratories at the Lautenberg Centre for Immunology and Cancer Research, IMRIC, Hebrew University Faculty of Medicine, 91120 Jerusalem, Israel
| | - Patrick Tschopp
- DUW Zoology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
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11
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Abstract
The principle of homology is central to conceptualizing the comparative aspects of morphological evolution. The distinctions between homologous or non-homologous structures have become blurred, however, as modern evolutionary developmental biology (evo-devo) has shown that novel features often result from modification of pre-existing developmental modules, rather than arising completely de novo. With this realization in mind, the term 'deep homology' was coined, in recognition of the remarkably conserved gene expression during the development of certain animal structures that would not be considered homologous by previous strict definitions. At its core, it can help to formulate an understanding of deeper layers of ontogenetic conservation for anatomical features that lack any clear phylogenetic continuity. Here, we review deep homology and related concepts in the context of a gene expression-based homology discussion. We then focus on how these conceptual frameworks have profited from the recent rise of high-throughput next-generation sequencing. These techniques have greatly expanded the range of organisms amenable to such studies. Moreover, they helped to elevate the traditional gene-by-gene comparison to a transcriptome-wide level. We will end with an outlook on the next challenges in the field and how technological advances might provide exciting new strategies to tackle these questions.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Patrick Tschopp
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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12
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Marin R, Cortez D, Lamanna F, Pradeepa MM, Leushkin E, Julien P, Liechti A, Halbert J, Brüning T, Mössinger K, Trefzer T, Conrad C, Kerver HN, Wade J, Tschopp P, Kaessmann H. Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage. Genome Res 2017; 27:1974-1987. [PMID: 29133310 PMCID: PMC5741051 DOI: 10.1101/gr.223727.117] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023]
Abstract
Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate for the almost complete Y Chromosome degeneration, X-linked genes have become twofold up-regulated, restoring ancestral expression levels. The highly efficient dosage compensation mechanism of Anolis represents the only vertebrate case identified so far to fully support Ohno's original dosage compensation hypothesis. Further analyses reveal that X up-regulation occurs only in males and is mediated by a male-specific chromatin machinery that leads to global hyperacetylation of histone H4 at lysine 16 specifically on the X Chromosome. The green anole dosage compensation mechanism is highly reminiscent of that of the fruit fly, Drosophila melanogaster. Altogether, our work unveils the convergent emergence of a Drosophila-like dosage compensation mechanism in an ancient reptilian sex chromosome system and highlights that the evolutionary pressures imposed by sex chromosome dosage reductions in different amniotes were resolved in fundamentally different ways.
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Affiliation(s)
- Ray Marin
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Diego Cortez
- Center for Genomic Sciences, UNAM, CP62210 Cuernavaca, Mexico
| | - Francesco Lamanna
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Madapura M Pradeepa
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Evgeny Leushkin
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Philippe Julien
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, 08003 Barcelona, Spain
| | - Angélica Liechti
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Thoomke Brüning
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Katharina Mössinger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Timo Trefzer
- Department of Theoretical Bioinformatics, German Cancer Research Center/BioQuant, D-69120 Heidelberg, Germany
| | - Christian Conrad
- Department of Theoretical Bioinformatics, German Cancer Research Center/BioQuant, D-69120 Heidelberg, Germany
| | - Halie N Kerver
- Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - Juli Wade
- Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA.,Department of Psychology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Patrick Tschopp
- Institute of Zoology, University of Basel, 4051 Basel, Switzerland
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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13
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Abstract
Critical steps in forming the vertebrate limb include the positioning of digits and the positioning of joints within each digit. Recent studies have proposed that the iterative series of digits is established by a Turing-like mechanism generating stripes of chondrogenic domains. However, re-examination of available data suggest that digits are actually patterned as evenly spaced spots, not stripes, which then elongate into rod-shaped digit rays by incorporating new cells at their tips. Moreover, extension of the digit rays and the patterning of the joints occur simultaneously at the distal tip, implying that an integrated model is required to fully understand these processes.
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Affiliation(s)
- Tom W Hiscock
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Tschopp
- Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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14
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Groner AC, Cato L, de Tribolet-Hardy J, Bernasocchi T, Janouskova H, Melchers D, Houtman R, Cato ACB, Tschopp P, Gu L, Corsinotti A, Zhong Q, Fankhauser C, Fritz C, Poyet C, Wagner U, Guo T, Aebersold R, Garraway LA, Wild PJ, Theurillat JP, Brown M. TRIM24 Is an Oncogenic Transcriptional Activator in Prostate Cancer. Cancer Cell 2016; 29:846-858. [PMID: 27238081 PMCID: PMC5124371 DOI: 10.1016/j.ccell.2016.04.012] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 12/15/2015] [Accepted: 04/27/2016] [Indexed: 01/22/2023]
Abstract
Androgen receptor (AR) signaling is a key driver of prostate cancer (PC). While androgen-deprivation therapy is transiently effective in advanced disease, tumors often progress to a lethal castration-resistant state (CRPC). We show that recurrent PC-driver mutations in speckle-type POZ protein (SPOP) stabilize the TRIM24 protein, which promotes proliferation under low androgen conditions. TRIM24 augments AR signaling, and AR and TRIM24 co-activated genes are significantly upregulated in CRPC. Expression of TRIM24 protein increases from primary PC to CRPC, and both TRIM24 protein levels and the AR/TRIM24 gene signature predict disease recurrence. Analyses in CRPC cells reveal that the TRIM24 bromodomain and the AR-interacting motif are essential to support proliferation. These data provide a rationale for therapeutic TRIM24 targeting in SPOP mutant and CRPC patients.
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Affiliation(s)
- Anna C Groner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Laura Cato
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas de Tribolet-Hardy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Hana Janouskova
- Institute of Oncology Research, Bellinzona 6500, Switzerland
| | | | - René Houtman
- PamGene International, Den Bosch 521HH, the Netherlands
| | - Andrew C B Cato
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Patrick Tschopp
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Lei Gu
- Division of Newborn Medicine, Children's Hospital Boston and Department of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
| | - Andrea Corsinotti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH16 4UU, UK; Laboratory Animal Resource Center, Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Qing Zhong
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Christian Fankhauser
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland; Department of Urology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Christine Fritz
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Cédric Poyet
- Department of Urology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Ulrich Wagner
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich 8093, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich 8093, Switzerland; Faculty of Science, University of Zurich, Zurich 8057, Switzerland
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich 8091, Switzerland
| | - Jean-Philippe Theurillat
- Institute of Oncology Research, Bellinzona 6500, Switzerland; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne 1011, Switzerland.
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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15
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Tschopp P, Sherratt E, Sanger TJ, Groner AC, Aspiras AC, Hu JK, Pourquié O, Gros J, Tabin CJ. A relative shift in cloacal location repositions external genitalia in amniote evolution. Nature 2014; 516:391-4. [PMID: 25383527 PMCID: PMC4294627 DOI: 10.1038/nature13819] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 08/20/2014] [Indexed: 12/23/2022]
Abstract
The move of vertebrates to a terrestrial lifestyle required major adaptations in their locomotory apparatus and reproductive organs. While the fin-to-limb transition has received considerable attention, little is known about the developmental and evolutionary origins of external genitalia. Similarities in gene expression have been interpreted as a potential evolutionary link between the limb and genitals; however, no underlying developmental mechanism has been identified. We re-examined this question using micro-computed tomography, lineage tracing in three amniote clades, and RNA-sequencing-based transcriptional profiling. Here we show that the developmental origin of external genitalia has shifted through evolution, and in some taxa limbs and genitals share a common primordium. In squamates, the genitalia develop directly from the budding hindlimbs, or the remnants thereof, whereas in mice the genital tubercle originates from the ventral and tail bud mesenchyme. The recruitment of different cell populations for genital outgrowth follows a change in the relative position of the cloaca, the genitalia organizing centre. Ectopic grafting of the cloaca demonstrates the conserved ability of different mesenchymal cells to respond to these genitalia-inducing signals. Our results support a limb-like developmental origin of external genitalia as the ancestral condition. Moreover, they suggest that a change in the relative position of the cloacal signalling centre during evolution has led to an altered developmental route for external genitalia in mammals, while preserving parts of the ancestral limb molecular circuitry owing to a common evolutionary origin.
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Affiliation(s)
- Patrick Tschopp
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Emma Sherratt
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Thomas J. Sanger
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Anna C. Groner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Ariel C. Aspiras
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Jimmy K. Hu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Jérôme Gros
- Developmental and Stem Cell Biology Department, Institut Pasteur, 75724 Paris Cedex 15, France
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16
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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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17
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Rohner N, Tschopp P, Tabin C. Development: Facial Makeup Enhancing Our Looks. Curr Biol 2014; 24:R36-R38. [DOI: 10.1016/j.cub.2013.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Schorderet P, Lonfat N, Darbellay F, Tschopp P, Gitto S, Soshnikova N, Duboule D. A genetic approach to the recruitment of PRC2 at the HoxD locus. PLoS Genet 2013; 9:e1003951. [PMID: 24244202 PMCID: PMC3820793 DOI: 10.1371/journal.pgen.1003951] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/27/2013] [Indexed: 01/01/2023] Open
Abstract
Polycomb group (PcG) proteins are essential for the repression of key factors during early development. In Drosophila, the polycomb repressive complexes (PRC) associate with defined polycomb response DNA elements (PREs). In mammals, however, the mechanisms underlying polycomb recruitment at targeted loci are poorly understood. We have used an in vivo approach to identify DNA sequences of importance for the proper recruitment of polycomb proteins at the HoxD locus. We report that various genomic re-arrangements of the gene cluster do not strongly affect PRC2 recruitment and that relatively small polycomb interacting sequences appear necessary and sufficient to confer polycomb recognition and targeting to ectopic loci. In addition, a high GC content, while not sufficient to recruit PRC2, may help its local spreading. We discuss the importance of PRC2 recruitment over Hox gene clusters in embryonic stem cells, for their subsequent coordinated transcriptional activation during development. Hox genes are essential for the proper organization of structures along the developing vertebrate body axis. These genes must be activated at a precise time and their premature transcription is deleterious to the organism. Early on, Hox gene clusters are covered by Polycomb Repressive protein Complexes (PRCs), which help keep these genes silent. However, the mechanism(s) that selectively recruit PRCs to these particular genomic loci remains elusive. We have used a collection of mutant mice carrying a set of deletions inside and outside the HoxD cluster to try and detect the presence of any DNA sequence of particular importance in this mechanism. We conclude that a range of low affinity sequences synergize to recruit PRCs over the gene cluster, which makes this process very robust and resistant to genetic perturbations.
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Affiliation(s)
- Patrick Schorderet
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Nicolas Lonfat
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Fabrice Darbellay
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Patrick Tschopp
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
| | - Sandra Gitto
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
| | - Natalia Soshnikova
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Denis Duboule
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
- * E-mail: ,
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19
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Mosimann C, Puller AC, Lawson KL, Tschopp P, Amsterdam A, Zon LI. Site-directed zebrafish transgenesis into single landing sites with the phiC31 integrase system. Dev Dyn 2013; 242:949-963. [PMID: 23723152 PMCID: PMC3775328 DOI: 10.1002/dvdy.23989] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Linear DNA-based and Tol2-mediated transgenesis are powerful tools for the generation of transgenic zebrafish. However, the integration of multiple copies or transgenes at random genomic locations complicates comparative transgene analysis and makes long-term transgene stability unpredictable with variable expression. Targeted, site-directed transgene integration into pre-determined genomic loci can circumvent these issues. The phiC31 integrase catalyzes the unidirectional recombination reaction between heterotypic attP and attB sites and is an efficient platform for site-directed transgenesis. RESULTS We report the implementation of the phiC31 integrase-mediated attP/attB recombination for site-directed zebrafish transgenics of attB-containing transgene vectors into single genomic attP landing sites. We generated Tol2-based single-insertion attP transgenic lines and established their performance in phiC31 integrase-catalyzed integration of an attB-containing transgene vector. We found stable germline transmission into the next generation of an attB reporter transgene in 34% of all tested animals. We further characterized two functional attP landing site lines and determined their genomic location. Our experiments also demonstrate tissue-specific transgene applications as well as long-term stability of phiC31-mediated transgenes. CONCLUSIONS Our results establish phiC31 integrase-controlled site-directed transgenesis into single, genomic attP sites as space-, time-, and labor-efficient zebrafish transgenesis technique. The described reagents are available for distribution to the zebrafish community.
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Affiliation(s)
- Christian Mosimann
- Howard Hughes Medical Institute, Boston, MA 02115, USA
- Stem Cell Program, Children’s Hospital Boston, Boston, MA 02115, USA
- Division of Hematology/Oncology, Children’s Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ann-Christin Puller
- Howard Hughes Medical Institute, Boston, MA 02115, USA
- Stem Cell Program, Children’s Hospital Boston, Boston, MA 02115, USA
- Division of Hematology/Oncology, Children’s Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Katy L. Lawson
- Howard Hughes Medical Institute, Boston, MA 02115, USA
- Stem Cell Program, Children’s Hospital Boston, Boston, MA 02115, USA
- Division of Hematology/Oncology, Children’s Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick Tschopp
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Adam Amsterdam
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02319, USA
| | - Leonard I. Zon
- Howard Hughes Medical Institute, Boston, MA 02115, USA
- Stem Cell Program, Children’s Hospital Boston, Boston, MA 02115, USA
- Division of Hematology/Oncology, Children’s Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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20
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Groner AC, Tschopp P, Challet L, Dietrich JE, Verp S, Offner S, Barde I, Rodriguez I, Hiiragi T, Trono D. The Krüppel-associated box repressor domain can induce reversible heterochromatization of a mouse locus in vivo. J Biol Chem 2012; 287:25361-9. [PMID: 22605343 DOI: 10.1074/jbc.m112.350884] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The study of chromatin and its regulators is key to understanding and manipulating transcription. We previously exploited the Krüppel-associated box (KRAB) transcriptional repressor domain, present in hundreds of vertebrate-specific zinc finger proteins, to assess the effect of its binding to gene bodies. These experiments revealed that the ectopic and doxycycline (dox)-controlled tet repressor KRAB fusion protein (tTRKRAB) can induce reversible and long-range silencing of cellular promoters. Here, we extend this system to in vivo applications and use tTRKRAB to achieve externally controllable repression of an endogenous mouse locus. We employed lentiviral-mediated transgenesis with promoterless TetO-containing gene traps to engineer a mouse line where the endogenous kinesin family member 2A (Kif2A) promoter drives a YFP reporter gene. When these mice were crossed to animals expressing the TetO-binding tTRKRAB repressor, this regulator was recruited to the Kif2A locus, and YFP expression was reduced. This effect was reversed when dox was given to embryos or adult mice, demonstrating that the cellular Kif2A promoter was only silenced upon repressor binding. Molecular analyses confirmed that tTRKRAB induced transcriptional repression through the spread of H3K9me3-containing heterochromatin, without DNA methylation of the trapped Kif2A promoter. Therefore, we demonstrate that targeting of tTRKRAB to a gene body in vivo results in reversible transcriptional repression through the spreading of facultative heterochromatin. This finding not only sheds light on KRAB-mediated transcriptional processes, but also suggests approaches for the externally controllable and reversible modulation of chromatin and transcription in vivo.
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Affiliation(s)
- Anna C Groner
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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21
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Abstract
The evolution of vertebrate genomes was accompanied by an astounding increase in the complexity of their regulatory modalities. Genetic redundancy resulting from large-scale genome duplications at the base of the chordate tree was repeatedly exploited by the functional redeployment of paralogous genes via innovations in their regulatory circuits. As a paradigm of such regulatory evolution, we have extensively studied those control mechanisms at work in-cis over vertebrate Hox gene clusters. Here, we review the portfolio of genetic strategies that have been developed to tackle the intricate relationship between genomic topography and the transcriptional activities in this gene family, and we describe some of the mechanistic insights we gained by using the HoxD cluster as an example. We discuss the high heuristic value of this system in our general understanding of how changes in transcriptional regulation can diversify gene function and thereby fuel morphological evolution.
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Affiliation(s)
- Patrick Tschopp
- National Center of Competence in Research, Frontiers in Genetics, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
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22
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Tschopp P, Christen AJ, Duboule D. Bimodal control of Hoxd gene transcription in the spinal cord defines two regulatory subclusters. Development 2012; 139:929-39. [PMID: 22278926 DOI: 10.1242/dev.076794] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The importance of Hox genes in the specification of neuronal fates in the spinal cord has long been recognized. However, the transcriptional controls underlying their collinear expression domains remain largely unknown. Here we show in mice that the correspondence between the physical order of Hoxd genes and their rostral expression boundaries, although respecting spatial collinearity, does not display a fully progressive distribution. Instead, two major anteroposterior boundaries are detected, coinciding with the functional subdivision of the spinal cord. Tiling array analyses reveal two distinct blocks of transcription, regulated independently from one another, that define the observed expression boundaries. Targeted deletions in vivo that remove the genomic fragments separating the two blocks induce ectopic expression of posterior genes. We further evaluate the independent regulatory potential and transcription profile of each gene locus by a tiling array approach using a contiguous series of transgenes combined with locus-specific deletions. Our work uncovers a bimodal type of HoxD spatial collinearity in the developing spinal cord that relies on two separate 'enhancer mini-hubs' to ensure correct Hoxd gene expression levels while maintaining their appropriate anteroposterior boundaries.
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Affiliation(s)
- Patrick Tschopp
- National Research Centre Frontiers in Genetics at Department of Genetics and Evolution, University of Geneva, Sciences III, Quai Ernest-Ansermet 30, Geneva 4, Switzerland
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23
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Tschopp P, Duboule D. A regulatory 'landscape effect' over the HoxD cluster. Dev Biol 2010; 351:288-96. [PMID: 21195707 DOI: 10.1016/j.ydbio.2010.12.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 12/22/2022]
Abstract
Faithful expression of Hox genes in both time and space is essential for proper patterning of the primary body axis. Transgenic approaches in vertebrates have suggested that this collinear activation process is regulated in a largely gene cluster-autonomous manner. In contrast, more recently co-opted expression specificities, required in other embryonic structures, depend upon long-range enhancer sequences acting from outside the gene clusters. This regulatory dichotomy was recently questioned, since gene activation along the trunk seems to be partially regulated by signals located outside of the cluster. We investigated these alternative regulatory strategies by engineering a large inversion that precisely separates the murine HoxD complex from its centromeric neighborhood. Mutant animals displayed posterior transformations along with subtle deregulations of Hoxd genes, indicating an impact of the centromeric landscape on the fine-tuning of Hoxd gene expression. Proximal limbs were also affected, suggesting that this 'landscape effect' is generic and impacts upon regulatory mechanisms of various qualities and evolutionary origins.
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Affiliation(s)
- Patrick Tschopp
- National Research Centre-Frontiers in Genetics, Department of Zoology and Animal Biology, University of Geneva, Sciences III, Quai Ernest-Ansermet 30, Geneva, Switzerland
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24
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Tschopp P, Tarchini B, Spitz F, Zakany J, Duboule D. Uncoupling time and space in the collinear regulation of Hox genes. PLoS Genet 2009; 5:e1000398. [PMID: 19266017 PMCID: PMC2642670 DOI: 10.1371/journal.pgen.1000398] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 01/30/2009] [Indexed: 12/23/2022] Open
Abstract
During development of the vertebrate body axis, Hox genes are transcribed sequentially, in both time and space, following their relative positions within their genomic clusters. Analyses of animal genomes support the idea that Hox gene clustering is essential for coordinating the various times of gene activations. However, the eventual collinear ordering of the gene specific transcript domains in space does not always require genomic clustering. We analyzed these complex regulatory relationships by using mutant alleles at the mouse HoxD locus, including one that splits the cluster into two pieces. We show that both positive and negative regulatory influences, located on either side of the cluster, control an early phase of collinear expression in the trunk. Interestingly, this early phase does not systematically impact upon the subsequent expression patterns along the main body axis, indicating that the mechanism underlying temporal collinearity is distinct from those acting during the second phase. We discuss the potential functions and evolutionary origins of these mechanisms, as well as their relationship with similar processes at work during limb development. Hox genes encode proteins that control embryonic development along the head-to-tail axis. These genes are clustered in one site on the chromosome and their respective positions within the cluster determine their time and place of activation. Here, by using a large set of targeted mutations disturbing the integrity of the gene cluster, we show that the spatial organization of expression domains does not directly depend upon the timing of activation as was previously suggested. This uncoupling between space and time in the regulation of these Hox genes coincides with the existence of two major phases of regulation. The first is time-dependent and involves global regulatory influences, located outside the gene cluster, whereas the second relies upon more local regulatory elements, likely interspersed between the genes, inside the cluster. These results provide the bases for future analyses of collinear mechanisms and indicate that different types of collinearities are not necessarily related, neither in function, nor in their evolutionary histories.
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Affiliation(s)
- Patrick Tschopp
- National Research Centre “Frontiers in Genetics”, Department of Zoology and Animal Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | - Basile Tarchini
- National Research Centre “Frontiers in Genetics”, Department of Zoology and Animal Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | - François Spitz
- National Research Centre “Frontiers in Genetics”, Department of Zoology and Animal Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | - Jozsef Zakany
- National Research Centre “Frontiers in Genetics”, Department of Zoology and Animal Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | - Denis Duboule
- National Research Centre “Frontiers in Genetics”, Department of Zoology and Animal Biology, University of Geneva, Sciences III, Geneva, Switzerland
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
- * E-mail:
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25
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Casez JP, Tschopp P, Sandberg Tschopp A, Lippuner K, Zingg E, Jaeger P. Effects of nasal calcitonin on bone mineral density following parathyroidectomy in patients with primary hyperparathyroidism. Horm Res Paediatr 2004; 59:263-9. [PMID: 12784089 DOI: 10.1159/000070623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2002] [Accepted: 12/19/2002] [Indexed: 11/19/2022] Open
Abstract
AIM To investigate whether nasal salmon calcitonin (CT; 200 U/day) given in addition to calcium helps to restore the bone mass after parathyroidectomy (PTX) in patients with primary hyperparathyroidism (PHPT). METHODS Twenty patients with PHPT were enrolled after successful PTX and received 1 g calcium per os daily for 1 year. They were randomly assigned either to nasal CT (CT group) or to no treatment. The bone mass was measured using dual-energy X-ray absorptiometry at multiple sites. RESULTS Eight patients in each group completed the study. After 12 months, the bone mass increased significantly at whole-body level and at lumbar spine in both groups, increased at hip and epiphyses of tibia or radius in the CT group only, and did not change at diaphyses of tibia and radius in either group. CONCLUSIONS Bone mass increases after PTX for PHPT in patients receiving oral calcium. CT may help to restore the bone mass at sites of the appendicular skeleton, where trabecular bone predominates.
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Affiliation(s)
- J-P Casez
- Department of Nephrology, University Hospital, Nice, France
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26
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Abstract
The presence of homocysteate and homocysteine sulfinate was demonstrated in extracts prepared from cultures of rat cortical and cerebellar astrocytes as well as from C6 glioblastoma cells by o-phthalaldehyde derivatization and subsequent HPLC analysis. Homocysteate-like immunoreactivity was found in cultured cortical astrocytes by postembedding immunocytochemistry at the level of light microscopy. These findings support the notion of a glial localization of the excitatory transmitter candidate homocysteate.
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Affiliation(s)
- P Tschopp
- Institut für Hirnforschung, University of Zürich, Switzerland
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27
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Tschopp P, Mumenthaler M. [Symptomatic cluster headache: coincidence or causal relation? Report of six cases]. Nervenarzt 1991; 62:383-7. [PMID: 1876223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- P Tschopp
- Neurologische Universitätsklinik, Inselspital, Bern, Schweiz
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Tschopp P. [Health 80. Survey of households in Geneva]. Krankenpfl Soins Infirm 1981:40-42. [PMID: 6270457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Tschopp P. [National research program on the economy and efficacy of the health system in Switzerland: scientific objective and practical aspects]. Soz Praventivmed 1981; 26:6-11. [PMID: 6795850 DOI: 10.1007/bf02076310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Scientific and policy targets of the National Research Program on Health Care Efficiency. Following a brief review of the general background, the specific goals of the program are presented: the realization of a solid scientific and interdisciplinary basis in the field of systematic health-system-research in Switzerland. After a review of the criteria which were employed to select out of one hundred offers some twenty research projects, a summary of these projects permits to illustrate the architecture of the whole program.
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Tschopp P. [The notion of effectiveness in the health field]. Soz Praventivmed 1978; 23:92-6. [PMID: 685495 DOI: 10.1007/bf02075231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The author emphasizes the necessity of an interdisciplinary approach in the field of exploring efficiency of the health system. He attempts to show how the notion of efficiency depends on the degree of aggregation of the considered components of the health system.
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Tschopp P. [Economic consequences in social medicine security]. Schweiz Rundsch Med Prax 1970; 59:556-9. [PMID: 5509523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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