1
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Mochii M, Akizuki K, Ossaka H, Kagawa N, Umesono Y, Suzuki KIT. A CRISPR-Cas9-mediated versatile method for targeted integration of a fluorescent protein gene to visualize endogenous gene expression in Xenopus laevis. Dev Biol 2024; 506:42-51. [PMID: 38052295 DOI: 10.1016/j.ydbio.2023.11.010] [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: 05/15/2023] [Revised: 11/10/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023]
Abstract
Xenopus laevis is a widely used model organism in developmental and regeneration studies. Despite several reports regarding targeted integration techniques in Xenopus, there is still room for improvement of them, especially in creating reporter lines that rely on endogenous regulatory enhancers/promoters. We developed a CRISPR-Cas9-based simple method to efficiently introduce a fluorescent protein gene into 5' untranslated regions (5'UTRs) of target genes in Xenopus laevis. A donor plasmid DNA encoding an enhanced green fluorescent protein (eGFP) flanked by a genomic fragment ranging from 66 bp to 878 bp including target 5'UTR was co-injected into fertilized eggs with a single guide RNA and Cas9 protein. Injections for krt12.2.L, myod1.S, sox2.L or brevican.S resulted in embryos expressing eGFP fluorescence in a tissue-specific manner, recapitulating endogenous expression of target genes. Integrations of the donor DNA into the target regions were examined by genotyping PCR for the eGFP-expressing embryos. The rate of embryos expressing the specific eGFP varied from 2.1% to 13.2% depending on the target locus and length of the genomic fragment in the donor plasmids. Germline transmission of an integrated DNA was observed. This simple method provides a powerful tool for exploring gene expression and function in developmental and regeneration research in X. laevis.
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Affiliation(s)
- Makoto Mochii
- Department of Life Science, Graduate School of Science, University of Hyogo, Akougun, Hyogo, 678-1297, Japan.
| | - Kai Akizuki
- Department of Life Science, Graduate School of Science, University of Hyogo, Akougun, Hyogo, 678-1297, Japan
| | - Hero Ossaka
- Department of Life Science, Graduate School of Science, University of Hyogo, Akougun, Hyogo, 678-1297, Japan
| | - Norie Kagawa
- Department of Life Science, Graduate School of Science, University of Hyogo, Akougun, Hyogo, 678-1297, Japan
| | - Yoshihiko Umesono
- Department of Life Science, Graduate School of Science, University of Hyogo, Akougun, Hyogo, 678-1297, Japan
| | - Ken-Ichi T Suzuki
- Emerging Model Organisms Facility, Trans-scale Biology Center, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan.
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2
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Min S, Whited JL. Limb blastema formation: How much do we know at a genetic and epigenetic level? J Biol Chem 2023; 299:102858. [PMID: 36596359 PMCID: PMC9898764 DOI: 10.1016/j.jbc.2022.102858] [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: 12/22/2021] [Revised: 12/13/2022] [Accepted: 12/23/2022] [Indexed: 01/02/2023] Open
Abstract
Regeneration of missing body parts is an incredible ability which is present in a wide number of species. However, this regenerative capability varies among different organisms. Urodeles (salamanders) are able to completely regenerate limbs after amputation through the essential process of blastema formation. The blastema is a collection of relatively undifferentiated progenitor cells that proliferate and repattern to form the internal tissues of a regenerated limb. Understanding blastema formation in salamanders may enable comparative studies with other animals, including mammals, with more limited regenerative abilities and may inspire future therapeutic approaches in humans. This review focuses on the current state of knowledge about how limb blastemas form in salamanders, highlighting both the possible roles of epigenetic controls in this process as well as limitations to scientific understanding that present opportunities for research.
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Affiliation(s)
- Sangwon Min
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jessica L Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.
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3
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Sousounis K, Courtemanche K, Whited JL. A Practical Guide for CRISPR-Cas9-Induced Mutations in Axolotls. Methods Mol Biol 2023; 2562:335-349. [PMID: 36272086 DOI: 10.1007/978-1-0716-2659-7_22] [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] [Indexed: 06/16/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is a powerful tool that enables editing of the axolotl genome. In this chapter, we will cover how to retrieve gene sequences, confirm annotation, design CRISPR targets, analyze indels, and screen for Crispant axolotls. This is a comprehensive guide on how to use CRISPR on your favorite gene and gain insights into its function.
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Affiliation(s)
- Konstantinos Sousounis
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Katharine Courtemanche
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jessica L Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- The Harvard Stem Cell Institute, Cambridge, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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4
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Maden M. Salamanders as Key Models for Development and Regeneration Research. Methods Mol Biol 2023; 2562:1-23. [PMID: 36272065 DOI: 10.1007/978-1-0716-2659-7_1] [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] [Indexed: 06/16/2023]
Abstract
For 70 years from the very beginning of developmental biology, the salamander embryo was the pre-eminent model for these studies. Here I review the major discoveries that were made using salamander embryos including regionalization of the mesoderm; patterning of the neural plate; limb development, with the pinnacle being Spemann's Nobel Prize for the discovery of the organizer; and the phenomenon of induction. Salamanders have also been the major organism for elucidating discoveries in organ regeneration, and these are described here too beginning with Spallanzani's experiments in 1768. These include the neurotrophic hypothesis of regeneration, studies of aneurogenic limbs, the concept of dedifferentiation and transdifferentiation, and advances in understanding pattern formation via molecules located on the cell surface. Also described is the prodigious power of brain and spinal cord regeneration and discoveries from lens regeneration, all of which reveal how important salamanders have been as research models.
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Affiliation(s)
- Malcolm Maden
- Department of Biology & UF Genetics Institute, University of Florida, Gainesville, FL, USA.
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5
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Fu S, Peng C, Zeng YY, Qiu Y, Liu Y, Fei JF. Establishing an Efficient Electroporation-Based Method to Manipulate Target Gene Expression in the Axolotl Brain. Cell Transplant 2023; 32:9636897231200059. [PMID: 37724837 PMCID: PMC10510365 DOI: 10.1177/09636897231200059] [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: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023] Open
Abstract
The tetrapod salamander species axolotl (Ambystoma mexicanum) is capable of regenerating injured brain. For better understanding the mechanisms of brain regeneration, it is very necessary to establish a rapid and efficient gain-of-function and loss-of-function approaches to study gene function in the axolotl brain. Here, we establish and optimize an electroporation-based method to overexpress or knockout/knockdown target gene in ependymal glial cells (EGCs) in the axolotl telencephalon. By orientating the electrodes, we were able to achieve specific expression of EGFP in EGCs located in dorsal, ventral, medial, or lateral ventricular zones. We then studied the role of Cdc42 in brain regeneration by introducing Cdc42 into EGCs through electroporation, followed by brain injury. Our findings showed that overexpression of Cdc42 in EGCs did not significantly affect EGC proliferation and production of newly born neurons, but it disrupted their apical polarity, as indicated by the loss of the ZO-1 tight junction marker. This disruption led to a ventricular accumulation of newly born neurons, which are failed to migrate into the neuronal layer where they could mature, thus resulted in a delayed brain regeneration phenotype. Furthermore, when electroporating CAS9-gRNA protein complexes against TnC (Tenascin-C) into EGCs of the brain, we achieved an efficient knockdown of TnC. In the electroporation-targeted area, TnC expression is dramatically reduced at both mRNA and protein levels. Overall, this study established a rapid and efficient electroporation-based gene manipulation approach allowing for investigation of gene function in the process of axolotl brain regeneration.
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Affiliation(s)
- Sulei Fu
- Key Laboratory of Brain, Cognition and Education Science, Ministry of Education, Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Cheng Peng
- Key Laboratory of Brain, Cognition and Education Science, Ministry of Education, Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yan-Yun Zeng
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuanhui Qiu
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yanmei Liu
- Key Laboratory of Brain, Cognition and Education Science, Ministry of Education, Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, China
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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6
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Wang L, Zeng YY, Liu Y, Fei JF. Applying a Knock-In Strategy to Create Reporter-Tagged Knockout Alleles in Axolotls. Methods Mol Biol 2023; 2562:351-368. [PMID: 36272087 DOI: 10.1007/978-1-0716-2659-7_23] [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] [Indexed: 06/16/2023]
Abstract
Tetrapod species axolotls exhibit the powerful capacity to fully regenerate their tail and limbs upon injury, hence serving as an excellent model organism in regenerative biology research. Developing proper molecular and genetic tools in axolotls is an absolute necessity for deep dissection of tissue regeneration mechanisms. Previously, CRISPR-/Cas9-based knockout and targeted gene knock-in approaches have been established in axolotls, allowing genetically deciphering gene function, labeling, and tracing particular types of cells. Here, we further extend the CRISPR/Cas9 technology application and describe a method to create reporter-tagged knockout allele in axolotls. This method combines gene knockout and knock-in and achieves loss of function of a given gene and simultaneous labeling of cells expressing this particular gene, that allows identification, tracking of the "knocking out" cells. Our method offers a useful gene function analysis tool to the field of axolotl developmental and regenerative research.
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Affiliation(s)
- Liqun Wang
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Yan-Yun Zeng
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Yanmei Liu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China.
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
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7
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Lovely AM, Duerr TJ, Stein DF, Mun ET, Monaghan JR. Hybridization Chain Reaction Fluorescence In Situ Hybridization (HCR-FISH) in Ambystoma mexicanum Tissue. Methods Mol Biol 2023; 2562:109-122. [PMID: 36272070 PMCID: PMC10949069 DOI: 10.1007/978-1-0716-2659-7_6] [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] [Indexed: 02/12/2023]
Abstract
In situ hybridization is a standard procedure for visualizing mRNA transcripts in tissues. The recent adoption of fluorescent probes and new signal amplification methods have facilitated multiplexed RNA imaging in tissue sections and whole tissues. Here we present protocols for multiplexed hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) staining, imaging, cell segmentation, and mRNA quantification in regenerating axolotl tissue sections. We also present a protocol for whole-mount staining and imaging of developing axolotl limbs.
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Affiliation(s)
- Alex M Lovely
- Department of Biology, Northeastern University, Boston, MA, USA
- Northeastern University, Institute for Chemical Imaging of Living Systems, Boston, MA, USA
| | - Timothy J Duerr
- Department of Biology, Northeastern University, Boston, MA, USA
| | - David F Stein
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Evan T Mun
- Department of Biology, Northeastern University, Boston, MA, USA
| | - James R Monaghan
- Department of Biology, Northeastern University, Boston, MA, USA.
- Northeastern University, Institute for Chemical Imaging of Living Systems, Boston, MA, USA.
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8
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Tanaka EM. Now that We Got There, What Next? Methods Mol Biol 2023; 2562:471-479. [PMID: 36272095 DOI: 10.1007/978-1-0716-2659-7_31] [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] [Indexed: 06/16/2023]
Abstract
As seen in the protocols in this book, the opportunities to pursue work at the cellular and molecular work in salamanders have considerably broadened over the last years. The availability of genomic information and genome editing, and the possibility to image tissues live and other methods enhance the spectrum of biological questions accessible to all researchers. Here I provide a personal perspective on what I consider exciting future questions open for investigation.
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Affiliation(s)
- Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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9
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Bölük A, Yavuz M, Demircan T. Axolotl: A resourceful vertebrate model for regeneration and beyond. Dev Dyn 2022; 251:1914-1933. [PMID: 35906989 DOI: 10.1002/dvdy.520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 01/30/2023] Open
Abstract
The regenerative capacity varies significantly among the animal kingdom. Successful regeneration program in some animals results in the functional restoration of tissues and lost structures. Among the highly regenerative animals, axolotl provides multiple experimental advantages with its many extraordinary characteristics. It has been positioned as a regeneration model organism due to its exceptional renewal capacity, including the internal organs, central nervous system, and appendages, in a scar-free manner. In addition to this unique regeneration ability, the observed low cancer incidence, its resistance to carcinogens, and the reversing effect of its cell extract on neoplasms strongly suggest its usability in cancer research. Axolotl's longevity and efficient utilization of several anti-aging mechanisms underline its potential to be employed in aging studies.
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Affiliation(s)
- Aydın Bölük
- School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Mervenur Yavuz
- Institute of Health Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Turan Demircan
- Department of Medical Biology, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
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10
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Shibata Y, Suzuki M, Hirose N, Takayama A, Sanbo C, Inoue T, Umesono Y, Agata K, Ueno N, Suzuki KIT, Mochii M. CRISPR/Cas9-based simple transgenesis in Xenopus laevis. Dev Biol 2022; 489:76-83. [PMID: 35690103 DOI: 10.1016/j.ydbio.2022.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
Transgenic techniques have greatly increased our understanding of the transcriptional regulation of target genes through live reporter imaging, as well as the spatiotemporal function of a gene using loss- and gain-of-function constructs. In Xenopus species, two well-established transgenic methods, restriction enzyme-mediated integration and I-SceI meganuclease-mediated transgenesis, have been used to generate transgenic animals. However, donor plasmids are randomly integrated into the Xenopus genome in both methods. Here, we established a new and simple targeted transgenesis technique based on CRISPR/Cas9 in Xenopus laevis. In this method, Cas9 ribonucleoprotein (RNP) targeting a putative harbor site (the transforming growth factor beta receptor 2-like (tgfbr2l) locus) and a preset donor plasmid DNA were co-injected into the one-cell stage embryos of X. laevis. Approximately 10% of faithful reporter expression was detected in F0 crispants in a promoter/enhancer-specific manner. Importantly, efficient germline transmission and stable transgene expression were observed in the F1 offspring. The simplicity of this method only required preparation of a donor vector containing the tgfbr2l genome fragment and Cas9 RNP targeting this site, which are common experimental procedures used in Xenopus laboratories. Our improved technique allows the simple generation of transgenic X. laevis, so is expected to become a powerful tool for reporter assay and gene function analysis.
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Affiliation(s)
- Yuki Shibata
- Center for the Development of New Model Organisms, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Miyuki Suzuki
- Laboratory for Biothermology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Nao Hirose
- Department of Life Science, Graduate School of Science, University of Hyogo, Akou-gun, Hyogo, Japan
| | - Ayuko Takayama
- Center for the Development of New Model Organisms, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Chiaki Sanbo
- Center for the Development of New Model Organisms, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Takeshi Inoue
- Division of Adaptation Physiology, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Yoshihiko Umesono
- Department of Life Science, Graduate School of Science, University of Hyogo, Akou-gun, Hyogo, Japan
| | - Kiyokazu Agata
- Laboratory of Regeneration Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Naoto Ueno
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Ken-Ichi T Suzuki
- Center for the Development of New Model Organisms, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
| | - Makoto Mochii
- Department of Life Science, Graduate School of Science, University of Hyogo, Akou-gun, Hyogo, Japan.
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11
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Adamson CJ, Morrison-Welch N, Rogers CD. The amazing and anomalous axolotls as scientific models. Dev Dyn 2022; 251:922-933. [PMID: 35322911 PMCID: PMC9536427 DOI: 10.1002/dvdy.470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 11/05/2022] Open
Abstract
Ambystoma mexicanum (axolotl) embryos and juveniles have been used as model organisms for developmental and regenerative research for many years. This neotenic aquatic species maintains the unique capability to regenerate most, if not all, of its tissues well into adulthood. With large externally developing embryos, axolotls were one of the original model species for developmental biology. However, increased access to, and use of, organisms with sequenced and annotated genomes, such as Xenopus laevis and tropicalis and Danio rerio, reduced the prevalence of axolotls as models in embryogenesis studies. Recent sequencing of the large axolotl genome opens up new possibilities for defining the recipes that drive the formation and regeneration of tissues like the limbs and spinal cord. However, to decode the large Ambystoma mexicanum genome will take a herculean effort, community resources, and the development of novel techniques. Here, we provide an updated axolotl-staging chart ranging from 1-cell stage to immature adult paired with a perspective on both historical and current axolotl research that spans from their use in early studies of development to the recent cutting-edge research, employment of transgenesis, high resolution imaging, and study of mechanisms deployed in regeneration. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Carly J Adamson
- Department of Anatomy, Physiology, and Cell Biology, UC Davis School of Veterinary Medicine, 1089 Veterinary Medicine Drive, Davis, CA
| | | | - Crystal D Rogers
- Department of Anatomy, Physiology, and Cell Biology, UC Davis School of Veterinary Medicine, 1089 Veterinary Medicine Drive, Davis, CA
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12
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Takeuchi T, Matsubara H, Minamitani F, Satoh Y, Tozawa S, Moriyama T, Maruyama K, Suzuki KIT, Shigenobu S, Inoue T, Tamura K, Agata K, Hayashi T. Newt Hoxa13 has an essential and predominant role in digit formation during development and regeneration. Development 2022; 149:274659. [DOI: 10.1242/dev.200282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/21/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The 5′Hox genes play crucial roles in limb development and specify regions in the proximal-distal axis of limbs. However, there is no direct genetic evidence that Hox genes are essential for limb development in non-mammalian tetrapods or for limb regeneration. Here, we produced single to quadruple Hox13 paralog mutants using the CRISPR/Cas9 system in newts (Pleurodeles waltl), which have strong regenerative capacities, and also produced germline mutants. We show that Hox13 genes are essential for digit formation in development, as in mice. In addition, Hoxa13 has a predominant role in digit formation, unlike in mice. The predominance is probably due to the restricted expression pattern of Hoxd13 in limb buds and the strong dependence of Hoxd13 expression on Hoxa13. Finally, we demonstrate that Hox13 genes are also necessary for digit formation in limb regeneration. Our findings reveal that the general function of Hox13 genes is conserved between limb development and regeneration, and across taxa. The predominance of Hoxa13 function both in newt limbs and fish fins, but not in mouse limbs, suggests a potential contribution of Hoxa13 function in fin-to-limb transition.
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Affiliation(s)
- Takashi Takeuchi
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Haruka Matsubara
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Fumina Minamitani
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Yukio Satoh
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Sayo Tozawa
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Tomoki Moriyama
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Kohei Maruyama
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Ken-ichi T. Suzuki
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Gakushuin University, Toyoshima-Ku, Tokyo 171-8588, Japan
| | - Koji Tamura
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Kiyokazu Agata
- Laboratory of Regeneration Biology, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
- Department of Life Science, Faculty of Science, Gakushuin University, Toyoshima-Ku, Tokyo 171-8588, Japan
| | - Toshinori Hayashi
- Division of Developmental Biology, School of Life Sciences, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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13
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Abstract
The salamander Ambystoma mexicanum, commonly called "the axolotl" has a long, illustrious history as a model organism, perhaps with one of the longest track records as a laboratory-bred vertebrate, yet it also holds a prominent place among the emerging model organisms. Or rather it is by now an "emerged" model organism, boasting a full cohort molecular genetic tools that allows an expanding community of researchers in the field to explore the remarkable traits of this animal including regeneration, at cellular and molecular precision-which had been a dream for researchers over the years. This chapter describes the journey to this status, that could be helpful for those developing their respective animal or plant models.
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Affiliation(s)
- Karen Echeverri
- Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Jifeng Fei
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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14
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Javaid N, Choi S. CRISPR/Cas System and Factors Affecting Its Precision and Efficiency. Front Cell Dev Biol 2021; 9:761709. [PMID: 34901007 PMCID: PMC8652214 DOI: 10.3389/fcell.2021.761709] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
The diverse applications of genetically modified cells and organisms require more precise and efficient genome-editing tool such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas). The CRISPR/Cas system was originally discovered in bacteria as a part of adaptive-immune system with multiple types. Its engineered versions involve multiple host DNA-repair pathways in order to perform genome editing in host cells. However, it is still challenging to get maximum genome-editing efficiency with fewer or no off-targets. Here, we focused on factors affecting the genome-editing efficiency and precision of CRISPR/Cas system along with its defense-mechanism, orthologues, and applications.
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Affiliation(s)
- Nasir Javaid
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
- S&K Therapeutics, Ajou University Campus Plaza, Suwon, South Korea
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15
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Tilley L, Papadopoulos SC, Pende M, Fei JF, Murawala P. The use of transgenics in the laboratory axolotl. Dev Dyn 2021; 251:942-956. [PMID: 33949035 DOI: 10.1002/dvdy.357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/10/2021] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
The ability to generate transgenic animals sparked a wave of research committed to implementing such technology in a wide variety of model organisms. Building a solid base of ubiquitous and tissue-specific reporter lines has set the stage for later interrogations of individual cells or genetic elements. Compared to other widely used model organisms such as mice, zebrafish and fruit flies, there are only a few transgenic lines available in the laboratory axolotl (Ambystoma mexicanum), although their number is steadily expanding. In this review, we discuss a brief history of the transgenic methodologies in axolotl and their advantages and disadvantages. Next, we discuss available transgenic lines and insights we have been able to glean from them. Finally, we list challenges when developing transgenic axolotl, and where further work is needed in order to improve their standing as both a developmental and regenerative model.
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Affiliation(s)
- Lydia Tilley
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, Maine, USA
| | - Sofia-Christina Papadopoulos
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, Maine, USA.,Clinic for Kidney and Hypertension Diseases, Hannover Medical School, Hannover, Germany
| | - Marko Pende
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, Maine, USA
| | - Ji-Feng Fei
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - Prayag Murawala
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, Maine, USA.,Clinic for Kidney and Hypertension Diseases, Hannover Medical School, Hannover, Germany
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16
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Nowoshilow S, Fei JF, Voss SR, Tanaka EM, Murawala P. Gene and transgenics nomenclature for the laboratory axolotl-Ambystoma mexicanum. Dev Dyn 2021; 251:913-921. [PMID: 33896069 DOI: 10.1002/dvdy.351] [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: 01/04/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 01/10/2023] Open
Abstract
The laboratory axolotl (Ambystoma mexicanum) is widely used in biological research. Recent advancements in genetic and molecular toolkits are greatly accelerating the work using axolotl, especially in the area of tissue regeneration. At this juncture, there is a critical need to establish gene and transgenic nomenclature to ensure uniformity in axolotl research. Here, we propose guidelines for genetic nomenclature when working with the axolotl.
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Affiliation(s)
- Sergej Nowoshilow
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Ji-Feng Fei
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou, China
| | - S Randal Voss
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA.,Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky, USA.,Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky, USA
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Prayag Murawala
- Mount Desert Island Biological laboratory (MDIBL), Salisbury Cove, USA.,Clinic for Kidney and Hypertension Diseases, Hannover Medical School, Hannover, Germany
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17
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Arenas Gómez CM, Echeverri K. Salamanders: The molecular basis of tissue regeneration and its relevance to human disease. Curr Top Dev Biol 2021; 145:235-275. [PMID: 34074531 PMCID: PMC8186737 DOI: 10.1016/bs.ctdb.2020.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Salamanders are recognized for their ability to regenerate a broad range of tissues. They have also have been used for hundreds of years for classical developmental biology studies because of their large accessible embryos. The range of tissues these animals can regenerate is fascinating, from full limbs to parts of the brain or heart, a potential that is missing in humans. Many promising research efforts are working to decipher the molecular blueprints shared across the organisms that naturally have the capacity to regenerate different tissues and organs. Salamanders are an excellent example of a vertebrate that can functionally regenerate a wide range of tissue types. In this review, we outline some of the significant insights that have been made that are aiding in understanding the cellular and molecular mechanisms of tissue regeneration in salamanders and discuss why salamanders are a worthy model in which to study regenerative biology and how this may benefit research fields like regenerative medicine to develop therapies for humans in the future.
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Affiliation(s)
- Claudia Marcela Arenas Gómez
- Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, University of Chicago, Woods Hole, MA, United States
| | - Karen Echeverri
- Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, University of Chicago, Woods Hole, MA, United States.
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18
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Dwaraka VB, Voss SR. Towards comparative analyses of salamander limb regeneration. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:129-144. [PMID: 31584252 PMCID: PMC8908358 DOI: 10.1002/jez.b.22902] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/13/2019] [Accepted: 08/31/2019] [Indexed: 08/29/2023]
Abstract
Among tetrapods, only salamanders can regenerate their limbs and tails throughout life. This amazing regenerative ability has attracted the attention of scientists for hundreds of years. Now that large, salamander genomes are beginning to be sequenced for the first time, omics tools and approaches can be used to integrate new perspectives into the study of tissue regeneration. Here we argue the need to move beyond the primary salamander models to investigate regeneration in other species. Salamanders at first glance come across as a phylogenetically conservative group that has not diverged greatly from their ancestors. While salamanders do present ancestral characteristics of basal tetrapods, including the ability to regenerate limbs, data from fossils and data from studies that have tested for species differences suggest there may be considerable variation in how salamanders develop and regenerate their limbs. We review the case for expanded studies of salamander tissue regeneration and identify questions and approaches that are most likely to reveal commonalities and differences in regeneration among species. We also address challenges that confront such an initiative, some of which are regulatory and not scientific. The time is right to gain evolutionary perspective about mechanisms of tissue regeneration from comparative studies of salamander species.
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Affiliation(s)
- Varun B. Dwaraka
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - S. Randal Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky
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19
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Daponte V, Tylzanowski P, Forlino A. Appendage Regeneration in Vertebrates: What Makes This Possible? Cells 2021; 10:cells10020242. [PMID: 33513779 PMCID: PMC7911911 DOI: 10.3390/cells10020242] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/26/2022] Open
Abstract
The ability to regenerate amputated or injured tissues and organs is a fascinating property shared by several invertebrates and, interestingly, some vertebrates. The mechanism of evolutionary loss of regeneration in mammals is not understood, yet from the biomedical and clinical point of view, it would be very beneficial to be able, at least partially, to restore that capability. The current availability of new experimental tools, facilitating the comparative study of models with high regenerative ability, provides a powerful instrument to unveil what is needed for a successful regeneration. The present review provides an updated overview of multiple aspects of appendage regeneration in three vertebrates: lizard, salamander, and zebrafish. The deep investigation of this process points to common mechanisms, including the relevance of Wnt/β-catenin and FGF signaling for the restoration of a functional appendage. We discuss the formation and cellular origin of the blastema and the identification of epigenetic and cellular changes and molecular pathways shared by vertebrates capable of regeneration. Understanding the similarities, being aware of the differences of the processes, during lizard, salamander, and zebrafish regeneration can provide a useful guide for supporting effective regenerative strategies in mammals.
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Affiliation(s)
- Valentina Daponte
- Biochemistry Unit, Department of Molecular Medicine, University of Pavia, via Taramelli 3/B, 27100 Pavia, Italy;
| | - Przemko Tylzanowski
- Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, University of Leuven, 3000 Leuven, Belgium;
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Antonella Forlino
- Biochemistry Unit, Department of Molecular Medicine, University of Pavia, via Taramelli 3/B, 27100 Pavia, Italy;
- Correspondence: ; Tel.: +39-0382-987235
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20
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Rozenblit F, Gollisch T. What the salamander eye has been telling the vision scientist's brain. Semin Cell Dev Biol 2020; 106:61-71. [PMID: 32359891 PMCID: PMC7493835 DOI: 10.1016/j.semcdb.2020.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 12/30/2022]
Abstract
Salamanders have been habitual residents of research laboratories for more than a century, and their history in science is tightly interwoven with vision research. Nevertheless, many vision scientists - even those working with salamanders - may be unaware of how much our knowledge about vision, and particularly the retina, has been shaped by studying salamanders. In this review, we take a tour through the salamander history in vision science, highlighting the main contributions of salamanders to our understanding of the vertebrate retina. We further point out specificities of the salamander visual system and discuss the perspectives of this animal system for future vision research.
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Affiliation(s)
- Fernando Rozenblit
- Department of Ophthalmology, University Medical Center Göttingen, 37073, Göttingen, Germany; Bernstein Center for Computational Neuroscience Göttingen, 37077, Göttingen, Germany
| | - Tim Gollisch
- Department of Ophthalmology, University Medical Center Göttingen, 37073, Göttingen, Germany; Bernstein Center for Computational Neuroscience Göttingen, 37077, Göttingen, Germany.
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21
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Square TA, Jandzik D, Massey JL, Romášek M, Stein HP, Hansen AW, Purkayastha A, Cattell MV, Medeiros DM. Evolution of the endothelin pathway drove neural crest cell diversification. Nature 2020; 585:563-568. [PMID: 32939088 DOI: 10.1038/s41586-020-2720-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Neural crest cells (NCCs) are migratory, multipotent embryonic cells that are unique to vertebrates and form an array of clade-defining adult features. The evolution of NCCs has been linked to various genomic events, including the evolution of new gene-regulatory networks1,2, the de novo evolution of genes3 and the proliferation of paralogous genes during genome-wide duplication events4. However, conclusive functional evidence linking new and/or duplicated genes to NCC evolution is lacking. Endothelin ligands (Edns) and endothelin receptors (Ednrs) are unique to vertebrates3,5,6, and regulate multiple aspects of NCC development in jawed vertebrates7-10. Here, to test whether the evolution of Edn signalling was a driver of NCC evolution, we used CRISPR-Cas9 mutagenesis11 to disrupt edn, ednr and dlx genes in the sea lamprey, Petromyzon marinus. Lampreys are jawless fishes that last shared a common ancestor with modern jawed vertebrates around 500 million years ago12. Thus, comparisons between lampreys and gnathostomes can identify deeply conserved and evolutionarily flexible features of vertebrate development. Using the frog Xenopus laevis to expand gnathostome phylogenetic representation and facilitate side-by-side analyses, we identify ancient and lineage-specific roles for Edn signalling. These findings suggest that Edn signalling was activated in NCCs before duplication of the vertebrate genome. Then, after one or more genome-wide duplications in the vertebrate stem, paralogous Edn pathways functionally diverged, resulting in NCC subpopulations with different Edn signalling requirements. We posit that this new developmental modularity facilitated the independent evolution of NCC derivatives in stem vertebrates. Consistent with this, differences in Edn pathway targets are associated with differences in the oropharyngeal skeleton and autonomic nervous system of lampreys and modern gnathostomes. In summary, our work provides functional genetic evidence linking the origin and duplication of new vertebrate genes with the stepwise evolution of a defining vertebrate novelty.
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Affiliation(s)
- Tyler A Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA. .,Department of Molecular and Cellular Biology, University of California, Berkeley, CA, USA.
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA. .,Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia. .,Department of Zoology, Charles University in Prague, Prague, Czech Republic.
| | - James L Massey
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Marek Romášek
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Gymnázium Jiřího Wolkera, Prostějov, Czech Republic
| | - Haley P Stein
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Andrew W Hansen
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Amrita Purkayastha
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Maria V Cattell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,Department of Biology, Metropolitan State University, Denver, CO, USA
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
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22
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Rasys AM, Park S, Ball RE, Alcala AJ, Lauderdale JD, Menke DB. CRISPR-Cas9 Gene Editing in Lizards through Microinjection of Unfertilized Oocytes. Cell Rep 2020; 28:2288-2292.e3. [PMID: 31461646 DOI: 10.1016/j.celrep.2019.07.089] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/28/2019] [Accepted: 07/24/2019] [Indexed: 12/29/2022] Open
Abstract
CRISPR-Cas9-mediated gene editing has enabled the direct manipulation of gene function in many species. However, the reproductive biology of reptiles presents unique barriers for the use of this technology, and there are no reptiles with effective methods for targeted mutagenesis. Here, we demonstrate that the microinjection of immature oocytes within the ovaries of Anolis sagrei females enables the production of CRISPR-Cas9-induced mutations. This method is capable of producing F0 embryos and hatchlings with monoallelic or biallelic mutations. We demonstrate that these mutations can be transmitted through the germline to establish genetically modified strains of lizards. Direct tests of gene function can now be performed in Anolis lizards, an important model for studies of reptile evolution and development.
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Affiliation(s)
- Ashley M Rasys
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sungdae Park
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Rebecca E Ball
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Aaron J Alcala
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - James D Lauderdale
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA; Neuroscience Division of the Biomedical Health Sciences Institute, University of Georgia, Athens, GA 30602, USA
| | - Douglas B Menke
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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23
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Quoseena M, Vuppaladadium S, Hussain S, Banu S, Bharathi S, Idris MM. Functional role of annexins in zebrafish caudal fin regeneration – A gene knockdown approach in regenerating tissue. Biochimie 2020; 175:125-131. [DOI: 10.1016/j.biochi.2020.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/18/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022]
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24
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Kim BH, Zhang G. Generating Stable Knockout Zebrafish Lines by Deleting Large Chromosomal Fragments Using Multiple gRNAs. G3 (BETHESDA, MD.) 2020; 10:1029-1037. [PMID: 31915253 PMCID: PMC7056962 DOI: 10.1534/g3.119.401035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/06/2020] [Indexed: 12/28/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) and Cas9 (CRISPR associated protein 9) system has been successfully adopted as a versatile genetic tool for functional manipulations, due to its convenience and effectiveness. Genetics lesions induced by single guide RNA (gRNA) are usually small indel (insertion-deletion) DNA mutations. The impact of this type of CRISPR-induced DNA mutation on the coded mRNA transcription processing and protein translation can be complex. Unexpected or unknown transcripts, generated through alternative splicing, may impede the generation of successful loss-of-function mutants. To create null or null-like loss-of-function mutant zebrafish, we employed simultaneous multiple gRNA injection into single-cell stage embryos. We demonstrated that DNA composed of multiple exons, up to 78kb in length, can be deleted in the smarca2 gene locus. Additionally, two different genes (rnf185 and rnf215) were successfully mutated in F1 fish with multiple exon deletions using this multiplex gRNA injection strategy. We expect this approach will be useful for knock-out studies in zebrafish and other vertebrate organisms, especially when the phenotype of a single gRNA-induced mutant is not clear.
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Affiliation(s)
| | - GuangJun Zhang
- Department of Comparative Pathobiology,
- Purdue University Center for Cancer Research
- Purdue Institute for Inflammation, Immunology and Infectious Diseases (PI4D), and
- Purdue Institute for Integrative Neuroscience; Purdue University, West Lafayette, Indiana 47907
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25
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Flowers GP, Crews CM. Remembering where we are: Positional information in salamander limb regeneration. Dev Dyn 2020; 249:465-482. [PMID: 32124513 DOI: 10.1002/dvdy.167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/26/2022] Open
Abstract
Fifty years ago, Lewis Wolpert defined an important question in developmental biology: how are cell fates determined by the positions of cells within a system? He proposed that cells retain positional values as if they lie within a coordinate system and that the interpretation of these values produces patterns in development. He referred to this concept as positional information. Though initially controversial, this concept of positional information has proven to be profoundly influential in developmental biology. One area in which the influence of Wolpert's theoretical work can be clearly demonstrated is the study of limb regeneration in salamanders. Here, we review the work in limb regeneration leading up to Wolpert defining the concept of positional information and how his theory has guided regeneration research over the subsequent 50 years.
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Affiliation(s)
- Grant Parker Flowers
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA.,Department of Chemistry, Yale University, New Haven, Connecticut, USA.,Department of Pharmacology, Yale University, New Haven, Connecticut, USA
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26
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Sanor LD, Flowers GP, Crews CM. Multiplex CRISPR/Cas screen in regenerating haploid limbs of chimeric Axolotls. eLife 2020; 9:48511. [PMID: 31989926 PMCID: PMC6986871 DOI: 10.7554/elife.48511] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 01/06/2020] [Indexed: 01/04/2023] Open
Abstract
Axolotls and other salamanders can regenerate entire limbs after amputation as adults, and much recent effort has sought to identify the molecular programs controlling this process. While targeted mutagenesis approaches like CRISPR/Cas9 now permit gene-level investigation of these mechanisms, genetic screening in the axolotl requires an extensive commitment of time and space. Previously, we quantified CRISPR/Cas9-generated mutations in the limbs of mosaic mutant axolotls before and after regeneration and found that the regenerated limb is a highfidelity replicate of the original limb (Flowers et al. 2017). Here, we circumvent aforementioned genetic screening limitations and present methods for a multiplex CRISPR/Cas9 haploid screen in chimeric axolotls (MuCHaChA), which is a novel platform for haploid genetic screening in animals to identify genes essential for limb regeneration.
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Affiliation(s)
- Lucas D Sanor
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, United States
| | - Grant Parker Flowers
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, United States
| | - Craig M Crews
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, United States.,Department of Chemistry, Yale University, New Haven, United States.,Department of Pharmacology, Yale University, New Haven, United States
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27
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Sibai M, Parlayan C, Tuğlu P, Öztürk G, Demircan T. Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues. Sci Rep 2019; 9:20280. [PMID: 31889169 PMCID: PMC6937273 DOI: 10.1038/s41598-019-56829-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/09/2019] [Indexed: 01/08/2023] Open
Abstract
Axolotl (Ambystoma mexicanum) is a urodele amphibian endowed with remarkable regenerative capacities manifested in scarless wound healing and restoration of amputated limbs, which makes it a powerful experimental model for regenerative biology and medicine. Previous studies have utilized microarrays and RNA-Seq technologies for detecting differentially expressed (DE) genes in different phases of the axolotl limb regeneration. However, sufficient consistency may be lacking due to statistical limitations arising from intra-laboratory analyses. This study aims to bridge such gaps by performing an integrative analysis of publicly available microarray and RNA-Seq data from axolotl limb samples having comparable study designs using the “merging” method. A total of 351 genes were found DE in regenerative samples compared to the control in data of both technologies, showing an adjusted p-value < 0.01 and log fold change magnitudes >1. Downstream analyses illustrated consistent correlations of the directionality of DE genes within and between data of both technologies, as well as concordance with the literature on regeneration related biological processes. qRT-PCR analysis validated the observed expression level differences of five of the top DE genes. Future studies may benefit from the utilized concept and approach for enhanced statistical power and robust discovery of biomarkers of regeneration.
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Affiliation(s)
- Mustafa Sibai
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Cüneyd Parlayan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey. .,Department of Biomedical Engineering, Faculty of Engineering, İstanbul Medipol University, Istanbul, Turkey.
| | - Pelin Tuğlu
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey.,Department of Physiology, International School of Medicine, İstanbul Medipol University, Istanbul, Turkey
| | - Turan Demircan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey. .,Department of Medical Biology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey.
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28
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Vieira WA, Wells KM, McCusker CD. Advancements to the Axolotl Model for Regeneration and Aging. Gerontology 2019; 66:212-222. [PMID: 31779024 DOI: 10.1159/000504294] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
Loss of regenerative capacity is a normal part of aging. However, some organisms, such as the Mexican axolotl, retain striking regenerative capacity throughout their lives. Moreover, the development of age-related diseases is rare in this organism. In this review, we will explore how axolotls are used as a model system to study regenerative processes, the exciting new technological advancements now available for this model, and how we can apply the lessons we learn from studying regeneration in the axolotl to understand, and potentially treat, age-related decline in humans.
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Affiliation(s)
- Warren A Vieira
- Department of Biology, University of Massachusetts, Boston, Massachusetts, USA
| | - Kaylee M Wells
- Department of Biology, University of Massachusetts, Boston, Massachusetts, USA
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29
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Efficient Gene Disruption via Base Editing Induced Stop in Newt Pleurodeles waltl. Genes (Basel) 2019; 10:genes10110837. [PMID: 31652881 PMCID: PMC6895984 DOI: 10.3390/genes10110837] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/16/2019] [Accepted: 10/21/2019] [Indexed: 11/17/2022] Open
Abstract
Loss-of-function approaches provide strong evidence for determining the role of particular genes. The prevalent CRISPR/Cas9 technique is widely used to disrupt target gene with uncontrolled non-homologous end joining after the double strand breaks, which results in mosaicism and multiple genotypes in the founders. In animal models with long generation time such as the salamanders, producing homozygous offspring mutants would be rather labor intensive and time consuming. Here we utilized the base editing technique to create the loss-of-function F0 mutants without the random indels. As a proof of principle, we successfully introduced premature stop codons into the tyrosinase locus and produced the albino phenotype in the newts (Pleurodeles waltl). We further demonstrated that the knockout efficiency could be greatly improved by using multiplex sgRNAs target the same gene. The F0 mutated animals showed fully loss-of-function by both genotyping and phenotyping analysis, which could enable direct functional analysis in the founders and avoid sophisticated breeding. This study not only presented the high efficiency of single base editing in a gigantic animal genome (>20 G), but also provided new tools for interrogating gene function in other salamander species.
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30
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Mehta AS, Singh A. Insights into regeneration tool box: An animal model approach. Dev Biol 2019; 453:111-129. [PMID: 30986388 PMCID: PMC6684456 DOI: 10.1016/j.ydbio.2019.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022]
Abstract
For ages, regeneration has intrigued countless biologists, clinicians, and biomedical engineers. In recent years, significant progress made in identification and characterization of a regeneration tool kit has helped the scientific community to understand the mechanism(s) involved in regeneration across animal kingdom. These mechanistic insights revealed that evolutionarily conserved pathways like Wnt, Notch, Hedgehog, BMP, and JAK/STAT are involved in regeneration. Furthermore, advancement in high throughput screening approaches like transcriptomic analysis followed by proteomic validations have discovered many novel genes, and regeneration specific enhancers that are specific to highly regenerative species like Hydra, Planaria, Newts, and Zebrafish. Since genetic machinery is highly conserved across the animal kingdom, it is possible to engineer these genes and regeneration specific enhancers in species with limited regeneration properties like Drosophila, and mammals. Since these models are highly versatile and genetically tractable, cross-species comparative studies can generate mechanistic insights in regeneration for animals with long gestation periods e.g. Newts. In addition, it will allow extrapolation of regenerative capabilities from highly regenerative species to animals with low regeneration potential, e.g. mammals. In future, these studies, along with advancement in tissue engineering applications, can have strong implications in the field of regenerative medicine and stem cell biology.
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Affiliation(s)
- Abijeet S Mehta
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA; Premedical Program, University of Dayton, Dayton, OH, 45469, USA; Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, 45469, USA; The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, 45469, USA; Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA.
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31
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Attenuation of Inherited and Acquired Retinal Degeneration Progression with Gene-based Techniques. Mol Diagn Ther 2019; 23:113-120. [PMID: 30569401 DOI: 10.1007/s40291-018-0377-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Inherited retinal dystrophies cause progressive vision loss and are major contributors to blindness worldwide. Advances in gene therapy have brought molecular approaches into the realm of clinical trials for these incurable illnesses. Select phase I, II and III trials are complete and provide some promise in terms of functional outcomes and safety, although questions do remain over the durability of their effects and the prevalence of inflammatory reactions. This article reviews gene therapy as it can be applied to inherited retinal dystrophies, provides an update of results from recent clinical trials, and discusses the future prospects of gene therapy and genome surgery.
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32
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Martinez-Redondo P, Izpisua Belmonte JC. Tailored chromatin modulation to promote tissue regeneration. Semin Cell Dev Biol 2019; 97:3-15. [PMID: 31028854 DOI: 10.1016/j.semcdb.2019.04.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 12/16/2022]
Abstract
Epigenetic regulation of gene expression is fundamental in the maintenance of cellular identity and the regulation of cellular plasticity during tissue repair. In fact, epigenetic modulation is associated with the processes of cellular de-differentiation, proliferation, and re-differentiation that takes place during tissue regeneration. In here we explore the epigenetic events that coordinate tissue repair in lower vertebrates with high regenerative capacity, and in mammalian adult stem cells, which are responsible for the homeostasis maintenance of most of our tissues. Finally we summarize promising CRISPR-based editing technologies developed during the last years, which look as promising tools to not only study but also promote specific events during tissue regeneration.
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Affiliation(s)
- Paloma Martinez-Redondo
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, United States
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, United States.
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33
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Zimmer AM, Pan YK, Chandrapalan T, Kwong RWM, Perry SF. Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing? ACTA ACUST UNITED AC 2019; 222:222/7/jeb175737. [PMID: 30948498 DOI: 10.1242/jeb.175737] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Loss-of-function technologies, such as morpholino- and RNAi-mediated gene knockdown, and TALEN- and CRISPR/Cas9-mediated gene knockout, are widely used to investigate gene function and its physiological significance. Here, we provide a general overview of the various knockdown and knockout technologies commonly used in comparative physiology and discuss the merits and drawbacks of these technologies with a particular focus on research conducted in zebrafish. Despite their widespread use, there is an ongoing debate surrounding the use of knockdown versus knockout approaches and their potential off-target effects. This debate is primarily fueled by the observations that, in some studies, knockout mutants exhibit phenotypes different from those observed in response to knockdown using morpholinos or RNAi. We discuss the current debate and focus on the discrepancies between knockdown and knockout phenotypes, providing literature and primary data to show that the different phenotypes are not necessarily a direct result of the off-target effects of the knockdown agents used. Nevertheless, given the recent evidence of some knockdown phenotypes being recapitulated in knockout mutants lacking the morpholino or RNAi target, we stress that results of knockdown experiments need to be interpreted with caution. We ultimately argue that knockdown experiments should not be discontinued if proper control experiments are performed, and that with careful interpretation, knockdown approaches remain useful to complement the limitations of knockout studies (e.g. lethality of knockout and compensatory responses).
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Affiliation(s)
- Alex M Zimmer
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Yihang K Pan
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | | | - Steve F Perry
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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34
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Sabin KZ, Jiang P, Gearhart MD, Stewart R, Echeverri K. AP-1 cFos/JunB/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration. Commun Biol 2019; 2:91. [PMID: 30854483 PMCID: PMC6403268 DOI: 10.1038/s42003-019-0335-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/04/2019] [Indexed: 12/30/2022] Open
Abstract
Salamanders have the remarkable ability to functionally regenerate after spinal cord transection. In response to injury, GFAP+ glial cells in the axolotl spinal cord proliferate and migrate to replace the missing neural tube and create a permissive environment for axon regeneration. Molecular pathways that regulate the pro-regenerative axolotl glial cell response are poorly understood. Here we show axolotl glial cells up-regulate AP-1cFos/JunB after injury, which promotes a pro-regenerative glial cell response. Injury induced upregulation of miR-200a in glial cells supresses c-Jun expression in these cells. Inhibition of miR-200a during regeneration causes defects in axonal regrowth and transcriptomic analysis revealed that miR-200a inhibition leads to differential regulation of genes involved with reactive gliosis, the glial scar, extracellular matrix remodeling and axon guidance. This work identifies a unique role for miR-200a in inhibiting reactive gliosis in axolotl glial cells during spinal cord regeneration. Keith Sabin et al. showed that upregulation of the AP-1 complex, composed of c-Fos and JunB, in the axolotl spinal cord promotes a pro-regenerative glial cell response. This response is impaired by inhibition of miR-200a; suggesting an important role for this microRNA in axolotl spinal cord regeneration.
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Affiliation(s)
- Keith Z Sabin
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA.,Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, 02543, MA, USA
| | - Peng Jiang
- Morgridge Institute for Research, Madison, 53715, WI, USA
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, 53715, WI, USA
| | - Karen Echeverri
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA. .,Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, 02543, MA, USA.
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35
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Freitas PD, Yandulskaya AS, Monaghan JR. Spinal Cord Regeneration in Amphibians: A Historical Perspective. Dev Neurobiol 2019; 79:437-452. [PMID: 30725532 DOI: 10.1002/dneu.22669] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/11/2022]
Abstract
In some vertebrates, a grave injury to the central nervous system (CNS) results in functional restoration, rather than in permanent incapacitation. Understanding how these animals mount a regenerative response by activating resident CNS stem cell populations is of critical importance in regenerative biology. Amphibians are of a particular interest in the field because the regenerative ability is present throughout life in urodele species, but in anuran species it is lost during development. Studying amphibians, who transition from a regenerative to a nonregenerative state, could give insight into the loss of ability to recover from CNS damage in mammals. Here, we highlight the current knowledge of spinal cord regeneration across vertebrates and identify commonalities and differences in spinal cord regeneration between amphibians.
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Affiliation(s)
- Polina D Freitas
- Department of Biology, Northeastern University, 360 Huntington Ave., 134 Mugar Hall, Boston, Massachusetts, 02115
| | - Anastasia S Yandulskaya
- Department of Biology, Northeastern University, 360 Huntington Ave., 134 Mugar Hall, Boston, Massachusetts, 02115
| | - James R Monaghan
- Department of Biology, Northeastern University, 360 Huntington Ave., 134 Mugar Hall, Boston, Massachusetts, 02115
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36
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Baker CVH, Modrell MS. Insights into Electroreceptor Development and Evolution from Molecular Comparisons with Hair Cells. Integr Comp Biol 2019; 58:329-340. [PMID: 29846597 DOI: 10.1093/icb/icy037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The vertebrate lateral line system comprises a mechanosensory division, with neuromasts containing hair cells that detect local water movement ("distant touch"); and an electrosensory division, with electrosensory organs that detect the weak, low-frequency electric fields surrounding other animals in water (primarily used for hunting). The entire lateral line system was lost in the amniote lineage with the transition to fully terrestrial life; the electrosensory division was lost independently in several lineages, including the ancestors of frogs and of teleost fishes. (Electroreception with different characteristics subsequently evolved independently within two teleost lineages.) Recent gene expression studies in a non-teleost actinopterygian fish suggest that electroreceptor ribbon synapses employ the same transmission mechanisms as hair cell ribbon synapses, and show that developing electrosensory organs express transcription factors essential for hair cell development, including Atoh1 and Pou4f3. Previous hypotheses for electroreceptor evolution suggest either that electroreceptors and hair cells evolved independently in the vertebrate ancestor from a common ciliated secondary cell, or that electroreceptors evolved from hair cells. The close developmental and putative physiological similarities implied by the gene expression data support the latter hypothesis, i.e., that electroreceptors evolved in the vertebrate ancestor as a "sister cell-type" to lateral line hair cells.
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Affiliation(s)
- Clare V H Baker
- Department of Physiology, Development and Neuroscience, University of Cambridge, Anatomy Building, Downing Street, Cambridge CB2 3DY, UK
| | - Melinda S Modrell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Anatomy Building, Downing Street, Cambridge CB2 3DY, UK
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37
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Mokalled MH, Poss KD. A Regeneration Toolkit. Dev Cell 2019; 47:267-280. [PMID: 30399333 DOI: 10.1016/j.devcel.2018.10.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/13/2022]
Abstract
The ability of animals to replace injured body parts has been a subject of fascination for centuries. The emerging importance of regenerative medicine has reinvigorated investigations of innate tissue regeneration, and the development of powerful genetic tools has fueled discoveries into how tissue regeneration occurs. Here, we present an overview of the armamentarium employed to probe regeneration in vertebrates, highlighting areas where further methodology advancement will deepen mechanistic findings.
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Affiliation(s)
- Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Kenneth D Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Regeneration Next, Duke University, Durham, NC 27710, USA.
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38
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Miniscule differences between sex chromosomes in the giant genome of a salamander. Sci Rep 2018; 8:17882. [PMID: 30552368 PMCID: PMC6294749 DOI: 10.1038/s41598-018-36209-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/12/2018] [Indexed: 11/08/2022] Open
Abstract
In the Mexican axolotl (Ambystoma mexicanum), sex is determined by a single Mendelian factor, yet its sex chromosomes do not exhibit morphological differentiation typical of many vertebrate taxa that possess a single sex-determining locus. As sex chromosomes are theorized to differentiate rapidly, species with undifferentiated sex chromosomes provide the opportunity to reconstruct early events in sex chromosome evolution. Whole genome sequencing of 48 salamanders, targeted chromosome sequencing and in situ hybridization were used to identify the homomorphic sex chromosome that carries an A. mexicanum sex-determining factor and sequences that are present only on the W chromosome. Altogether, these sequences cover ~300 kb of validated female-specific (W chromosome) sequence, representing ~1/100,000th of the 32 Gb genome. Notably, a recent duplication of ATRX, a gene associated with mammalian sex-determining pathways, is one of few functional (non-repetitive) genes identified among these W-specific sequences. This duplicated gene (ATRW) was used to develop highly predictive markers for diagnosing sex and represents a strong candidate for a recently-acquired sex determining locus (or sexually antagonistic gene) in A. mexicanum.
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39
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Fei JF, Lou WPK, Knapp D, Murawala P, Gerber T, Taniguchi Y, Nowoshilow S, Khattak S, Tanaka EM. Application and optimization of CRISPR-Cas9-mediated genome engineering in axolotl (Ambystoma mexicanum). Nat Protoc 2018; 13:2908-2943. [PMID: 30429597 DOI: 10.1038/s41596-018-0071-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genomic manipulation is essential to the use of model organisms to understand development, regeneration and adult physiology. The axolotl (Ambystoma mexicanum), a type of salamander, exhibits an unparalleled regenerative capability in a spectrum of complex tissues and organs, and therefore serves as a powerful animal model for dissecting mechanisms of regeneration. We describe here an optimized stepwise protocol to create genetically modified axolotls using the CRISPR-Cas9 system. The protocol, which takes 7-8 weeks to complete, describes generation of targeted gene knockouts and knock-ins and includes site-specific integration of large targeting constructs. The direct use of purified CAS9-NLS (CAS9 containing a C-terminal nuclear localization signal) protein allows the prompt formation of guide RNA (gRNA)-CAS9-NLS ribonucleoprotein (RNP) complexes, which accelerates the creation of double-strand breaks (DSBs) at targeted genomic loci in single-cell-stage axolotl eggs. With this protocol, a substantial number of F0 individuals harboring a homozygous-type frameshift mutation can be obtained, allowing phenotype analysis in this generation. In the presence of targeting constructs, insertions of exogenous genes into targeted axolotl genomic loci can be achieved at efficiencies of up to 15% in a non-homologous end joining (NHEJ) manner. Our protocol bypasses the long generation time of axolotls and allows direct functional analysis in F0 genetically manipulated axolotls. This protocol can be potentially applied to other animal models, especially to organisms with a well-characterized transcriptome but lacking a well-characterized genome.
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Affiliation(s)
- Ji-Feng Fei
- Institute for Brain Research and Rehabilitation (IBRR), Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China.
| | - Wilson Pak-Kin Lou
- School of Life Sciences, South China Normal University, Guangzhou, China
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Dunja Knapp
- DFG Center for Regenerative Therapies, Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Prayag Murawala
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Tobias Gerber
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Yuka Taniguchi
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Sergej Nowoshilow
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Shahryar Khattak
- DFG Center for Regenerative Therapies, Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - Elly M Tanaka
- The Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
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40
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Suzuki M, Hayashi T, Inoue T, Agata K, Hirayama M, Suzuki M, Shigenobu S, Takeuchi T, Yamamoto T, Suzuki KIT. Cas9 ribonucleoprotein complex allows direct and rapid analysis of coding and noncoding regions of target genes in Pleurodeles waltl development and regeneration. Dev Biol 2018; 443:127-136. [DOI: 10.1016/j.ydbio.2018.09.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022]
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41
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Stocum DL. Nerves and Proliferation of Progenitor Cells in Limb Regeneration. Dev Neurobiol 2018; 79:468-478. [PMID: 30303627 DOI: 10.1002/dneu.22643] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/12/2018] [Accepted: 09/22/2018] [Indexed: 01/15/2023]
Abstract
Nerves, in conjunction with the apical epidermal cap (AEC), play an important role in the proliferation of the mesenchymal progenitor cells comprising the blastema of regenerating urodele amphibian limbs. Reinnervation after amputation requires factors supplied by the forming blastema, and neurotrophic factors must be present at or above a quantitative threshold for mitosis of the blastema cells. The AEC forms independently of nerves, but requires nerves to be maintained. Urodele limb buds are independent of nerves for regeneration, but innervation imposes a regenerative requirement for nerve factors on their cells as they differentiate. There are three main ideas on the functional relationship between nerves, AEC, and blastema cells: (1) nerves and AEC produce factors with different roles in maintaining progenitor status and mitosis; (2) the AEC produces the factors that promote blastema cell mitosis, but requires nerves to express them; (3) blastema cells, nerves, and AEC all produce the same factor(s) that additively attain the required threshold for mitosis.
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Affiliation(s)
- David L Stocum
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 W. Michigan St., Indianapolis, IN, 46202
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42
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Klaassen H, Wang Y, Adamski K, Rohner N, Kowalko JE. CRISPR mutagenesis confirms the role of oca2 in melanin pigmentation in Astyanax mexicanus. Dev Biol 2018; 441:313-318. [DOI: 10.1016/j.ydbio.2018.03.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 01/02/2023]
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43
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Evans T, Johnson AD, Loose M. Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence. Sci Rep 2018; 8:618. [PMID: 29330416 PMCID: PMC5766544 DOI: 10.1038/s41598-017-19128-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/19/2017] [Indexed: 11/09/2022] Open
Abstract
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence. These assemblies are then linked and refined to generate gene models including upstream and downstream genomic, and intronic, sequence. Our assemblies are validated by comparison with previously published axolotl bacterial artificial chromosome (BAC) sequences. Our analyses of axolotl intron length, intron-exon structure, repeat content and synteny provide novel insights into the genic structure of this model species. This resource will enable new experimental approaches in axolotl, such as ChIP-Seq and CRISPR and aid in future whole genome sequencing efforts. The assembled sequences and annotations presented here are freely available for download from https://tinyurl.com/y8gydc6n . The software pipeline is available from https://github.com/LooseLab/iterassemble .
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Affiliation(s)
- Teri Evans
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Andrew D Johnson
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
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44
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Abstract
Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
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45
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Flowers GP, Sanor LD, Crews CM. Lineage tracing of genome-edited alleles reveals high fidelity axolotl limb regeneration. eLife 2017; 6:25726. [PMID: 28917058 PMCID: PMC5621835 DOI: 10.7554/elife.25726] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 09/08/2017] [Indexed: 12/21/2022] Open
Abstract
Salamanders are unparalleled among tetrapods in their ability to regenerate many structures, including entire limbs, and the study of this ability may provide insights into human regenerative therapies. The complex structure of the limb poses challenges to the investigation of the cellular and molecular basis of its regeneration. Using CRISPR/Cas, we genetically labelled unique cell lineages within the developing axolotl embryo and tracked the frequency of each lineage within amputated and fully regenerated limbs. This allowed us, for the first time, to assess the contributions of multiple low frequency cell lineages to the regenerating limb at once. Our comparisons reveal that regenerated limbs are high fidelity replicas of the originals even after repeated amputations.
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Affiliation(s)
- Grant Parker Flowers
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Lucas D Sanor
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,Department of Chemistry, Yale University, New Haven, United States.,Department of Pharmacology, Yale University, New Haven, United States
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46
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Russell JJ, Theriot JA, Sood P, Marshall WF, Landweber LF, Fritz-Laylin L, Polka JK, Oliferenko S, Gerbich T, Gladfelter A, Umen J, Bezanilla M, Lancaster MA, He S, Gibson MC, Goldstein B, Tanaka EM, Hu CK, Brunet A. Non-model model organisms. BMC Biol 2017; 15:55. [PMID: 28662661 PMCID: PMC5492503 DOI: 10.1186/s12915-017-0391-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Model organisms are widely used in research as accessible and convenient systems to study a particular area or question in biology. Traditionally only a handful of organisms have been widely studied, but modern research tools are enabling researchers to extend the set of model organisms to include less-studied and more unusual systems. This Forum highlights a range of 'non-model model organisms' as emerging systems for tackling questions across the whole spectrum of biology (and beyond), the opportunities and challenges, and the outlook for the future.
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Affiliation(s)
- James J Russell
- Department of Biology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA
| | - Julie A Theriot
- Departments of Biochemistry and of Microbiology & Immunology, Howard Hughes Medical Institute Stanford University, Stanford, CA, 94305, USA.
| | - Pranidhi Sood
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA
| | - Wallace F Marshall
- Department of Biochemistry & Biophysics, University of California San Francisco, 600 16th St, San Francisco, CA, 94158, USA.
| | - Laura F Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, NY, 10032, USA
| | | | - Jessica K Polka
- Visiting Scholar, Whitehead Institute, 9 Cambridge Center, Cambridge, MA, 02142, USA
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Therese Gerbich
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Amy Gladfelter
- 516 Fordham Hall, University of North Carolina Chapel Hill, Chapel Hill, NC, 27514, USA
| | - James Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd, St. Louis, MO, 63132, USA
| | | | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, CB2 0QH, Cambridge, UK
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Bob Goldstein
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, CA, 94305, USA
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47
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Abstract
Humans and other mammals are limited in their natural abilities to regenerate lost body parts. By contrast, many salamanders are highly regenerative and can spontaneously replace lost limbs even as adults. Because salamander limbs are anatomically similar to human limbs, knowing how they regenerate should provide important clues for regenerative medicine. Although interest in understanding the mechanics of this process has never wavered, until recently researchers have been vexed by seemingly impenetrable logistics of working with these creatures at a molecular level. Chief among the problems has been the very large size of salamander genomes, and not a single salamander genome has been fully sequenced to date. Recently the enormous gap in sequence information has been bridged by approaches that leverage mRNA as the starting point. Together with functional experimentation, these data are rapidly enabling researchers to finally uncover the molecular mechanisms underpinning the astonishing biological process of limb regeneration.
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Affiliation(s)
- Brian J Haas
- Broad Institute of Massachusetts Institute of Technology(MIT) and Harvard, Klarman Cell Observatory, 415 Main Street, Cambridge, MA 02142, USA.
| | - Jessica L Whited
- Harvard Medical School, Harvard Stem Cell Institute, and Brigham and Women's Hospital Department of Orthopedic Surgery, 60 Fenwood Road, Boston, MA 02115, USA.
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48
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Knowlton MN, Smith CL. Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. Mamm Genome 2017; 28:367-376. [PMID: 28589392 PMCID: PMC5569137 DOI: 10.1007/s00335-017-9698-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/27/2017] [Indexed: 12/29/2022]
Abstract
The widespread use of CRISPR/Cas and other targeted endonuclease technologies in many species has led to an explosion in the generation of new mutations and alleles. The ability to generate many different mutations from the same target sequence either by homology-directed repair with a donor sequence or non-homologous end joining-induced insertions and deletions necessitates a means for representing these mutations in literature and databases. Standardized nomenclature can be used to generate unambiguous, concise, and specific symbols to represent mutations and alleles. The research communities of a variety of species using CRISPR/Cas and other endonuclease-mediated mutation technologies have developed different approaches to naming and identifying such alleles and mutations. While some organism-specific research communities have developed allele nomenclature that incorporates the method of generation within the official allele or mutant symbol, others use metadata tags that include method of generation or mutagen. Organism-specific research community databases together with organism-specific nomenclature committees are leading the way in providing standardized nomenclature and metadata to facilitate the integration of data from alleles and mutations generated using CRISPR/Cas and other targeted endonucleases.
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Affiliation(s)
| | - Cynthia L Smith
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, 04609, USA
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49
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Cabral T, DiCarlo JE, Justus S, Sengillo JD, Xu Y, Tsang SH. CRISPR applications in ophthalmologic genome surgery. Curr Opin Ophthalmol 2017; 28:252-259. [PMID: 28141764 PMCID: PMC5511789 DOI: 10.1097/icu.0000000000000359] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PURPOSE OF REVIEW The present review seeks to summarize and discuss the application of clustered regularly interspaced short palindromic repeats (CRISPR)-associated systems (Cas) for genome editing, also called genome surgery, in the field of ophthalmology. RECENT FINDINGS Precision medicine is an emerging approach for disease treatment and prevention that takes into account the variability of an individual's genetic sequence. Various groups have used CRISPR-Cas genome editing to make significant progress in mammalian preclinical models of eye disease, the basic science of eye development in zebrafish, the in vivo modification of ocular tissue, and the correction of stem cells with therapeutic applications. In addition, investigators have creatively used the targeted mutagenic potential of CRISPR-Cas systems to target pathogenic alleles in vitro. SUMMARY Over the past year, CRISPR-Cas genome editing has been used to correct pathogenic mutations in vivo and in transplantable stem cells. Although off-target mutagenesis remains a concern, improvement in CRISPR-Cas technology and careful screening for undesired mutations will likely lead to clinical eye therapeutics employing CRISPR-Cas systems in the near future.
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Affiliation(s)
- Thiago Cabral
- Jonas Children’s Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA
- Edward S Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
- Department of Ophthalmology, Federal University of Espírito Santo, Vitoria, Brazil
- Department of Ophthalmology, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - James E DiCarlo
- Jonas Children’s Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA
- Edward S Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Sally Justus
- Jonas Children’s Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA
- Edward S Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Jesse D Sengillo
- Jonas Children’s Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA
- Edward S Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
- State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Yu Xu
- Jonas Children’s Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA
- Edward S Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
- Department of Ophthalmology, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University
| | - Stephen H Tsang
- Jonas Children’s Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA
- Edward S Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
- Department of Pathology & Cell Biology, Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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50
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Modrell MS, Lyne M, Carr AR, Zakon HH, Buckley D, Campbell AS, Davis MC, Micklem G, Baker CV. Insights into electrosensory organ development, physiology and evolution from a lateral line-enriched transcriptome. eLife 2017; 6. [PMID: 28346141 PMCID: PMC5429088 DOI: 10.7554/elife.24197] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/23/2017] [Indexed: 01/22/2023] Open
Abstract
The anamniote lateral line system, comprising mechanosensory neuromasts and electrosensory ampullary organs, is a useful model for investigating the developmental and evolutionary diversification of different organs and cell types. Zebrafish neuromast development is increasingly well understood, but neither zebrafish nor Xenopus is electroreceptive and our molecular understanding of ampullary organ development is rudimentary. We have used RNA-seq to generate a lateral line-enriched gene-set from late-larval paddlefish (Polyodon spathula). Validation of a subset reveals expression in developing ampullary organs of transcription factor genes critical for hair cell development, and genes essential for glutamate release at hair cell ribbon synapses, suggesting close developmental, physiological and evolutionary links between non-teleost electroreceptors and hair cells. We identify an ampullary organ-specific proneural transcription factor, and candidates for the voltage-sensing L-type Cav channel and rectifying Kv channel predicted from skate (cartilaginous fish) ampullary organ electrophysiology. Overall, our results illuminate ampullary organ development, physiology and evolution.
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Affiliation(s)
- Melinda S Modrell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Mike Lyne
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Adrian R Carr
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Harold H Zakon
- Department of Neuroscience, The University of Texas at Austin, Austin, United States.,Department of Integrative Biology, The University of Texas at Austin, Austin, United States
| | - David Buckley
- Departmento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales-MNCN-CSIC, Madrid, Spain.,Department of Natural Sciences, Saint Louis University - Madrid Campus, Madrid, Spain
| | - Alexander S Campbell
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Marcus C Davis
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, United States
| | - Gos Micklem
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Clare Vh Baker
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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