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Shi YB, Fu L, Tanizaki Y. Intestinal remodeling during Xenopus metamorphosis as a model for studying thyroid hormone signaling and adult organogenesis. Mol Cell Endocrinol 2024; 586:112193. [PMID: 38401883 PMCID: PMC10999354 DOI: 10.1016/j.mce.2024.112193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
Intestinal development takes places in two phases, the initial formation of neonatal (mammals)/larval (anurans) intestine and its subsequent maturation into the adult form. This maturation occurs during postembryonic development when plasma thyroid hormone (T3) level peaks. In anurans such as the highly related Xenopus laevis and Xenopus tropicalis, the larval/tadpole intestine is drastically remodeled from a simple tubular structure to a complex, multi-folded adult organ during T3-dependent metamorphosis. This involved complete degeneration of larval epithelium via programmed cell death and de novo formation of adult epithelium, with concurrent maturation of the muscles and connective tissue. Here, we will summarize our current understanding of the underlying molecular mechanisms, with a focus on more recent genetic and genome-wide studies.
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Affiliation(s)
- Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| | - Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
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2
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Ran R, Li L, Xu T, Huang J, He H, Chen Y. Revealing mitf functions and visualizing allografted tumor metastasis in colorless and immunodeficient Xenopus tropicalis. Commun Biol 2024; 7:275. [PMID: 38443437 PMCID: PMC10915148 DOI: 10.1038/s42003-024-05967-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 02/23/2024] [Indexed: 03/07/2024] Open
Abstract
Transparent immunodeficient animal models not only enhance in vivo imaging investigations of visceral organ development but also facilitate in vivo tracking of transplanted tumor cells. However, at present, transparent and immunodeficient animal models are confined to zebrafish, presenting substantial challenges for real-time, in vivo imaging studies addressing specific biological inquiries. Here, we employed a mitf-/-/prkdc-/-/il2rg-/- triple-knockout strategy to establish a colorless and immunodeficient amphibian model of Xenopus tropicalis. By disrupting the mitf gene, we observed the loss of melanophores, xanthophores, and granular glands in Xenopus tropicalis. Through the endogenous mitf promoter to drive BRAFV600E expression, we confirmed mitf expression in melanophores, xanthophores and granular glands. Moreover, the reconstruction of the disrupted site effectively reinstated melanophores, xanthophores, and granular glands, further highlighting the crucial role of mitf as a regulator in their development. By crossing mitf-/- frogs with prkdc-/-/il2rg-/- frogs, we generated a mitf-/-/prkdc-/-/il2rg-/- Xenopus tropicalis line, providing a colorless and immunodeficient amphibian model. Utilizing this model, we successfully observed intravital metastases of allotransplanted xanthophoromas and migrations of allotransplanted melanomas. Overall, colorless and immunodeficient Xenopus tropicalis holds great promise as a valuable platform for tumorous and developmental biology research.
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Affiliation(s)
- Rensen Ran
- Department of Chemical Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, 519000, Zhuhai, China.
| | - Lanxin Li
- Department of Chemical Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Tingting Xu
- Fujian Medical University Union Hospital, 350001, Fuzhou, China
| | - Jixuan Huang
- Department of Chemical Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Huanhuan He
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, 519000, Zhuhai, China
| | - Yonglong Chen
- Department of Chemical Biology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
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3
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Zoller JA, Parasyraki E, Lu AT, Haghani A, Niehrs C, Horvath S. DNA methylation clocks for clawed frogs reveal evolutionary conservation of epigenetic aging. GeroScience 2024; 46:945-960. [PMID: 37270437 PMCID: PMC10828168 DOI: 10.1007/s11357-023-00840-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
To address how conserved DNA methylation-based epigenetic aging is in diverse branches of the tree of life, we generated DNA methylation data from African clawed frogs (Xenopus laevis) and Western clawed frogs (Xenopus tropicalis) and built multiple epigenetic clocks. Dual species clocks were developed that apply to both humans and frogs (human-clawed frog clocks), supporting that epigenetic aging processes are evolutionary conserved outside mammals. Highly conserved positively age-related CpGs are located in neural-developmental genes such as uncx, tfap2d as well as nr4a2 implicated in age-associated disease. We conclude that signatures of epigenetic aging are evolutionary conserved between frogs and mammals and that the associated genes relate to neural processes, altogether opening opportunities to employ Xenopus as a model organism to study aging.
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Affiliation(s)
- Joseph A Zoller
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.
- German Cancer Research Center (DKFZ), Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Steve Horvath
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
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4
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Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, Rokhsar DS. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs. Nat Commun 2024; 15:579. [PMID: 38233380 PMCID: PMC10794172 DOI: 10.1038/s41467-023-43012-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/27/2023] [Indexed: 01/19/2024] Open
Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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Affiliation(s)
- Jessen V Bredeson
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Austin B Mudd
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sofia Medina-Ruiz
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Therese Mitros
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Owen Kabnick Smith
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Kelly E Miller
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Jessica B Lyons
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California Berkeley, 2626 Hearst Avenue, Berkeley, CA, 94720, USA
| | - Joseph Park
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Kodiak C Berkoff
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Christopher Plott
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guadalupe Aguirre-Figueroa
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Maura Lane
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Isabelle Philipp
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Mara Laslo
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - James Hanken
- Department of Organismic and Evolutionary Biology, and Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Gwenneg Kerdivel
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Buisine
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Laurent M Sachs
- Département Adaptation du Vivant, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Heidi Smith-Parker
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Marcos Gridi-Papp
- Department of Biological Sciences, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael J Ryan
- Department of Integrative Biology, Patterson Labs, 2401 Speedway, University of Texas, Austin, TX, 78712, USA
| | - Robert D Denton
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John H Malone
- Department of Molecular and Cell Biology and Institute of Systems Genomics, University of Connecticut, 181 Auditorium Road, Unit 3197, Storrs, CT, 06269, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Patterson Labs, 2401 Speedway, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Beckman Center 409, Stanford, CA, 94305-5307, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Weill Hall, University of California, Berkeley, CA, 94720, USA.
- DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.
- Chan-Zuckerberg BioHub, 499 Illinois Street, San Francisco, CA, 94158, USA.
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan.
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5
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Tulkens D, Boelens M, Naert T, Carron M, Demuynck S, Dewaele S, Van Isterdael G, Creytens D, Pieters T, Goossens S, Van Vlierberghe P, Vleminckx K. Mutations in the histone methyltransferase Ezh2 drive context-dependent leukemia in Xenopus tropicalis. Leukemia 2023; 37:2404-2413. [PMID: 37794102 DOI: 10.1038/s41375-023-02052-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
CRISPR-mediated simultaneous targeting of candidate tumor suppressor genes in Xenopus tropicalis allows fast functional assessment of co-driver genes for various solid tumors. Genotyping of tumors that emerge in the mosaic mutant animals rapidly exposes the gene mutations under positive selection for tumor establishment. However, applying this simple approach to the blood lineage has not been attempted. Multiple hematologic malignancies have mutations in EZH2, encoding the catalytic subunit of the Polycomb Repressive Complex 2. Interestingly, EZH2 can act as an oncogene or a tumor suppressor, depending on cellular context and disease stage. We show here that mosaic CRISPR/Cas9 mediated ezh2 disruption in the blood lineage resulted in early and penetrant acute myeloid leukemia (AML) induction. While animals were co-targeted with an sgRNA that induces notch1 gain-of-function mutations, sequencing of leukemias revealed positive selection towards biallelic ezh2 mutations regardless of notch1 mutational status. Co-targeting dnm2, recurrently mutated in T/ETP-ALL, induced a switch from myeloid towards acute T-cell leukemia. Both myeloid and T-cell leukemias engrafted in immunocompromised hosts. These data underline the potential of Xenopus tropicalis for modeling human leukemia, where mosaic gene disruption, combined with deep amplicon sequencing of the targeted genomic regions, can rapidly and efficiently expose co-operating driver gene mutations.
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Affiliation(s)
- Dieter Tulkens
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Marthe Boelens
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Marjolein Carron
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Suzan Demuynck
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Sylviane Dewaele
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Gert Van Isterdael
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
| | - David Creytens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Pathology, Ghent University and Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tim Pieters
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Steven Goossens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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Morselli M, Bennett R, Shaidani NI, Horb M, Peshkin L, Pellegrini M. Age-associated DNA methylation changes in Xenopus frogs. Epigenetics 2023; 18:2201517. [PMID: 37092296 PMCID: PMC10128463 DOI: 10.1080/15592294.2023.2201517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 04/06/2023] [Indexed: 04/25/2023] Open
Abstract
Age-associated changes in DNA methylation have been characterized across various animals, but not yet in amphibians, which are of particular interest because they include widely studied model organisms. In this study, we present clear evidence that the aquatic vertebrate species Xenopus tropicalis displays patterns of age-associated changes in DNA methylation. We have generated whole-genome bisulfite sequencing (WGBS) profiles from skin samples of nine frogs representing young, mature, and old adults and characterized the gene- and chromosome-scale DNA methylation changes with age. Many of the methylation features and changes we observe are consistent with what is known in mammalian species, suggesting that the mechanism of age-related changes is conserved. Moreover, we selected a few thousand age-associated CpG sites to build an assay based on targeted DNA methylation analysis (TBSseq) to expand our findings in future studies involving larger cohorts of individuals. Preliminary results of a pilot TBSeq experiment recapitulate the findings obtained with WGBS setting the basis for the development of an epigenetic clock assay. The results of this study will allow us to leverage the unique resources available for Xenopus to study how DNA methylation relates to other hallmarks of ageing.
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Affiliation(s)
- Marco Morselli
- Molecular, Cell & Developmental Biology, UCLA, Los Angeles, CA, USA
| | - Ronan Bennett
- Molecular, Cell & Developmental Biology, UCLA, Los Angeles, CA, USA
| | - Nikko-Ideen Shaidani
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Marko Horb
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Leonid Peshkin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, USA
- Systems Biology, Harvard Medical School, Boston, MA, USA
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Hossain N, Igawa T, Suzuki M, Tazawa I, Nakao Y, Hayashi T, Suzuki N, Ogino H. Phenotype-genotype relationships in Xenopus sox9 crispants provide insights into campomelic dysplasia and vertebrate jaw evolution. Dev Growth Differ 2023; 65:481-497. [PMID: 37505799 DOI: 10.1111/dgd.12884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023]
Abstract
Since CRISPR-based genome editing technology works effectively in the diploid frog Xenopus tropicalis, a growing number of studies have successfully modeled human genetic diseases in this species. However, most of their targets were limited to non-syndromic diseases that exhibit abnormalities in a small fraction of tissues or organs in the body. This is likely because of the complexity of interpreting the phenotypic variations resulting from somatic mosaic mutations generated in the founder animals (crispants). In this study, we attempted to model the syndromic disease campomelic dysplasia (CD) by generating sox9 crispants in X. tropicalis. The resulting crispants failed to form neural crest cells at neurula stages and exhibited various combinations of jaw, gill, ear, heart, and gut defects at tadpole stages, recapitulating part of the syndromic phenotype of CD patients. Genotyping of the crispants with a variety of allelic series of mutations suggested that the heart and gut defects depend primarily on frame-shift mutations expected to be null, whereas the jaw, gill, and ear defects could be induced not only by such mutations but also by in-frame deletion mutations expected to delete part of the jawed vertebrate-specific domain from the encoded Sox9 protein. These results demonstrate that Xenopus crispants are useful for investigating the phenotype-genotype relationships behind syndromic diseases and examining the tissue-specific role of each functional domain within a single protein, providing novel insights into vertebrate jaw evolution.
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Affiliation(s)
- Nusrat Hossain
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Makoto Suzuki
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Ichiro Tazawa
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuta Nakao
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Toshinori Hayashi
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Nanoka Suzuki
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
| | - Hajime Ogino
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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Marquez J, Aslam F, Khokha MK. Expanding EMC foldopathies: Topogenesis deficits alter the neural crest. Genesis 2023; 61:e23520. [PMID: 37318954 PMCID: PMC10524326 DOI: 10.1002/dvg.23520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 04/13/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is essential for the insertion of a wide variety of transmembrane proteins into the plasma membrane across cell types. Each EMC is composed of Emc1-7, Emc10, and either Emc8 or Emc9. Recent human genetics studies have implicated variants in EMC genes as the basis for a group of human congenital diseases. The patient phenotypes are varied but appear to affect a subset of tissues more prominently than others. Namely, craniofacial development seems to be commonly affected. We previously developed an array of assays in Xenopus tropicalis to assess the effects of emc1 depletion on the neural crest, craniofacial cartilage, and neuromuscular function. We sought to extend this approach to additional EMC components identified in patients with congenital malformations. Through this approach, we determine that EMC9 and EMC10 are important for neural crest development and the development of craniofacial structures. The phenotypes observed in patients and our Xenopus model phenotypes similar to EMC1 loss of function likely due to a similar mechanism of dysfunction in transmembrane protein topogenesis.
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Affiliation(s)
- Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Faiza Aslam
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
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9
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Kitamura K, Yamamoto T, Ochi H, Suzuki M, Suzuki N, Igawa T, Yoshida T, Futakuchi M, Ogino H, Michiue T. Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis. Sci Rep 2023; 13:13214. [PMID: 37580380 PMCID: PMC10425369 DOI: 10.1038/s41598-023-40193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/06/2023] [Indexed: 08/16/2023] Open
Abstract
Cancer treatment is still challenging because the disease is often caused by multiple mutations. Although genomic studies have identified many oncogenes and tumor suppressor genes, gene sets involved in tumorigenesis remain poorly understood. Xenopus, a genus of aquatic frogs, is a useful model to identify gene sets because it can be genetically and experimentally analyzed. Here, we analyzed gene expression in tumor tissues of three individuals in Xenopus tropicalis and identified 55 differentially expressed genes (DEGs). Gene ontology (GO) analysis showed that the upregulated genes in the tumor tissues were enriched in GO terms related to the extracellular matrix and collagen fibril organization. Hierarchical clustering showed that the gene expression patterns of tumor tissues in X. tropicalis were comparable to those of human connective, soft, and subcutaneous tissue-derived cancers. Additionally, pathway analysis revealed that these DEGs were associated with multiple pathways, including the extracellular matrix, collagen fibril organization, MET signaling, and keratan sulfate. We also found that the expression tendency of some DEGs that have not been well analyzed in the cancer field clearly determines the prognosis of human cancer patients. This study provides a remarkable reference for future experimental work on X. tropicalis to identify gene sets involved in human cancer.
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Affiliation(s)
- Kazuki Kitamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Takayoshi Yamamoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata City, Yamagata, 990-9585, Japan
| | - Makoto Suzuki
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Nanoka Suzuki
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Tadashi Yoshida
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan
| | - Mitsuru Futakuchi
- Department of Pathology, Faculty of Medicine, Yamagata University, 2-2-2 Iida-Nishi, Yamagata City, Yamagata, 990-9585, Japan
| | - Hajime Ogino
- Amphibian Research Center, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Tatsuo Michiue
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-Ku, Tokyo, 153-8902, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.
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10
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Tang S, Xu X, Yu D, Long M, Xia H, Lu Y, Gan Z. Evolutionary and functional conservation of myeloid differentiation factor 88 (MyD88) in amphibian Xenopus tropicalis. Gene 2023; 865:147332. [PMID: 36871675 DOI: 10.1016/j.gene.2023.147332] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/29/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
As a universal adaptor used by most TLR members, the myeloid differentiation factor 88 (MyD88) plays essential roles in TLR-mediated inflammatory response of invertebrate and vertebrate animals, and functional features of MyD88 remain largely unknown in amphibians. In this study, a MyD88 gene named Xt-MyD88 was characterized in the Western clawed frog (Xenopus tropicalis). Xt-MyD88 and MyD88 in other species of vertebrates share similar structural characteristics, genomic structures, and flanking genes, suggesting that MyD88 is structurally conserved in different phyla of vertebrates ranging from fish to mammals. Moreover, Xt-MyD88 was widely expressed in different organs/tissues, and was induced by poly(I:C) in spleen, kidney, and liver. Importantly, overexpression of Xt-MyD88 triggered a marked activation of both NF-κB promoter and interferon-stimulated response elements (ISREs), implying that it may be play important roles in inflammatory responses of amphibians. The research represents the first characterization on the immune functions of amphibian MyD88, and reveals considerable functional conservation of MyD88 in early tetrapods.
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Affiliation(s)
- Shaoshuai Tang
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China
| | - Xinlan Xu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Dapeng Yu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China
| | - Meng Long
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China
| | - Hongli Xia
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China
| | - Yishan Lu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhen Gan
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang 524088, China.
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11
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Long Q, Yan K, Wang C, Wen Y, Qi F, Wang H, Shi P, Liu X, Chan WY, Lu X, Zhao H. Modification of maternally defined H3K4me3 regulates the inviability of interspecific Xenopus hybrids. Sci Adv 2023; 9:eadd8343. [PMID: 37027476 PMCID: PMC10081845 DOI: 10.1126/sciadv.add8343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Increasing evidence suggests that interspecific hybridization is crucial to speciation. However, chromatin incompatibility during interspecific hybridization often renders this process. Genomic imbalances such as chromosomal DNA loss and rearrangements leading to infertility have been commonly noted in hybrids. The mechanism underlying reproductive isolation of interspecific hybridization remains elusive. Here, we identified that modification of maternally defined H3K4me3 in Xenopus laevis and Xenopus tropicalis hybrids determines the different fates of the two types of hybrids as te×ls with developmental arrest and viable le×ts. Transcriptomics highlighted that the P53 pathway was overactivated, and the Wnt signaling pathway was suppressed in te×ls hybrids. Moreover, the lack of maternal H3K4me3 in te×ls disturbed the balance of gene expression between the L and S subgenomes in this hybrid. Attenuation of p53 can postpone the arrested development of te×ls. Our study suggests an additional model of reproductive isolation based on modifications of maternally defined H3K4me3.
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Affiliation(s)
- Qi Long
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong; GMU-GIBH Joint School of Life Sciences, the Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Hong Kong SAR, China
- Guangzhou Institutes of Biomedicine and Health, The Chinese Academy of Sciences, Guangzhou 511436, China
| | - Kai Yan
- State Key Laboratory of Genetic Resources and Evolution/Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China
- Kunming Institute of Zoology Chinese Academy of Sciences, The Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, The Chinese Academy of Sciences, Kunming 650223, China
| | - Chendong Wang
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong; GMU-GIBH Joint School of Life Sciences, the Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Hong Kong SAR, China
| | - Yanling Wen
- State Key Laboratory of Genetic Resources and Evolution/Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China
| | - Furong Qi
- State Key Laboratory of Genetic Resources and Evolution/Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China
| | - Hui Wang
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong; GMU-GIBH Joint School of Life Sciences, the Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Hong Kong SAR, China
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution/Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China
- Kunming Institute of Zoology Chinese Academy of Sciences, The Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, The Chinese Academy of Sciences, Kunming 650223, China
| | - Xingguo Liu
- Guangzhou Institutes of Biomedicine and Health, The Chinese Academy of Sciences, Guangzhou 511436, China
| | - Wai-Yee Chan
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong; GMU-GIBH Joint School of Life Sciences, the Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Hong Kong SAR, China
- Kunming Institute of Zoology Chinese Academy of Sciences, The Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, New Territories, Hong Kong SAR, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution/Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming 650223, China
- Kunming Institute of Zoology Chinese Academy of Sciences, The Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, The Chinese Academy of Sciences, Kunming 650223, China
| | - Hui Zhao
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong; GMU-GIBH Joint School of Life Sciences, the Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Hong Kong SAR, China
- Kunming Institute of Zoology Chinese Academy of Sciences, The Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, New Territories, Hong Kong SAR, China
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12
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Paul B, Dockery R, Valverde VM, Buchholz DR. Characterization of a novel corticosterone response gene in Xenopus tropicalis tadpole tails. Front Endocrinol (Lausanne) 2023; 14:1121002. [PMID: 36777337 PMCID: PMC9910334 DOI: 10.3389/fendo.2023.1121002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Corticosteroids are critical for development and for mediating stress responses across diverse vertebrate taxa. Study of frog metamorphosis has made significant breakthroughs in our understanding of corticosteroid signaling during development in non-mammalian vertebrate species. However, lack of adequate corticosterone (CORT) response genes in tadpoles make identification and quantification of CORT responses challenging. Here, we characterized a CORT-response gene frzb (frizzled related protein) previously identified in Xenopus tropicalis tadpole tail skin by an RNA-seq study. We validated the RNA-seq results that CORT and not thyroid hormone induces frzb in the tails using quantitative PCR. Further, maximum frzb expression was achieved by 100-250 nM CORT within 12-24 hours. frzb is not significantly induced in the liver and brain in response to 100 nM CORT. We also found no change in frzb expression across natural metamorphosis when endogenous CORT levels peak. Surprisingly, frzb is only induced by CORT in X. tropicalis tails and not in Xenopus laevis tails. The exact downstream function of increased frzb expression in tails in response to CORT is not known, but the specificity of hormone response and its high mRNA expression levels in the tail render frzb a useful marker of exogenous CORT-response independent of thyroid hormone for exogenous hormone treatments and in-vivo endocrine disruption studies.
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Affiliation(s)
- Bidisha Paul
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Rejenae Dockery
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Valery M. Valverde
- School of Medicine and Health Sciences TecSalud Instituto Tecnológico y de Estudios Superiores de Monterrey (ITESM), Monterrey, Nuevo Leon, Mexico
| | - Daniel R. Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
- *Correspondence: Daniel R. Buchholz,
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13
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Godden AM, Antonaci M, Wheeler GN. An Efficient CRISPR-Cas9 Method to Knock Out MiRNA Expression in Xenopus Tropicalis. Methods Mol Biol 2023; 2630:231-241. [PMID: 36689186 DOI: 10.1007/978-1-0716-2982-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In recent years CRISPR-Cas9 knockouts (KO) have become increasingly utilized to study gene function. MicroRNAs (miRNAs) are short noncoding RNAs, 20-25 nucleotides long, which affect gene expression through posttranscriptional repression. As miRNAs are so small and due to the limitations of known PAM sequences, it is difficult to design CRISPR sgRNAs that reproducibly lead to a KO. We have therefore developed a novel approach using two guide RNAs to effectively "drop out" a miRNA. Validation of efficient CRISPR miRNA KO and phenotype analysis included use of q-RT-PCR and Sanger sequencing. To show specificity of the phenotype, we provide a protocol to use miRNA mimics to rescue the KO phenotype.
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Affiliation(s)
- Alice M Godden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Marco Antonaci
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Grant N Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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14
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Rigolet M, Buisine N, Scharwatt M, Duvernois-Berthet E, Buchholz DR, Sachs LM. Crosstalk between Thyroid Hormone and Corticosteroid Signaling Targets Cell Proliferation in Xenopus tropicalis Tadpole Liver. Int J Mol Sci 2022; 23:ijms232213715. [PMID: 36430192 PMCID: PMC9692397 DOI: 10.3390/ijms232213715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
Thyroid hormones (TH) and glucocorticoids (GC) are involved in numerous developmental and physiological processes. The effects of individual hormones are well documented, but little is known about the joint actions of the two hormones. To decipher the crosstalk between these two hormonal pathways, we conducted a transcriptional analysis of genes regulated by TH, GC, or both hormones together in liver of Xenopus tropicalis tadpoles using RNA-Seq. Among the differentially expressed genes (DE), 70.5% were regulated by TH only, 0.87% by GC only, and 15% by crosstalk between the two hormones. Gene ontology analysis of the crosstalk-regulated genes identified terms referring to DNA replication, DNA repair, and cell-cycle regulation. Biological network analysis identified groups of genes targeted by the hormonal crosstalk and corroborated the gene ontology analysis. Specifically, we found two groups of functionally linked genes (chains) mainly composed of crosstalk-regulated hubs (highly interactive genes), and a large subnetwork centred around the crosstalk-regulated genes psmb6 and cdc7. Most of the genes in the chains are involved in cell-cycle regulation, as are psmb6 and cdc7, which regulate the G2/M transition. Thus, the biological action of these two hormonal pathways acting together in the liver targets cell-cycle regulation.
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Affiliation(s)
- Muriel Rigolet
- UMR PhyMA CNRS, Muséum National d’Histoire Naturelle, 75005 Paris, France
| | - Nicolas Buisine
- UMR PhyMA CNRS, Muséum National d’Histoire Naturelle, 75005 Paris, France
| | - Marylou Scharwatt
- UMR PhyMA CNRS, Muséum National d’Histoire Naturelle, 75005 Paris, France
| | | | - Daniel R. Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Laurent M. Sachs
- UMR PhyMA CNRS, Muséum National d’Histoire Naturelle, 75005 Paris, France
- UMR7221 CNRS, Muséum National d’Histoire Naturelle, CP32, 7 Rue Cuvier, CEDEX 05, 75231 Paris, France
- Correspondence: ; Tel.: +33-1-40-79-36-17
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15
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Fu L, Liu R, Ma V, Shi YB. Upregulation of proto-oncogene ski by thyroid hormone in the intestine and tail during Xenopus metamorphosis. Gen Comp Endocrinol 2022; 328:114102. [PMID: 35944650 PMCID: PMC9530006 DOI: 10.1016/j.ygcen.2022.114102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022]
Abstract
Thyroid hormone (T3) is important for adult organ function and vertebrate development, particularly during the postembryonic period when many organs develop/mature into their adult forms. Amphibian metamorphosis is totally dependent on T3 and can be easily manipulated, thus offering a unique opportunity for studying how T3 controls postembryonic development in vertebrates. Numerous early studies have demonstrated that T3 affects frog metamorphosis through T3 receptor (TR)-mediated regulation of T3 response genes, where TR forms a heterodimer with RXR (9-cis retinoic acid receptor) and binds to T3 response elements (TREs) in T3 response genes to regulate their expression. We have previously identified many candidate direct T3 response genes in Xenopus tropicalis tadpole intestine. Among them is the proto-oncogene Ski, which encodes a nuclear protein with complex function in regulating cell fate. We show here that Ski is upregulated in the intestine and tail of premetamorphic tadpoles upon T3 treatment and its expression peaks at stage 62, the climax of metamorphosis. We have further discovered a putative TRE in the first exon that can bind to TR/RXR in vitro and mediate T3 regulation of the promoter in vivo. These data demonstrate that Ski is activated by T3 through TR binding to a TRE in the first exon during Xenopus tropicalis metamorphosis, implicating a role of Ski in regulating cell fate during metamorphosis.
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Affiliation(s)
- Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert Liu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD 20892, USA
| | - Vincent Ma
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD 20892, USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, MD 20892, USA.
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Wang J, Lu C, Wei S. Whole-genome sequencing identifies I-SceI-mediated transgene integration sites in Xenopus tropicalis snai2:eGFP line. G3 (Bethesda) 2022; 12:jkac037. [PMID: 35171990 PMCID: PMC9073676 DOI: 10.1093/g3journal/jkac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 01/21/2022] [Indexed: 11/23/2022]
Abstract
Transgenesis with the meganuclease I-SceI is a safe and efficient method, but the underlying mechanisms remain unclear due to the lack of information on transgene localization. Using I-SceI, we previously developed a transgenic Xenopus tropicalis line expressing enhanced green fluorescent protein driven by the neural crest-specific snai2 promoter/enhancer, which is a powerful tool for studying neural crest development and craniofacial morphogenesis. Here, we carried out whole-genome shotgun sequencing for the snai2:eGFP embryos to identify the transgene integration sites. With a 19x sequencing coverage, we estimated that 6 copies of the transgene were inserted into the Xenopus tropicalis genome in the hemizygous transgenic embryos. Two transgene integration loci adjacent to each other were identified in a noncoding region on chromosome 1, possibly as a result of duplication after a single transgene insertion. Interestingly, genomic DNA at the boundaries of the transgene integration loci contains short sequences homologous to the I-SceI recognition site, suggesting that the integration was not random but probably mediated by sequence homology. To our knowledge, our work represents the first genome-wide sequencing study on a transgenic organism generated with I-SceI, which is useful for evaluating the potential genetic effects of I-SceI-mediated transgenesis and further understanding the mechanisms underlying this transgenic method.
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Affiliation(s)
- Jian Wang
- Department of Biological Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Congyu Lu
- Department of Biological Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Shuo Wei
- Department of Biological Sciences and Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
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Papenfuss M, Lützow S, Wilms G, Babendreyer A, Flaßhoff M, Kunick C, Becker W. Differential maturation and chaperone dependence of the paralogous protein kinases DYRK1A and DYRK1B. Sci Rep 2022; 12:2393. [PMID: 35165364 PMCID: PMC8844047 DOI: 10.1038/s41598-022-06423-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/28/2022] [Indexed: 11/16/2022] Open
Abstract
The HSP90/CDC37 chaperone system not only assists the maturation of many protein kinases but also maintains their structural integrity after folding. The interaction of mature kinases with the HSP90/CDC37 complex is governed by the conformational stability of the catalytic domain, while the initial folding of the protein kinase domain is mechanistically less well characterized. DYRK1A (Dual-specificity tyrosine (Y)-phosphorylation Regulated protein Kinase 1A) and DYRK1B are closely related protein kinases with discordant HSP90 client status. DYRK kinases stoichiometrically autophosphorylate on a tyrosine residue immediately after folding, which served us as a traceable marker of successful maturation. In the present study, we used bacterial expression systems to compare the capacity of autonomous maturation of DYRK1A and DYRK1B in the absence of eukaryotic cofactors or chaperones. Under these conditions, autophosphorylation of human DYRK1B was severely compromised when compared with DYRK1A or DYRK1B orthologs from zebrafish and Xenopus. Maturation of human DYRK1B could be restored by bacterial expression at lower temperatures, suggesting that folding was not absolutely dependent on eukaryotic chaperones. The differential folding properties of DYRK1A and DYRK1B were largely due to divergent sequences of the C-terminal lobes of the catalytic domain. Furthermore, the mature kinase domain of DYRK1B featured lower thermal stability than that of DYRK1A when exposed to heat challenge in vitro or in living cells. In summary, our study enhances the mechanistic understanding of the differential thermodynamic properties of two closely related protein kinases during initial folding and as mature kinases.
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Affiliation(s)
- Marco Papenfuss
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Svenja Lützow
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Gerrit Wilms
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Aaron Babendreyer
- Institute of Molecular Pharmacology, RWTH Aachen University, 52074, Aachen, Germany
| | - Maren Flaßhoff
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Conrad Kunick
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, 38106, Braunschweig, Germany
| | - Walter Becker
- Institute of Pharmacology and Toxicology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany.
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18
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Arshinoff BI, Cary GA, Karimi K, Foley S, Agalakov S, Delgado F, Lotay VS, Ku CJ, Pells TJ, Beatman TR, Kim E, Cameron RA, Vize PD, Telmer C, Croce JC, Ettensohn CA, Hinman VF. Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms. Nucleic Acids Res 2022; 50:D970-D979. [PMID: 34791383 PMCID: PMC8728261 DOI: 10.1093/nar/gkab1005] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 12/16/2022] Open
Abstract
Echinobase (www.echinobase.org) is a third generation web resource supporting genomic research on echinoderms. The new version was built by cloning the mature Xenopus model organism knowledgebase, Xenbase, refactoring data ingestion pipelines and modifying the user interface to adapt to multispecies echinoderm content. This approach leveraged over 15 years of previous database and web application development to generate a new fully featured informatics resource in a single year. In addition to the software stack, Echinobase uses the private cloud and physical hosts that support Xenbase. Echinobase currently supports six echinoderm species, focused on those used for genomics, developmental biology and gene regulatory network analyses. Over 38 000 gene pages, 18 000 publications, new improved genome assemblies, JBrowse genome browser and BLAST + services are available and supported by the development of a new echinoderm anatomical ontology, uniformly applied formal gene nomenclature, and consistent orthology predictions. A novel feature of Echinobase is integrating support for multiple, disparate species. New genomes from the diverse echinoderm phylum will be added and supported as data becomes available. The common code development design of the integrated knowledgebases ensures parallel improvements as each resource evolves. This approach is widely applicable for developing new model organism informatics resources.
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Affiliation(s)
- Bradley I Arshinoff
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Gregory A Cary
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Saoirse Foley
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sergei Agalakov
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Francisco Delgado
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Vaneet S Lotay
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Carolyn J Ku
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Troy J Pells
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Thomas R Beatman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Eugene Kim
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - R Andrew Cameron
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Cheryl A Telmer
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jenifer C Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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19
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Fu L, Crawford L, Tong A, Luu N, Tanizaki Y, Shi YB. Sperm associated antigen 7 is activated by T3 during Xenopus tropicalis metamorphosis via a thyroid hormone response element within the first intron. Dev Growth Differ 2022; 64:48-58. [PMID: 34862790 PMCID: PMC8810736 DOI: 10.1111/dgd.12764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 01/03/2023]
Abstract
Thyroid hormone (T3) affects many diverse physiological processes such as metabolism, organogenesis, and growth. The two highly related frog species, diploid Xenopus tropicalis and pseudo tetraploid Xenopus laevis, have been used as models for analyzing the effects of T3 during vertebrate development. T3 regulates T3-inducible gene transcription through T3 receptor (TR)-binding to T3-response elements (TREs). We have previously identified sperm associated antigen 7 (spag7) as a candidate T3 target gene that is potentially involved in adult stem cell development and/or proliferation during intestinal metamorphosis. To investigate whether T3 regulates spag7 directly at the transcriptional level via TR, we first conducted qRT-PCR to analyze its expression during natural and T3-induced metamorphosis and found that spag7 was up-regulated during natural metamorphosis in the intestine, tail, brain and hindlimb, peaking at the climax of metamorphosis in all those organs, and upon T3 treatment of premetamorphic tadpoles. Next, we demonstrated that an intronic TRE in spag7, first identified through bioinformatic analysis, could bind to TR in vitro and in vivo during metamorphosis. A dual luciferase assay utilizing a reconstituted frog oocyte transcription system showed that the TRE could mediate promoter activation by liganded TR. These results indicate that spag7 expression is directly regulated by T3 through the TRE in the first intron during metamorphosis, implicating a role for spag7 early during T3-regulated tissue remodeling and resorption.
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Affiliation(s)
- Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland, USA
| | - LaTaijah Crawford
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew Tong
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland, USA
| | - Nga Luu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland, USA
| | - Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland, USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland, USA
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20
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Roco ÁS, Ruiz-García A, Bullejos M. Interaction between sex-determining genes from two species: clues from Xenopus hybrids. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200104. [PMID: 34304589 PMCID: PMC8310712 DOI: 10.1098/rstb.2020.0104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
Hybrids provide an interesting model to study the evolution of sex-determining genes and sex chromosome systems as they offer the opportunity to see how independently evolving sex-determining pathways interact in vivo. In this context, the genus Xenopus represents a stimulating model, since species with non-homologous sex chromosomes and different sex-determining genes have been identified. In addition, the possibility of interspecies breeding is favoured in this group, which arose by alloploidization events, with species ploidy ranging from 2n = 2x = 20 in X. tropicalis (the only diploid representative of the genus) to 2n = 12x = 108 in X. ruwenzoriensis. To study how two sex-determining genes interact in vivo, X. laevis × X. tropicalis hybrids were produced. Gonadal differentiation in these hybrids revealed that the dm-w gene is dominant over X. tropicalis male-determining sex chromosomes (Y or Z), even though the Y chromosome is dominant in X. tropicalis (Y > W>Z). In the absence of the dm-w gene (the Z chromosome from X. laevis is present), the W chromosome from X. tropicalis is able to trigger ovarian development. Testicular differentiation will take place in the absence of W chromosomes from any of the parental species. The dominance/recessivity relationships between these sex-determining loci in the context of either parental genome remains unknown. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Álvaro S. Roco
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain
| | - Adrián Ruiz-García
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain
| | - Mónica Bullejos
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain
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21
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Holler K, Neuschulz A, Drewe-Boß P, Mintcheva J, Spanjaard B, Arsiè R, Ohler U, Landthaler M, Junker JP. Spatio-temporal mRNA tracking in the early zebrafish embryo. Nat Commun 2021; 12:3358. [PMID: 34099733 PMCID: PMC8184788 DOI: 10.1038/s41467-021-23834-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/18/2021] [Indexed: 01/17/2023] Open
Abstract
Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.
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Affiliation(s)
- Karoline Holler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Anika Neuschulz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Philipp Drewe-Boß
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Janita Mintcheva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Bastiaan Spanjaard
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Roberto Arsiè
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Department of Biology, Humboldt University, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- IRI Life Science, Institute of Biology, Humboldt University, Berlin, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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22
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Tarashansky AJ, Musser JM, Khariton M, Li P, Arendt D, Quake SR, Wang B. Mapping single-cell atlases throughout Metazoa unravels cell type evolution. eLife 2021; 10:e66747. [PMID: 33944782 PMCID: PMC8139856 DOI: 10.7554/elife.66747] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories and diversifications in expression programs. Previously, we introduced the self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds from single-cell data (Tarashansky et al., 2019). Here, we build on SAM to map cell atlas manifolds across species. This new method, SAMap, identifies homologous cell types with shared expression programs across distant species within phyla, even in complex examples where homologous tissues emerge from distinct germ layers. SAMap also finds many genes with more similar expression to their paralogs than their orthologs, suggesting paralog substitution may be more common in evolution than previously appreciated. Lastly, comparing species across animal phyla, spanning sponge to mouse, reveals ancient contractile and stem cell families, which may have arisen early in animal evolution.
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Affiliation(s)
| | - Jacob M Musser
- European Molecular Biology Laboratory, Developmental Biology UnitHeidelbergGermany
| | | | - Pengyang Li
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology UnitHeidelbergGermany
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
| | - Stephen R Quake
- Department of Bioengineering, Stanford UniversityStanfordUnited States
- Department of Applied Physics, Stanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Bo Wang
- Department of Bioengineering, Stanford UniversityStanfordUnited States
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
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23
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Roco ÁS, Liehr T, Ruiz-García A, Guzmán K, Bullejos M. Comparative Distribution of Repetitive Sequences in the Karyotypes of Xenopus tropicalis and Xenopus laevis (Anura, Pipidae). Genes (Basel) 2021; 12:617. [PMID: 33919402 PMCID: PMC8143290 DOI: 10.3390/genes12050617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 11/29/2022] Open
Abstract
Xenopus laevis and its diploid relative, Xenopus tropicalis, are the most used amphibian models. Their genomes have been sequenced, and they are emerging as model organisms for research into disease mechanisms. Despite the growing knowledge on their genomes based on data obtained from massive genome sequencing, basic research on repetitive sequences in these species is lacking. This study conducted a comparative analysis of repetitive sequences in X. laevis and X. tropicalis. Genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) with Cot DNA of both species revealed a conserved enrichment of repetitive sequences at the ends of the chromosomes in these Xenopus species. The repeated sequences located on the short arm of chromosome 3 from X. tropicalis were not related to the sequences on the short arm of chromosomes 3L and 3S from X. laevis, although these chromosomes were homoeologous, indicating that these regions evolved independently in these species. Furthermore, all the other repetitive sequences in X. tropicalis and X. laevis may be species-specific, as they were not revealed in cross-species hybridizations. Painting experiments in X. laevis with chromosome 7 from X. tropicalis revealed shared sequences with the short arm of chromosome 3L. These regions could be related by the presence of the nucleolus organizer region (NOR) in both chromosomes, although the region revealed by chromosome painting in the short arm of chromosome 3L in X. laevis did not correspond to 18S + 28S rDNA sequences, as they did not colocalize. The identification of these repeated sequences is of interest as they provide an explanation to some problems already described in the genome assemblies of these species. Furthermore, the distribution of repetitive DNA in the genomes of X. laevis and X. tropicalis might be a valuable marker to assist us in understanding the genome evolution in a group characterized by numerous polyploidization events coupled with hybridizations.
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Affiliation(s)
- Álvaro S. Roco
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany;
| | - Adrián Ruiz-García
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Kateryna Guzmán
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas S/N, 23071 Jaén, Spain; (Á.S.R.); (A.R.-G.); (K.G.)
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24
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Tanizaki Y, Bao L, Shi B, Shi YB. A Role of Endogenous Histone Acetyltransferase Steroid Hormone Receptor Coactivator 3 in Thyroid Hormone Signaling During Xenopus Intestinal Metamorphosis. Thyroid 2021; 31:692-702. [PMID: 33076783 PMCID: PMC8195878 DOI: 10.1089/thy.2020.0410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Background: Thyroid hormone (triiodothyronine [T3]) plays an important role in regulating vertebrate developmental, cellular, and metabolic processes via T3 receptor (TR). Liganded TR recruit coactivator complexes that include steroid receptor coactivators (SRC1, SRC2 or SRC3), which are histone acetyltransferases, to T3-responsive promoters. The functions of endogenous coactivators during T3-dependent mammalian adult organ development remain largely unclear, in part, due to the difficulty to access and manipulate late-stage embryos and neonates. We use Xenopus metamorphosis as a model for postembryonic development in vertebrates. This process is controlled by T3, involves drastic changes in every organ/tissue, and can be easily manipulated. We have previously found that SRC3 was upregulated in the intestine during amphibian metamorphosis. Methods: To determine the function of endogenous SRC3 during intestinal remodeling, we have generated Xenopus tropicalis animals lacking a functional SRC3 gene and analyzed the resulting phenotype. Results: Although removing SRC3 had no apparent effect on external development and animal gross morphology, the SRC3 (-/-) tadpoles displayed a reduction in the acetylation of histone H4 in the intestine compared with that in wild-type animals. Further, the expression of TR target genes was also reduced in SRC3 (-/-) tadpoles during intestinal remodeling. Importantly, SRC3 (-/-) tadpoles had inhibited/delayed intestinal remodeling during natural and T3-induced metamorphosis, including reduced adult intestinal stem cell proliferation and apoptosis of larval epithelial cells. Conclusion: Our results, thus, demonstrate that SRC3 is a critical component of the TR-signaling pathway in vivo during intestinal remodeling.
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Affiliation(s)
- Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Lingyu Bao
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an, P.R. China
| | - Bingyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University School of Medicine, Xi'an, P.R. China
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Address correspondence to: Yun-Bo Shi, PhD, Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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25
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Shibata Y, Tanizaki Y, Zhang H, Lee H, Dasso M, Shi YB. Thyroid Hormone Receptor Is Essential for Larval Epithelial Apoptosis and Adult Epithelial Stem Cell Development but Not Adult Intestinal Morphogenesis during Xenopus tropicalis Metamorphosis. Cells 2021; 10:cells10030536. [PMID: 33802526 PMCID: PMC8000126 DOI: 10.3390/cells10030536] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 12/23/2022] Open
Abstract
Vertebrate postembryonic development is regulated by thyroid hormone (T3). Of particular interest is anuran metamorphosis, which offers several unique advantages for studying the role of T3 and its two nuclear receptor genes, TRα and TRβ, during postembryonic development. We have recently generated TR double knockout (TRDKO) Xenopus tropicalis animals and reported that TR is essential for the completion of metamorphosis. Furthermore, TRDKO tadpoles are stalled at the climax of metamorphosis before eventual death. Here we show that TRDKO intestine lacked larval epithelial cell death and adult stem cell formation/proliferation during natural metamorphosis. Interestingly, TRDKO tadpole intestine had premature formation of adult-like epithelial folds and muscle development. In addition, T3 treatment of premetamorphic TRDKO tadpoles failed to induce any metamorphic changes in the intestine. Furthermore, RNA-seq analysis revealed that TRDKO altered the expression of many genes in biological pathways such as Wnt signaling and the cell cycle that likely underlay the inhibition of larval epithelial cell death and adult stem cell development caused by removing both TR genes. Our data suggest that liganded TR is required for larval epithelial cell degeneration and adult stem cell formation, whereas unliganded TR prevents precocious adult tissue morphogenesis such as smooth-muscle development and epithelial folding.
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Affiliation(s)
- Yuki Shibata
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (Y.S.); (Y.T.)
| | - Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (Y.S.); (Y.T.)
| | - Hongen Zhang
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA;
| | - Hangnoh Lee
- Section on Cell Cycle Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (H.L.); (M.D.)
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Mary Dasso
- Section on Cell Cycle Regulation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (H.L.); (M.D.)
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (Y.S.); (Y.T.)
- Correspondence: ; Tel.: +1-301-402-1004; Fax: +1-301-402-1323
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26
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Narahari AK, Kreutzberger AJB, Gaete PS, Chiu YH, Leonhardt SA, Medina CB, Jin X, Oleniacz PW, Kiessling V, Barrett PQ, Ravichandran KS, Yeager M, Contreras JE, Tamm LK, Bayliss DA. ATP and large signaling metabolites flux through caspase-activated Pannexin 1 channels. eLife 2021; 10:e64787. [PMID: 33410749 PMCID: PMC7806264 DOI: 10.7554/elife.64787] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Pannexin 1 (Panx1) is a membrane channel implicated in numerous physiological and pathophysiological processes via its ability to support release of ATP and other cellular metabolites for local intercellular signaling. However, to date, there has been no direct demonstration of large molecule permeation via the Panx1 channel itself, and thus the permselectivity of Panx1 for different molecules remains unknown. To address this, we expressed, purified, and reconstituted Panx1 into proteoliposomes and demonstrated that channel activation by caspase cleavage yields a dye-permeable pore that favors flux of anionic, large-molecule permeants (up to ~1 kDa). Large cationic molecules can also permeate the channel, albeit at a much lower rate. We further show that Panx1 channels provide a molecular pathway for flux of ATP and other anionic (glutamate) and cationic signaling metabolites (spermidine). These results verify large molecule permeation directly through caspase-activated Panx1 channels that can support their many physiological roles.
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Affiliation(s)
- Adishesh K Narahari
- Department of Pharmacology, University of VirginiaCharlottesvilleUnited States
| | - Alex JB Kreutzberger
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleUnited States
| | - Pablo S Gaete
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers New Jersey Medical SchoolNewarkUnited States
| | - Yu-Hsin Chiu
- Department of Pharmacology, University of VirginiaCharlottesvilleUnited States
| | - Susan A Leonhardt
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleUnited States
| | - Christopher B Medina
- Department of Microbiology, Immunology, and Cancer Biology, University of VirginiaCharlottesvilleUnited States
| | - Xueyao Jin
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleUnited States
| | - Patrycja W Oleniacz
- Department of Pharmacology, University of VirginiaCharlottesvilleUnited States
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleUnited States
| | - Paula Q Barrett
- Department of Pharmacology, University of VirginiaCharlottesvilleUnited States
| | - Kodi S Ravichandran
- Department of Microbiology, Immunology, and Cancer Biology, University of VirginiaCharlottesvilleUnited States
| | - Mark Yeager
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleUnited States
| | - Jorge E Contreras
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers New Jersey Medical SchoolNewarkUnited States
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleUnited States
| | - Douglas A Bayliss
- Department of Pharmacology, University of VirginiaCharlottesvilleUnited States
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27
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Medina-Muñoz SG, Kushawah G, Castellano LA, Diez M, DeVore ML, Salazar MJB, Bazzini AA. Crosstalk between codon optimality and cis-regulatory elements dictates mRNA stability. Genome Biol 2021; 22:14. [PMID: 33402205 PMCID: PMC7783504 DOI: 10.1186/s13059-020-02251-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The regulation of messenger RNA (mRNA) stability has a profound impact on gene expression dynamics during embryogenesis. For example, in animals, maternally deposited mRNAs are degraded after fertilization to enable new developmental trajectories. Regulatory sequences in 3' untranslated regions (3'UTRs) have long been considered the central determinants of mRNA stability. However, recent work indicates that the coding sequence also possesses regulatory information. Specifically, translation in cis impacts mRNA stability in a codon-dependent manner. However, the strength of this mechanism during embryogenesis, as well as its relationship with other known regulatory elements, such as microRNA, remains unclear. RESULTS Here, we show that codon composition is a major predictor of mRNA stability in the early embryo. We show that this mechanism works in combination with other cis-regulatory elements to dictate mRNA stability in zebrafish and Xenopus embryos as well as in mouse and human cells. Furthermore, we show that microRNA targeting efficacy can be affected by substantial enrichment of optimal (stabilizing) or non-optimal (destabilizing) codons. Lastly, we find that one microRNA, miR-430, antagonizes the stabilizing effect of optimal codons during early embryogenesis in zebrafish. CONCLUSIONS By integrating the contributions of different regulatory mechanisms, our work provides a framework for understanding how combinatorial control of mRNA stability shapes the gene expression landscape.
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Affiliation(s)
- Santiago Gerardo Medina-Muñoz
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
- Present Address: National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, 36824, Irapuato, Mexico
| | - Gopal Kushawah
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | | | - Michay Diez
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - Michelle Lynn DeVore
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
| | - María José Blanco Salazar
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA
- Present Address: Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, México City, Mexico
| | - Ariel Alejandro Bazzini
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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Tanizaki Y, Shibata Y, Zhang H, Shi YB. Analysis of Thyroid Hormone Receptor α-Knockout Tadpoles Reveals That the Activation of Cell Cycle Program Is Involved in Thyroid Hormone-Induced Larval Epithelial Cell Death and Adult Intestinal Stem Cell Development During Xenopus tropicalis Metamorphosis. Thyroid 2021; 31:128-142. [PMID: 32515287 PMCID: PMC7840310 DOI: 10.1089/thy.2020.0022] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background: There are two highly conserved thyroid hormone (triiodothyronine [T3]) receptor (TR) genes, TRα and TRβ, in all vertebrates, and the expression of TRα but not TRβ is activated earlier than T3 synthesis during development. In human, high levels of T3 are present during the several months around birth, and T3 deficiency during this period causes severe developmental abnormalities including skeletal and intestinal defects. It is, however, difficult to study this period in mammals as the embryos and neonates depend on maternal supply of nutrients for survival. However, Xenopus tropicalis undergoes a T3-dependent metamorphosis, which drastically changes essentially every organ in a tadpole. Of interest is intestinal remodeling, which involves near complete degeneration of the larval epithelium through apoptosis. Concurrently, adult intestinal stem cells are formed de novo and subsequently give rise to the self-renewing adult epithelial system, resembling intestinal maturation around birth in mammals. We have previously demonstrated that T3 signaling is essential for the formation of adult intestinal stem cells during metamorphosis. Methods: We studied the function of endogenous TRα in the tadpole intestine by using knockout animals and RNA-seq analysis. Results: We observed that removing endogenous TRα caused defects in intestinal remodeling, including drastically reduced larval epithelial cell death and adult intestinal stem cell proliferation. Using RNA-seq on intestinal RNA from premetamorphic wild-type and TRα-knockout tadpoles treated with or without T3 for one day, before any detectable T3-induced cell death and stem cell formation in the tadpole intestine, we identified more than 1500 genes, which were regulated by T3 treatment of the wild-type but not TRα-knockout tadpoles. Gene Ontology and biological pathway analyses revealed that surprisingly, these TRα-regulated genes were highly enriched with cell cycle-related genes, in addition to genes related to stem cells and apoptosis. Conclusions: Our findings suggest that TRα-mediated T3 activation of the cell cycle program is involved in larval epithelial cell death and adult epithelial stem cell development during intestinal remodeling.
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Affiliation(s)
- Yuta Tanizaki
- Section on Molecular Morphogenesis, Cell Regulation and Development Affinity Group, Division of Molecular and Cellular Biology, and Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Yuki Shibata
- Section on Molecular Morphogenesis, Cell Regulation and Development Affinity Group, Division of Molecular and Cellular Biology, and Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Hongen Zhang
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Cell Regulation and Development Affinity Group, Division of Molecular and Cellular Biology, and Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Address correspondence to: Yun-Bo Shi, PhD, Section on Molecular Morphogenesis, Cell Regulation and Development Affinity Group, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Building 49 Room 6A82, Bethesda, MD 20814, USA
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Gan Z, Cheng J, Hou J, Xia L, Lu Y, Nie P. Molecular and functional characterization of interferon regulatory factor 1 (IRF1) in amphibian Xenopus tropicalis. Int J Biol Macromol 2020; 167:719-725. [PMID: 33279564 DOI: 10.1016/j.ijbiomac.2020.11.217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022]
Abstract
Interferon regulatory factor 1 (IRF1) is an important regulator in controlling the transcription of type I interferon genes, and its functions have been well-characterized in mammals, birds and fish. However, little information is available regarding the function of amphibian IRF1. In this study, an IRF1 gene homolog named as Xt-IRF1 was identified in the Western clawed frog (Xenopus tropicalis), an amphibian model specie widely used for comparative immunology research. Xt-IRF1 and IRF1 in other vertebrates possess similar genomic structure and flanking genes, and were grouped together to form a separate clade in phylogenetic tree. In addition, Xt-IRF1 gene was constitutively expressed in all tissues examined, with the highest expression level observed in spleen, and was inducible after poly(I:C) stimulation. Importantly, the expression of Xt-IRF1 was markedly induced by recombinant type I interferon, and Xt-IRF1 induced a strong activation of both IFNβ and ISRE promoters. The present study opens the door to investigate the roles of IRF1 in amphibians, and thus contributes to a better understanding of the functional evolution of IRFs in lower tetrapods.
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Affiliation(s)
- Zhen Gan
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; College of Fishery, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen 518120, China; Shenzhen Dapeng New District Science and Technology Innovation Service Center, Shenzhen 518120, China
| | - Jun Cheng
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; College of Fishery, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen 518120, China
| | - Jing Hou
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; College of Fishery, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen 518120, China; Shenzhen Dapeng New District Science and Technology Innovation Service Center, Shenzhen 518120, China
| | - Liqun Xia
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; College of Fishery, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen 518120, China
| | - Yishan Lu
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; College of Fishery, Guangdong Ocean University, Zhanjiang 524025, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen 518120, China.
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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Zlatow AL, Wilson SS, Bouley DM, Tetens-Woodring J, Buchholz DR, Green SL. Axial Skeletal Malformations in Genetically Modified Xenopus laevis and Xenopus tropicalis. Comp Med 2020; 70:532-541. [PMID: 33203505 PMCID: PMC7754201 DOI: 10.30802/aalas-cm-20-000069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Skeletal malformations in captive-bred, adult Xenopus spp., have not previously been reported. Here we describe 10 sexually mature, genetically modified laboratory frogs (6 Xenopus laevis and 4 Xenopus tropicalis) with axial skeletal abnormalities. The young adult frogs were described by veterinary staff as presenting with "hunchbacks," but were otherwise considered to be in good health. All affected frogs were genetically engineered using various techniques: transcription activator-like effector nucleases (TALEN) editing using thyroid hormone receptor α TALEN mRNA, restriction enzyme-mediated integration methods involving insertion of the inducible transgene pCAR/TRDN, or via I-SceI meganuclease transgenesis using either pDRTREdpTR-HS4 or pDPCrtTA-TREG-HS4 plasmid sequences. Radiographic findings (6 frogs) and gross necropsy (10 frogs) revealed vertebral column malformations and sacroiliac deformities that resulted in moderate to severe kyphosis and kyphoscoliosis. These findings were confirmed and additional skeletal abnormalities were identified using computed tomography to create a 3D reconstruction of 4 frogs. Additional findings visible on the 3D reconstructions included incomplete vertebral segmentation, malformed transverse processes, and a short and/or curved urostyle. Histopathologic findings included misshapen intervertebral joints with nonconforming articular surfaces, narrowed joint cavities, flattened or irregularly-formed articular cartilage, irregular maturation lines and nonpolarized chondrocytes, excess fibrocartilage, and evidence of irregular bone resorption and growth. While the specific etiology of the vertebral skeletal abnormalities remains unclear, possibilities include: 1) egg/oocyte physical manipulation (dejellying, microinjection, fertilization, etc.), 2) induction and expression of the transgenes, 3) inactivation (knockout) of existing genes by insertional mutagenesis, or 4) a combination of the above. Furthermore, the possibility of undetected changes in the macro or microenvironment, or a feature of the genetic background of the affected frogs cannot be ruled out.
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Affiliation(s)
- Anne L Zlatow
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California
| | - Sabrina S Wilson
- Diagnostic Imaging Service, William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, California
| | - Donna M Bouley
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California
| | | | - Daniel R Buchholz
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Sherril L Green
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California;,
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31
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Raj S, Kyono Y, Sifuentes CJ, Arellanes-Licea EDC, Subramani A, Denver RJ. Thyroid Hormone Induces DNA Demethylation in Xenopus Tadpole Brain. Endocrinology 2020; 161:bqaa155. [PMID: 32865566 PMCID: PMC7947600 DOI: 10.1210/endocr/bqaa155] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/25/2020] [Indexed: 12/29/2022]
Abstract
Thyroid hormone (T3) plays pivotal roles in vertebrate development, acting via nuclear T3 receptors (TRs) that regulate gene transcription by promoting post-translational modifications to histones. Methylation of cytosine residues in deoxyribonucleic acid (DNA) also modulates gene transcription, and our recent finding of predominant DNA demethylation in the brain of Xenopus tadpoles at metamorphosis, a T3-dependent developmental process, caused us to hypothesize that T3 induces these changes in vivo. Treatment of premetamorphic tadpoles with T3 for 24 or 48 hours increased immunoreactivity in several brain regions for the DNA demethylation intermediates 5-hydroxymethylcytosine (5-hmC) and 5-carboxylcytosine, and the methylcytosine dioxygenase ten-eleven translocation 3 (TET3). Thyroid hormone treatment induced locus-specific DNA demethylation in proximity to known T3 response elements within the DNA methyltransferase 3a and Krüppel-like factor 9 genes, analyzed by 5-hmC immunoprecipitation and methylation sensitive restriction enzyme digest. Chromatin-immunoprecipitation (ChIP) assay showed that T3 induced TET3 recruitment to these loci. Furthermore, the messenger ribonucleic acid for several genes encoding DNA demethylation enzymes were induced by T3 in a time-dependent manner in tadpole brain. A TR ChIP-sequencing experiment identified putative TR binding sites at several of these genes, and we provide multiple lines of evidence to support that tet2 contains a bona fide T3 response element. Our findings show that T3 can promote DNA demethylation in developing tadpole brain, in part by promoting TET3 recruitment to discrete genomic regions, and by inducing genes that encode DNA demethylation enzymes.
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Affiliation(s)
- Samhitha Raj
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Yasuhiro Kyono
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Christopher J Sifuentes
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | | | - Arasakumar Subramani
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Robert J Denver
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
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32
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Furman BLS, Cauret CMS, Knytl M, Song XY, Premachandra T, Ofori-Boateng C, Jordan DC, Horb ME, Evans BJ. A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome. PLoS Genet 2020; 16:e1009121. [PMID: 33166278 PMCID: PMC7652241 DOI: 10.1371/journal.pgen.1009121] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/16/2020] [Indexed: 11/18/2022] Open
Abstract
In many species, sexual differentiation is a vital prelude to reproduction, and disruption of this process can have severe fitness effects, including sterility. It is thus interesting that genetic systems governing sexual differentiation vary among-and even within-species. To understand these systems more, we investigated a rare example of a frog with three sex chromosomes: the Western clawed frog, Xenopus tropicalis. We demonstrate that natural populations from the western and eastern edges of Ghana have a young Y chromosome, and that a male-determining factor on this Y chromosome is in a very similar genomic location as a previously known female-determining factor on the W chromosome. Nucleotide polymorphism of expressed transcripts suggests genetic degeneration on the W chromosome, emergence of a new Y chromosome from an ancestral Z chromosome, and natural co-mingling of the W, Z, and Y chromosomes in the same population. Compared to the rest of the genome, a small sex-associated portion of the sex chromosomes has a 50-fold enrichment of transcripts with male-biased expression during early gonadal differentiation. Additionally, X. tropicalis has sex-differences in the rates and genomic locations of recombination events during gametogenesis that are similar to at least two other Xenopus species, which suggests that sex differences in recombination are genus-wide. These findings are consistent with theoretical expectations associated with recombination suppression on sex chromosomes, demonstrate that several characteristics of old and established sex chromosomes (e.g., nucleotide divergence, sex biased expression) can arise well before sex chromosomes become cytogenetically distinguished, and show how these characteristics can have lingering consequences that are carried forward through sex chromosome turnovers.
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Affiliation(s)
- Benjamin L. S. Furman
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
- Department of Zoology, University of British Columbia, 6270 University Blvd Vancouver, British Columbia, V6T 1Z4 Canada
| | - Caroline M. S. Cauret
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Martin Knytl
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
- Department of Cell Biology, Charles University, 7 Vinicna Street, Prague, 12843, Czech Republic
| | - Xue-Ying Song
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Tharindu Premachandra
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | | | - Danielle C. Jordan
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543 USA
| | - Marko E. Horb
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543 USA
| | - Ben J. Evans
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
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Xu TH, Liu M, Zhou XE, Liang G, Zhao G, Xu HE, Melcher K, Jones PA. Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Nature 2020; 586:151-155. [PMID: 32968275 PMCID: PMC7540737 DOI: 10.1038/s41586-020-2747-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/30/2020] [Indexed: 12/31/2022]
Abstract
CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer1. These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core2, and they favour the methylation of linker DNA at positioned nucleosomes3,4. Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.
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Affiliation(s)
- Ting-Hai Xu
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Minmin Liu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Gongpu Zhao
- David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Institute, Grand Rapids, MI, USA
| | - H Eric Xu
- Center for Structure and Function of Drug Targets, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Peter A Jones
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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Farley-Barnes KI, Deniz E, Overton MM, Khokha MK, Baserga SJ. Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development. PLoS Genet 2020; 16:e1008967. [PMID: 32813698 PMCID: PMC7437866 DOI: 10.1371/journal.pgen.1008967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/30/2020] [Indexed: 12/30/2022] Open
Abstract
Dysregulation of ribosome production can lead to a number of developmental disorders called ribosomopathies. Despite the ubiquitous requirement for these cellular machines used in protein synthesis, ribosomopathies manifest in a tissue-specific manner, with many affecting the development of the face. Here we reveal yet another connection between craniofacial development and making ribosomes through the protein Paired Box 9 (PAX9). PAX9 functions as an RNA Polymerase II transcription factor to regulate the expression of proteins required for craniofacial and tooth development in humans. We now expand this function of PAX9 by demonstrating that PAX9 acts outside of the cell nucleolus to regulate the levels of proteins critical for building the small subunit of the ribosome. This function of PAX9 is conserved to the organism Xenopus tropicalis, an established model for human ribosomopathies. Depletion of pax9 leads to craniofacial defects due to abnormalities in neural crest development, a result consistent with that found for depletion of other ribosome biogenesis factors. This work highlights an unexpected layer of how the making of ribosomes is regulated in human cells and during embryonic development.
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Affiliation(s)
- Katherine I. Farley-Barnes
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Engin Deniz
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Maya M. Overton
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Susan J. Baserga
- Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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Wiechmann AF, Martin TA, Horb ME. CRISPR/Cas9 mediated mutation of the mtnr1a melatonin receptor gene causes rod photoreceptor degeneration in developing Xenopus tropicalis. Sci Rep 2020; 10:13757. [PMID: 32792587 PMCID: PMC7426423 DOI: 10.1038/s41598-020-70735-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/03/2020] [Indexed: 11/21/2022] Open
Abstract
Nighttime surges in melatonin levels activate melatonin receptors, which synchronize cellular activities with the natural light/dark cycle. Melatonin receptors are expressed in several cell types in the retina, including the photon-sensitive rods and cones. Previous studies suggest that long-term photoreceptor survival and retinal health is in part reliant on melatonin orchestration of circadian homeostatic activities. This scenario would accordingly envisage that disruption of melatonin receptor signaling is detrimental to photoreceptor health. Using in vivo CRISPR/Cas9 genomic editing, we discovered that a small deletion mutation of the Mel1a melatonin receptor (mtnr1a) gene causes a loss of rod photoreceptors in retinas of developing Xenopus tropicalis heterozygous, but not homozygous mutant tadpoles. Cones were relatively spared from degeneration, and the rod loss phenotype was not obvious after metamorphosis. Localization of Mel1a receptor protein appeared to be about the same in wild type and mutant retinas, suggesting that the mutant protein is expressed at some level in mutant retinal cells. The severe impact on early rod photoreceptor viability may signify a previously underestimated critical role in circadian influences on long-term retinal health and preservation of sight. These data offer evidence that disturbance of homeostatic, circadian signaling, conveyed through a mutated melatonin receptor, is incompatible with rod photoreceptor survival.
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Affiliation(s)
- Allan F Wiechmann
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - Teryn A Martin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Marko E Horb
- Marine Biological laboratory, Woods Hole, MA, USA
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Willsey HR, Xu Y, Everitt A, Dea J, Exner CRT, Willsey AJ, State MW, Harland RM. The neurodevelopmental disorder risk gene DYRK1A is required for ciliogenesis and control of brain size in Xenopus embryos. Development 2020; 147:dev189290. [PMID: 32467234 PMCID: PMC10755402 DOI: 10.1242/dev.189290] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/11/2020] [Indexed: 12/30/2023]
Abstract
DYRK1A [dual specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A] is a high-confidence autism risk gene that encodes a conserved kinase. In addition to autism, individuals with putative loss-of-function variants in DYRK1A exhibit microcephaly, intellectual disability, developmental delay and/or congenital anomalies of the kidney and urinary tract. DYRK1A is also located within the critical region for Down syndrome; therefore, understanding the role of DYRK1A in brain development is crucial for understanding the pathobiology of multiple developmental disorders. To characterize the function of this gene, we used the diploid frog Xenopus tropicalis We discover that Dyrk1a is expressed in ciliated tissues, localizes to ciliary axonemes and basal bodies, and is required for ciliogenesis. We also demonstrate that Dyrk1a localizes to mitotic spindles and that its inhibition leads to decreased forebrain size, abnormal cell cycle progression and cell death during brain development. These findings provide hypotheses about potential mechanisms of pathobiology and underscore the utility of X. tropicalis as a model system for understanding neurodevelopmental disorders.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Amanda Everitt
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
| | - Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard M Harland
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
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37
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Kakebeen AD, Chitsazan AD, Williams MC, Saunders LM, Wills AE. Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors. eLife 2020; 9:e52648. [PMID: 32338593 PMCID: PMC7250574 DOI: 10.7554/elife.52648] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/25/2020] [Indexed: 12/24/2022] Open
Abstract
Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. To better understand how a regenerative program is fulfilled by neural progenitor cells (NPCs) of the spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, we find that NPCs place an early priority on neuronal differentiation. Late in regeneration, the priority returns to proliferation. Our analyses identify Pbx3 and Meis1 as critical regulators of tail regeneration and axon organization. Overall, we use transcriptional regulatory dynamics to present a new model for cell fate decisions and their regulators in NPCs during regeneration.
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Affiliation(s)
| | | | | | - Lauren M Saunders
- Department of Genome Sciences, University of WashingtonSeattleUnited States
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38
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Li N, Wang J, Wallace SS, Chen J, Zhou J, D’Andrea AD. Cooperation of the NEIL3 and Fanconi anemia/BRCA pathways in interstrand crosslink repair. Nucleic Acids Res 2020; 48:3014-3028. [PMID: 31980815 PMCID: PMC7102959 DOI: 10.1093/nar/gkaa038] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 12/12/2019] [Accepted: 01/22/2020] [Indexed: 12/19/2022] Open
Abstract
The NEIL3 DNA glycosylase is a base excision repair enzyme that excises bulky base lesions from DNA. Although NEIL3 has been shown to unhook interstrand crosslinks (ICL) in Xenopus extracts, how NEIL3 participants in ICL repair in human cells and its corporation with the canonical Fanconi anemia (FA)/BRCA pathway remain unclear. Here we show that the NEIL3 and the FA/BRCA pathways are non-epistatic in psoralen-ICL repair. The NEIL3 pathway is the major pathway for repairing psoralen-ICL, and the FA/BRCA pathway is only activated when NEIL3 is not present. Mechanistically, NEIL3 is recruited to psoralen-ICL in a rapid, PARP-dependent manner. Importantly, the NEIL3 pathway repairs psoralen-ICLs without generating double-strand breaks (DSBs), unlike the FA/BRCA pathway. In addition, we found that the RUVBL1/2 complex physically interact with NEIL3 and function within the NEIL3 pathway in psoralen-ICL repair. Moreover, TRAIP is important for the recruitment of NEIL3 but not FANCD2, and knockdown of TRAIP promotes FA/BRCA pathway activation. Interestingly, TRAIP is non-epistatic with both NEIL3 and FA pathways in psoralen-ICL repair, suggesting that TRAIP may function upstream of the two pathways. Taken together, the NEIL3 pathway is the major pathway to repair psoralen-ICL through a unique DSB-free mechanism in human cells.
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Affiliation(s)
- Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - Jing Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Susan F. Smith Center for Women's Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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39
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Abstract
For decades, the early development of the Xenopus embryo has been an essential model system to study the gene regulatory mechanisms that govern cellular specification. At the top of the hierarchy of gene regulatory networks, maternally deposited transcription factors initiate this process and regulate the expression of zygotic genes that give rise to three distinctive germ layer cell types (ectoderm, mesoderm, and endoderm), and subsequent generation of organ precursors. The onset of germ layer specification is also closely coupled with changes associated with chromatin modifications. This review will examine the timing of maternal transcription factors initiating the zygotic genome activation, the epigenetic landscape of embryonic chromatin, and the network structure that governs the process.
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Affiliation(s)
- Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States; Center for Complex Biological Systems, University of California, Irvine, CA, United States
| | - Jin S Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States
| | - Junseok Yong
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, United States; Center for Complex Biological Systems, University of California, Irvine, CA, United States.
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40
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Nakajima K, Tanizaki Y, Luu N, Zhang H, Shi YB. Comprehensive RNA-Seq analysis of notochord-enriched genes induced during Xenopus tropicalis tail resorption. Gen Comp Endocrinol 2020; 287:113349. [PMID: 31794731 PMCID: PMC6956247 DOI: 10.1016/j.ygcen.2019.113349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/15/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022]
Abstract
Anuran metamorphosis is perhaps the most dramatic developmental process regulated by thyroid hormone (TH). One of the unique processes that occur during metamorphosis is the complete resorption of the tail, including the notochord. Interestingly, recent gene knockout studies have shown that of the two known vertebrate TH receptors, TRα and TRβ, TRβ appears to be critical for notochord regression during tail resorption in Xenopus tropicalis. To determine the mechanisms underlying notochord regression, we carried out a comprehensive gene expression analysis in the notochord during metamorphosis by using RNA-Seq analyses of whole tail at stage 60 before any noticeable tail length reduction, whole tail at stage 63 when the tail length is reduced by about one half, and the rest of the tail at stage 63 after removing the notochord. This allowed us to identify many notochord-enriched, metamorphosis-induced genes at stage 63. Future studies on these genes should help to determine if they are regulated by TRβ and play any roles in notochord regression.
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Affiliation(s)
- Keisuke Nakajima
- Division of Embryology, Amphibian Research Center, Hiroshima University, Higashihiroshima 739 8526, Japan.
| | - Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nga Luu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hongen Zhang
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yun Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA.
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41
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Schwenty-Lara J, Nehl D, Borchers A. The histone methyltransferase KMT2D, mutated in Kabuki syndrome patients, is required for neural crest cell formation and migration. Hum Mol Genet 2020; 29:305-319. [PMID: 31813957 PMCID: PMC7003132 DOI: 10.1093/hmg/ddz284] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 12/30/2022] Open
Abstract
Kabuki syndrome is an autosomal dominant developmental disorder with high similarities to CHARGE syndrome. It is characterized by a typical facial gestalt in combination with short stature, intellectual disability, skeletal findings and additional features like cardiac and urogenital malformations, cleft palate, hearing loss and ophthalmological anomalies. The major cause of Kabuki syndrome are mutations in KMT2D, a gene encoding a histone H3 lysine 4 (H3K4) methyltransferase belonging to the group of chromatin modifiers. Here we provide evidence that Kabuki syndrome is a neurocrestopathy, by showing that Kmt2d loss-of-function inhibits specific steps of neural crest (NC) development. Using the Xenopus model system, we find that Kmt2d loss-of-function recapitulates major features of Kabuki syndrome including severe craniofacial malformations. A detailed marker analysis revealed defects in NC formation as well as migration. Transplantation experiments confirm that Kmt2d function is required in NC cells. Furthermore, analyzing in vivo and in vitro NC migration behavior demonstrates that Kmt2d is necessary for cell dispersion but not protrusion formation of migrating NC cells. Importantly, Kmt2d knockdown correlates with a decrease in H3K4 monomethylation and H3K27 acetylation supporting a role of Kmt2d in the transcriptional activation of target genes. Consistently, using a candidate approach, we find that Kmt2d loss-of-function inhibits Xenopus Sema3F expression, and overexpression of Sema3F can partially rescue Kmt2d loss-of-function defects. Taken together, our data reveal novel functions of Kmt2d in multiple steps of NC development and support the hypothesis that major features of Kabuki syndrome are caused by defects in NC development.
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Affiliation(s)
- Janina Schwenty-Lara
- Department of Biology, Molecular Embryology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Denise Nehl
- Department of Biology, Molecular Embryology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps-Universität Marburg, Marburg 35043, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg 35043, Germany
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42
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Abstract
Antisense morpholino oligonucleotides (MOs) have become a valuable method to knockdown protein levels, to block with mRNA splicing and to interfere with miRNA function. MOs are widely used to alter gene expression in development of Xenopus and Zebrafish, where they are typically injected into the fertilized egg or blastomeres. Here we present methods to use electroporation to target delivery of MOs to the central nervous system of Xenopus laevis or Xenopus tropicalis tadpoles. Briefly, MO electroporation is accomplished by injecting MO solution into the brain ventricle and driving the MOs into cells of the brain with current passing between 2 platinum plate electrodes, positioned on either side of the target brain area. The method is relatively straightforward and uses standard equipment found in many neuroscience labs. A major advantage of electroporation is that it allows spatial and temporal control of MO delivery and therefore knockdown. Co-electroporation of MOs with cell type-specific fluorescent protein expression plasmids allows morphological analysis of cellular phenotypes. Furthermore, co-electroporation of MOs with rescuing plasmids allows assessment of specificity of the knockdown and phenotypic outcome. By combining MO-mediated manipulations with sophisticated assays of neuronal function, such as electrophysiological recording, behavioral assays, or in vivo time-lapse imaging of neuronal development, the functions of specific proteins and miRNAs within the developing nervous system can be elucidated. These methods can be adapted to apply antisense morpholinos to study protein and RNA function in a variety of complex tissues.
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Affiliation(s)
| | - Hollis T Cline
- The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA, USA.
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43
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Gentsch GE, Spruce T, Owens NDL, Smith JC. Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals. Nat Commun 2019; 10:4269. [PMID: 31537794 PMCID: PMC6753111 DOI: 10.1038/s41467-019-12263-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/30/2019] [Indexed: 12/14/2022] Open
Abstract
Embryonic development yields many different cell types in response to just a few families of inductive signals. The property of signal-receiving cells that determines how they respond to inductive signals is known as competence, and it differs in different cell types. Here, we explore the ways in which maternal factors modify chromatin to specify initial competence in the frog Xenopus tropicalis. We identify early-engaged regulatory DNA sequences, and infer from them critical activators of the zygotic genome. Of these, we show that the pioneering activity of the maternal pluripotency factors Pou5f3 and Sox3 determines competence for germ layer formation by extensively remodelling compacted chromatin before the onset of inductive signalling. This remodelling includes the opening and marking of thousands of regulatory elements, extensive chromatin looping, and the co-recruitment of signal-mediating transcription factors. Our work identifies significant developmental principles that inform our understanding of how pluripotent stem cells interpret inductive signals.
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Affiliation(s)
- George E Gentsch
- Developmental Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
| | - Thomas Spruce
- Centre for Genomic Regulation, Barcelona Institute for Science and Technology, 08003, Barcelona, Spain
| | - Nick D L Owens
- Department of Stem Cell and Developmental Biology, Pasteur Institute, 75015, Paris, France
| | - James C Smith
- Developmental Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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44
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Davis PE, Wilkinson EC, Dores RM. Identifying Common Features in the Activation of Melanocortin-2 Receptors: Studies on the Xenopus tropicalis Melanocortin-2 Receptor. Int J Mol Sci 2019; 20:ijms20174166. [PMID: 31454910 PMCID: PMC6747542 DOI: 10.3390/ijms20174166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 12/03/2022] Open
Abstract
The interaction between the pituitary hormone, adrenocorticotropin (ACTH), and melanocortin-2 receptor (MC2R) orthologs involves the H6 F7 R8 W9 and R/K15 K16 R17 R18 motifs in ACTH making contact with corresponding contact sites on MC2R. Earlier studies have localized the common HFRW binding site of all melanocortin receptors to residues in TM2, TM3, and TM6 that are located close to the extracellular space. The current study has identified residues in Xenopus tropicalis (xt) MC2R in TM4 (I158, F161), in EC2 (M166), and in TM5 (V172) that also are involved in activation of xtMC2R, and may be in the R/KKRR contact site of xtMC2R. These results are compared to earlier studies on the corresponding domains of human MC2R and rainbow trout MC2R in an effort to identify common features in the activation of teleost and tetrapod MC2R orthologs following stimulation with ACTH.
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Affiliation(s)
- Perry E Davis
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - Emily C Wilkinson
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - Robert M Dores
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA.
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45
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Hou P, Shi J, White KM, Gao Y, Cui J. ML277 specifically enhances the fully activated open state of KCNQ1 by modulating VSD-pore coupling. eLife 2019; 8:e48576. [PMID: 31329101 PMCID: PMC6684268 DOI: 10.7554/elife.48576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/22/2019] [Indexed: 12/16/2022] Open
Abstract
Upon membrane depolarization, the KCNQ1 potassium channel opens at the intermediate (IO) and activated (AO) states of the stepwise voltage-sensing domain (VSD) activation. In the heart, KCNQ1 associates with KCNE1 subunits to form IKs channels that regulate heart rhythm. KCNE1 suppresses the IO state so that the IKs channel opens only to the AO state. Here, we tested modulations of human KCNQ1 channels by an activator ML277 in Xenopus oocytes. It exclusively changes the pore opening properties of the AO state without altering the IO state, but does not affect VSD activation. These observations support a distinctive mechanism responsible for the VSD-pore coupling at the AO state that is sensitive to ML277 modulation. ML277 provides insights and a tool to investigate the gating mechanism of KCNQ1 channels, and our study reveals a new strategy for treating long QT syndrome by specifically enhancing the AO state of native IKs currents.
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Affiliation(s)
- Panpan Hou
- Department of Biomedical EngineeringWashington UniversitySt. LouisUnited States
- Center for the Investigation of Membrane Excitability DisordersWashington UniversitySt. LouisUnited States
- Cardiac Bioelectricity and Arrhythmia CenterWashington UniversitySt. LouisUnited States
| | - Jingyi Shi
- Department of Biomedical EngineeringWashington UniversitySt. LouisUnited States
- Center for the Investigation of Membrane Excitability DisordersWashington UniversitySt. LouisUnited States
- Cardiac Bioelectricity and Arrhythmia CenterWashington UniversitySt. LouisUnited States
| | - Kelli McFarland White
- Department of Biomedical EngineeringWashington UniversitySt. LouisUnited States
- Center for the Investigation of Membrane Excitability DisordersWashington UniversitySt. LouisUnited States
- Cardiac Bioelectricity and Arrhythmia CenterWashington UniversitySt. LouisUnited States
| | | | - Jianmin Cui
- Department of Biomedical EngineeringWashington UniversitySt. LouisUnited States
- Center for the Investigation of Membrane Excitability DisordersWashington UniversitySt. LouisUnited States
- Cardiac Bioelectricity and Arrhythmia CenterWashington UniversitySt. LouisUnited States
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46
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Abstract
Frog species of the genus Xenopus are widely used for studies of cell and developmental biology, and recent genome sequencing has revealed interesting phylogenetic relationships. Here we describe methods to generate haploid, triploid, and hybrid species starting from eggs and sperm of Xenopus laevis and Xenopus tropicalis that enable investigation of how genome size and content affect physiology at the organismal, cellular, and subcellular levels.
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Affiliation(s)
- Romain Gibeaux
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rebecca Heald
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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47
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Huang QT, Sheng CW, Jiang J, Jia ZQ, Han ZJ, Zhao CQ, Liu GY. Functional integrity of honeybee (Apis mellifera L.) resistant to dieldrin γ-aminobutyric acid receptor channels conjugated with three fluorescent proteins. Insect Mol Biol 2019; 28:313-320. [PMID: 30421825 DOI: 10.1111/imb.12552] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To generate an efficient tool used in Xenopus oocyte expression for in situ investigation of channel receptor expression, distribution and function, the C-terminus of the honeybee (Apis mellifera L.) resistant to dieldrin (RDL) subunit was fused with *FP, including monomeric red, enhanced yellow or enhanced green fluorescent protein (referred to as mRFP, EYFP and EGFP, respectively). In the present study, all fused *FP-AmRDLs could be visualized using fluorescence and laser confocal microscopy in cRNA-injected oocytes. Fluorescence was distributed isotropically in the cellular membrane. The potencies of the agonist γ-aminobutyric acid (GABA), but not β-alanine, and the test antagonists (fipronil, flufiprole, dieldrin, α-endosulfan, bifenazate and avermectin B1a) in the *FP-AmRDL receptor did not significantly differ from that of the untagged receptor with two-electrode voltage clamp detection. The half maximal effective concentrations (EC50 s) of GABA in AmRDL, EGFP-AmRDL, EYFP-AmRDL and mRFP-AmRDL receptors were 11.98, 12.61, 18.92 and 22.11 μM, respectively, and those of β-alanine were 651.6, 629.6, 1643.0 and 2146.0 μM, respectively. Inhibition percentages of test antagonists against *FP-AmRDL and AmRDL were not significantly different from each other. Overall, the consistency in functional properties between *FP-AmRDL and AmRDL receptors makes pGH19-*FP a promising tool for further in situ investigation of GABA receptors.
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Affiliation(s)
- Q-T Huang
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - C-W Sheng
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - J Jiang
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Z-Q Jia
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Z-J Han
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - C-Q Zhao
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - G-Y Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
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48
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Champeyroux C, Bellati J, Barberon M, Rofidal V, Maurel C, Santoni V. Regulation of a plant aquaporin by a Casparian strip membrane domain protein-like. Plant Cell Environ 2019; 42:1788-1801. [PMID: 30767240 DOI: 10.1111/pce.13537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 02/11/2019] [Indexed: 05/11/2023]
Abstract
The absorption of soil water by roots allows plants to maintain their water status. At the endodermis, water transport can be affected by initial formation of a Casparian strip and further deposition of suberin lamellas and regulated by the function of aquaporins. Four Casparian strip membrane domain protein-like (CASPL; CASPL1B1, CASPL1B2, CASPL1D1, and CASPL1D2) were previously shown to interact with PIP2;1. The present work shows that CASPL1B1, CASPL1B2, and CASPL1D2 are exclusively expressed in suberized endodermal cells, suggesting a cell-specific role in suberization and/or water transport regulation. When compared with wild-type plants, and by contrast to caspl1b1*caspl1b2 double loss of function, caspl1d1*caspl1d2 double mutants showed, in some control or NaCl stress experiments and not upon abscisic acid (ABA) treatment, a weak enlargement of the continuous suberization zone. None of the mutants showed root hydraulic conductivity (Lpr ) phenotype, whether in control, NaCl, or ABA treatment conditions. The data suggest a slight negative role for CASPL1D1 and CASPL1D2 in suberization under control or salt stress conditions, with no major impact on whole root transport functions. At the molecular level, CASPL1B1 was able to physically interact with PIP2;1 and potentially could influence the regulation of aquaporins by acting on their phosphorylated form.
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Affiliation(s)
- Chloé Champeyroux
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - Jorge Bellati
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - Marie Barberon
- Department of Botany and Plant Biology, Université de Genève, Geneva, Switzerland
| | - Valérie Rofidal
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - Christophe Maurel
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
| | - Véronique Santoni
- BPMP, Univ Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
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49
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Lara-Jacobo LR, Willard B, Wallace SJ, Langlois VS. Cytochrome P450 1A transcript is a suitable biomarker of both exposure and response to diluted bitumen in developing frog embryos. Environ Pollut 2019; 246:501-508. [PMID: 30583158 DOI: 10.1016/j.envpol.2018.12.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
In order for Alberta's thick bitumen to be transported through pipelines, condensates are added creating a diluted bitumen (dilbit) mixture. Recent pipeline expansion projects have generated concern about potential dilbit spills on aquatic wildlife health. Studies have suggested that polycyclic aromatic compounds (PACs) are toxic to aquatic vertebrates and could potentially also interfere with their endocrine system. The research objectives of this study were to investigate the toxicity of dilbit to developing frog embryos and to identify the molecular mechanisms of action involved. Fertilized embryos of Western clawed frog (Silurana tropicalis) were exposed for 72 h to water accommodated fractions (WAF; 0.7-8.9 μg/L TPACs) and chemically-enhanced WAFs (CEWAF; 0.09-56.7 μg/L TPACs) of Access Western Blend (AWB) and Cold Lake Blend (CLB) dilbits. Both dilbit's CEWAFs significantly increased embryonic mortality and malformation incidence in the highest treatments tested, while WAF treatments led to no visible toxic effects. Increases of the cytochrome P450 1A (cyp1a) mRNA levels were observed for all WAF and CEWAF dilbit treatments suggesting that phase I detoxification is activated in the dilbit-exposed larvae. When exposed to PAC concentrations ranging from 0.09 to 8.9 μg/L, the frogs displayed no observable malformations, but expressed significant increases of cyp1a mRNA levels (2- to 25-fold; indicating a suitable biomarker of exposure); however, when concentrations were of 46.6 μg/L or higher, both malformed frog phenotype and induction of cyp1a mRNA level (>250-fold) were measured (indicating a suitable biomarker of response). The expression of several genes related to cellular detoxification and endocrine disruption were also measured, but were not significantly altered by the treatments. In sum, cyp1a mRNA level is a highly sensitive endpoint to measure subtle molecular changes induced by PAC exposure in the frog embryos and larvae, and data suggest that PAC concentration higher than 46 μg/L would be toxic to the developing S. tropicalis.
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Affiliation(s)
- Linda R Lara-Jacobo
- Centre Eau Terre Environnment, Institut national de la recherche scientifique (INRS), Quebec City, QC, Canada
| | - Brianna Willard
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Sarah J Wallace
- Centre Eau Terre Environnment, Institut national de la recherche scientifique (INRS), Quebec City, QC, Canada; Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, Canada
| | - Valerie S Langlois
- Centre Eau Terre Environnment, Institut national de la recherche scientifique (INRS), Quebec City, QC, Canada; Department of Biology, Queen's University, Kingston, ON, Canada; Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, Canada.
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Abstract
At this time, no molecular targeted therapies exist for treatment of retinoblastoma. This can be, in part, attributed to the lack of animal models that allow for both rapid identification of novel therapeutic targets and hypothesis driven drug testing. Within this scope, we have recently reported the first genuine genetic nonmammalian retinoblastoma cancer model within the aquatic model organism Xenopus tropicalis (Naert et al., Sci Rep 6: 35263, 2016). Here we describe the methods to generate rb1 mosaic mutant Xenopus tropicalis by employing the CRISPR/Cas9 technology. In depth, we discuss short guide RNA (sgRNA) design parameters, generation, quality control, quantification, and delivery followed by several methods for assessing genome editing efficiencies. As such the reader should be capable, by minor changes to the methods described here, to (co-) target rb1 or any one or multiple gene(s) within the Xenopus tropicalis genome by multiplex CRISPR/Cas9 methodology.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
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