1
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Leclercq J, Torres-Paz J, Policarpo M, Agnès F, Rétaux S. Evolution of the regulation of developmental gene expression in blind Mexican cavefish. Development 2024; 151:dev202610. [PMID: 39007346 DOI: 10.1242/dev.202610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Developmental evolution and diversification of morphology can arise through changes in the regulation of gene expression or protein-coding sequence. To unravel mechanisms underlying early developmental evolution in cavefish of the species Astyanax mexicanus, we compared transcriptomes of surface-dwelling and blind cave-adapted morphs at the end of gastrulation. Twenty percent of the transcriptome was differentially expressed. Allelic expression ratios in cave X surface hybrids showed that cis-regulatory changes are the quasi-exclusive contributors to inter-morph variations in gene expression. Among a list of 108 genes with change at the cis-regulatory level, we explored the control of expression of rx3, which is a master eye gene. We discovered that cellular rx3 levels are cis-regulated in a cell-autonomous manner, whereas rx3 domain size depends on non-autonomous Wnt and Bmp signalling. These results highlight how uncoupled mechanisms and regulatory modules control developmental gene expression and shape morphological changes. Finally, a transcriptome-wide search for fixed coding mutations and differential exon use suggested that variations in coding sequence have a minor contribution. Thus, during early embryogenesis, changes in gene expression regulation are the main drivers of cavefish developmental evolution.
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Affiliation(s)
- Julien Leclercq
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Jorge Torres-Paz
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Maxime Policarpo
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - François Agnès
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Sylvie Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
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2
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Treccani S, Ferruti P, Alongi J, Monti E, Zizioli D, Ranucci E. Ecotoxicity Assessment of α-Amino Acid-Derived Polyamidoamines Using Zebrafish as a Vertebrate Model. Polymers (Basel) 2024; 16:2087. [PMID: 39065404 PMCID: PMC11280761 DOI: 10.3390/polym16142087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The aquatic ecotoxicity of three α-amino acid-derived polyamidoamines (PAAs) was studied using zebrafish embryos as a viable vertebrate model organism. The PAAs examined were water-soluble amphoteric polyelectrolytes with a primarily negative charge, which were efficient flame retardants for cotton. The fish embryo acute toxicity test performed with PAA water solutions using 1.5-500 mg L-1 concentrations showed that toxicity did not statistically differ from the control. The survival rates were indeed >90%, even at the highest concentration; the hatching rates were >80%; and the numbers of morphological defects were comparable to those of the control. Tests using transgenic zebrafish lines indicated that the numbers of microscopic vascular and musculoskeletal defects were comparable to the control, with one random concentration showing doubled alterations. Sensory-motor tests in response to visual and tactile stimuli were also performed. In the presence of PAAs, embryos exposed to alternating light/dark cycles showed an insignificant mobility reduction during the dark phase. Touch-evoked response tests revealed a mild effect of PAAs on the neuromotor system at concentrations > 10 mg L-1. The cystine/glycine copolymer at 100 mg L-1 exhibited the greatest effect. Overall, the studied PAAs showed a minimal impact on aquatic systems and should be further considered as promising ecofriendly materials.
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Affiliation(s)
- Sofia Treccani
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy; (S.T.); (P.F.); (J.A.)
| | - Paolo Ferruti
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy; (S.T.); (P.F.); (J.A.)
| | - Jenny Alongi
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy; (S.T.); (P.F.); (J.A.)
| | - Eugenio Monti
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy;
| | - Daniela Zizioli
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy;
| | - Elisabetta Ranucci
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy; (S.T.); (P.F.); (J.A.)
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3
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Clements WK, Khoury H. The molecular and cellular hematopoietic stem cell specification niche. Exp Hematol 2024; 136:104280. [PMID: 39009276 DOI: 10.1016/j.exphem.2024.104280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/17/2024]
Abstract
Hematopoietic stem cells (HSCs) are a population of tissue-specific stem cells that reside in the bone marrow of adult mammals, where they self-renew and continuously regenerate the adult hematopoietic lineages over the life of the individual. Prominence as a stem cell model and clinical usefulness have driven interest in understanding the physiologic processes that lead to the specification of HSCs during embryonic development. High-efficiency directed differentiation of HSCs by the instruction of defined progenitor cells using sequentially defined instructive molecules and conditions remains impossible, indicating that comprehensive knowledge of the complete set of precursor intermediate identities and required inductive inputs remains incompletely understood. Recently, interest in the molecular and cellular microenvironment where HSCs are specified from endothelial precursors-the "specification niche"-has increased. Here we review recent progress in understanding these niche spaces across vertebrate phyla, as well as how a better characterization of the origin and molecular phenotypes of the niche cell populations has helped inform and complicate previous understanding of signaling required for HSC emergence and maturation.
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Affiliation(s)
- Wilson K Clements
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN.
| | - Hanane Khoury
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN
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4
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Abitua PB, Stump LM, Aksel DC, Schier AF. Axis formation in annual killifish: Nodal and β-catenin regulate morphogenesis without Huluwa prepatterning. Science 2024; 384:1105-1110. [PMID: 38843334 DOI: 10.1126/science.ado7604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/08/2024] [Indexed: 06/16/2024]
Abstract
Axis formation in fish and amphibians typically begins with a prepattern of maternal gene products. Annual killifish embryogenesis, however, challenges prepatterning models as blastomeres disperse and then aggregate to form the germ layers and body axes. We show that huluwa, a prepatterning factor thought to break symmetry by stabilizing β-catenin, is truncated and inactive in Nothobranchius furzeri. Nuclear β-catenin is not selectively stabilized on one side of the blastula but accumulates in cells forming the aggregate. Blocking β-catenin activity or Nodal signaling disrupts aggregate formation and germ layer specification. Nodal signaling coordinates cell migration, establishing an early role for this signaling pathway. These results reveal a surprising departure from established mechanisms of axis formation: Huluwa-mediated prepatterning is dispensable, and β-catenin and Nodal regulate morphogenesis.
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Affiliation(s)
- Philip B Abitua
- Genome Sciences, University of Washington, Seattle, WA 98105, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Laura M Stump
- Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Deniz C Aksel
- Biophysics Program, Harvard University, Cambridge, MA 02138, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
- Biozentrum, University of Basel, 4051 Basel, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA 98195, USA
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5
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Fishman L, Modak A, Nechooshtan G, Razin T, Erhard F, Regev A, Farrell JA, Rabani M. Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nat Commun 2024; 15:3104. [PMID: 38600066 PMCID: PMC11006943 DOI: 10.1038/s41467-024-47290-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Avani Modak
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Talya Razin
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
- Chair of Computational Immunology, University of Regensburg, Regensburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge, MA, 02139, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard Cambridge, Cambridge, MA, 02142, USA
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA.
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel.
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6
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Chang NC, Wells JN, Wang AY, Schofield P, Huang YC, Truong VH, Simoes-Costa M, Feschotte C. Gag proteins encoded by endogenous retroviruses are required for zebrafish development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586437. [PMID: 38585793 PMCID: PMC10996621 DOI: 10.1101/2024.03.25.586437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. The process by which TEs become coopted remains obscure because most cases involve ancient, transpositionally inactive elements. Reports of active TEs serving beneficial functions are scarce and often contentious due to difficulties in manipulating repetitive sequences. Here we show that recently active TEs in zebrafish encode products critical for embryonic development. Knockdown and rescue experiments demonstrate that the endogenous retrovirus family BHIKHARI-1 (Bik-1) encodes a Gag protein essential for mesoderm development. Mechanistically, Bik-1 Gag associates with the cell membrane and its ectopic expression in chicken embryos alters cell migration. Similarly, depletion of BHIKHARI-2 Gag, a relative of Bik-1, causes defects in neural crest development in zebrafish. We propose an "addiction" model to explain how active TEs can be integrated into conserved developmental processes.
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Affiliation(s)
- Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Andrew Y Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Phillip Schofield
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Yi-Chia Huang
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Vinh H Truong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Marcos Simoes-Costa
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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7
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Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg CP. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development 2024; 151:dev202316. [PMID: 38372390 PMCID: PMC10911127 DOI: 10.1242/dev.202316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/04/2024] [Indexed: 02/20/2024]
Abstract
Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm.
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Affiliation(s)
- Alexandra Schauer
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
| | | | - Robert Hauschild
- Institute of Science and Technology Austria, Klosterneuburg 3400, Austria
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8
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Kocere A, Chiavacci E, Soneson C, Wells HH, Méndez-Acevedo KM, MacGowan JS, Jacobson ST, Hiltabidle MS, Raghunath A, Shavit JA, Panáková D, Williams MLK, Robinson MD, Mosimann C, Burger A. Rbm8a deficiency causes hematopoietic defects by modulating Wnt/PCP signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.12.536513. [PMID: 37090609 PMCID: PMC10120739 DOI: 10.1101/2023.04.12.536513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Defects in blood development frequently occur among syndromic congenital anomalies. Thrombocytopenia-Absent Radius (TAR) syndrome is a rare congenital condition with reduced platelets (hypomegakaryocytic thrombocytopenia) and forelimb anomalies, concurrent with more variable heart and kidney defects. TAR syndrome associates with hypomorphic gene function for RBM8A/Y14 that encodes a component of the exon junction complex involved in mRNA splicing, transport, and nonsense-mediated decay. How perturbing a general mRNA-processing factor causes the selective TAR Syndrome phenotypes remains unknown. Here, we connect zebrafish rbm8a perturbation to early hematopoietic defects via attenuated non-canonical Wnt/Planar Cell Polarity (PCP) signaling that controls developmental cell re-arrangements. In hypomorphic rbm8a zebrafish, we observe a significant reduction of cd41-positive thrombocytes. rbm8a-mutant zebrafish embryos accumulate mRNAs with individual retained introns, a hallmark of defective nonsense-mediated decay; affected mRNAs include transcripts for non-canonical Wnt/PCP pathway components. We establish that rbm8a-mutant embryos show convergent extension defects and that reduced rbm8a function interacts with perturbations in non-canonical Wnt/PCP pathway genes wnt5b, wnt11f2, fzd7a, and vangl2. Using live-imaging, we found reduced rbm8a function impairs the architecture of the lateral plate mesoderm (LPM) that forms hematopoietic, cardiovascular, kidney, and forelimb skeleton progenitors as affected in TAR Syndrome. Both mutants for rbm8a and for the PCP gene vangl2 feature impaired expression of early hematopoietic/endothelial genes including runx1 and the megakaryocyte regulator gfi1aa. Together, our data propose aberrant LPM patterning and hematopoietic defects as consequence of attenuated non-canonical Wnt/PCP signaling upon reduced rbm8a function. These results also link TAR Syndrome to a potential LPM origin and a developmental mechanism.
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Affiliation(s)
- Agnese Kocere
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Elena Chiavacci
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Charlotte Soneson
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Harrison H. Wells
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Jacalyn S. MacGowan
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Seth T. Jacobson
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Max S. Hiltabidle
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Azhwar Raghunath
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jordan A. Shavit
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniela Panáková
- Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany
- University Hospital Schleswig Holstein, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg, Kiel, Lübeck, Germany
| | - Margot L. K. Williams
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mark D. Robinson
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alexa Burger
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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9
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Jumde G, Spanjaard B, Junker JP. Inference of differentiation trajectories by transfer learning across biological processes. Cell Syst 2024; 15:75-82.e5. [PMID: 38128536 DOI: 10.1016/j.cels.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/28/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Stem cells differentiate into distinct fates by transitioning through a series of transcriptional states. Current computational approaches allow reconstruction of differentiation trajectories from single-cell transcriptomics data, but it remains unknown to what degree differentiation can be predicted across biological processes. Here, we use transfer learning to infer differentiation processes and quantify predictability in early embryonic development and adult hematopoiesis. Overall, we find that non-linear methods outperform linear approaches, and we achieved the best predictions with a custom variational autoencoder that explicitly models changes in transcriptional variance. We observed a high accuracy of predictions in embryonic development, but we found somewhat lower agreement with the real data in adult hematopoiesis. We demonstrate that this discrepancy can be explained by a higher degree of concordant transcriptional processes along embryonic differentiation compared with adult homeostasis. In summary, we establish a framework for quantifying and exploiting predictability of cellular differentiation trajectories.
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Affiliation(s)
- Gaurav Jumde
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Humboldt Universität zu Berlin, Faculty of Life Sciences, Department of Biology, 10115 Berlin, Germany
| | - Bastiaan Spanjaard
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
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10
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Toulany N, Morales-Navarrete H, Čapek D, Grathwohl J, Ünalan M, Müller P. Uncovering developmental time and tempo using deep learning. Nat Methods 2023; 20:2000-2010. [PMID: 37996754 PMCID: PMC10703695 DOI: 10.1038/s41592-023-02083-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 10/15/2023] [Indexed: 11/25/2023]
Abstract
During animal development, embryos undergo complex morphological changes over time. Differences in developmental tempo between species are emerging as principal drivers of evolutionary novelty, but accurate description of these processes is very challenging. To address this challenge, we present here an automated and unbiased deep learning approach to analyze the similarity between embryos of different timepoints. Calculation of similarities across stages resulted in complex phenotypic fingerprints, which carry characteristic information about developmental time and tempo. Using this approach, we were able to accurately stage embryos, quantitatively determine temperature-dependent developmental tempo, detect naturally occurring and induced changes in the developmental progression of individual embryos, and derive staging atlases for several species de novo in an unsupervised manner. Our approach allows us to quantify developmental time and tempo objectively and provides a standardized way to analyze early embryogenesis.
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Affiliation(s)
- Nikan Toulany
- Systems Biology of Development, University of Konstanz, Konstanz, Germany
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- University Hospital and Faculty of Medicine, University of Tübingen, Tübingen, Germany
| | - Hernán Morales-Navarrete
- Systems Biology of Development, University of Konstanz, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, Konstanz, Germany
| | - Daniel Čapek
- Systems Biology of Development, University of Konstanz, Konstanz, Germany
| | - Jannis Grathwohl
- Systems Biology of Development, University of Konstanz, Konstanz, Germany
| | - Murat Ünalan
- Systems Biology of Development, University of Konstanz, Konstanz, Germany.
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
| | - Patrick Müller
- Systems Biology of Development, University of Konstanz, Konstanz, Germany.
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
- University Hospital and Faculty of Medicine, University of Tübingen, Tübingen, Germany.
- Centre for the Advanced Study of Collective Behaviour, Konstanz, Germany.
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11
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Guinle C, Núñez-Vázquez EJ, Fernández-Herrera LJ, Corona-Rojas DA, Tovar-Ramírez D. Toxicogenomic Effects of Dissolved Saxitoxin on the Early Life Stages of the Longfin Yellowtail ( Seriola rivoliana). Mar Drugs 2023; 21:597. [PMID: 37999421 PMCID: PMC10671919 DOI: 10.3390/md21110597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/09/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
Harmful algal blooms (HABs) can produce a variety of noxious effects and, in some cases, the massive mortality of wild and farmed marine organisms. Some HAB species produce toxins that are released into seawater or transferred via food webs (particulate toxin fraction). The objective of the present study was to identify the toxicological effects of subacute exposure to saxitoxin (STX) during embryonic and early larval stages in Seriola rivoliana. Eggs were exposed to dissolved 19 STX (100 μg L-1). The toxic effects of STX were evaluated via the hatching percentage, the activity of three enzymes (protein and alkaline phosphatases and peroxidase), and the expression of four genes (HSF2, Nav1.4b, PPRC1, and DUSP8). A low hatching percentage (less than 5%) was observed in 44 hpf (hours post fertilization) embryos exposed to STX compared to 71% in the unexposed control. At this STX concentration, no oxidative stress in the embryos was evident. However, STX induced the expression of the NaV1.4 channel α-subunit (NaV1.4b), which is the primary target of this toxin. Our results revealed the overexpression of all four candidate genes in STX-intoxicated lecithotrophic larvae, reflecting the activation of diverse cellular processes involved in stress responses (HSF2), lipid metabolism (PPRC1), and MAP kinase signaling pathways associated with cell proliferation and differentiation (DUSP8). The effects of STX were more pronounced in young larvae than in embryos, indicating a stage-specific sensitivity to the toxin.
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Affiliation(s)
- Colleen Guinle
- Centro de Investigaciones Biológicas del Noroeste, Laboratorio de Fisiología Comparada y Genómica Funcional, Av. Instituto Politécnico Nacional 195 Playa Palo de Santa Rita, La Paz 23096, Mexico; (C.G.); (D.A.C.-R.)
| | - Erick Julián Núñez-Vázquez
- Centro de Investigaciones Biológicas del Noroeste, Laboratorio de Toxinas Marinas y Aminoácidos, Av. Instituto Politécnico Nacional 195 Playa Palo de Santa Rita, La Paz 23096, Mexico;
| | - Leyberth José Fernández-Herrera
- Centro de Investigaciones Biológicas del Noroeste, Laboratorio de Toxinas Marinas y Aminoácidos, Av. Instituto Politécnico Nacional 195 Playa Palo de Santa Rita, La Paz 23096, Mexico;
| | - Daniela Alejandra Corona-Rojas
- Centro de Investigaciones Biológicas del Noroeste, Laboratorio de Fisiología Comparada y Genómica Funcional, Av. Instituto Politécnico Nacional 195 Playa Palo de Santa Rita, La Paz 23096, Mexico; (C.G.); (D.A.C.-R.)
| | - Dariel Tovar-Ramírez
- Centro de Investigaciones Biológicas del Noroeste, Laboratorio de Fisiología Comparada y Genómica Funcional, Av. Instituto Politécnico Nacional 195 Playa Palo de Santa Rita, La Paz 23096, Mexico; (C.G.); (D.A.C.-R.)
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12
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Karvas RM, Zemke JE, Ali SS, Upton E, Sane E, Fischer LA, Dong C, Park KM, Wang F, Park K, Hao S, Chew B, Meyer B, Zhou C, Dietmann S, Theunissen TW. 3D-cultured blastoids model human embryogenesis from pre-implantation to early gastrulation stages. Cell Stem Cell 2023; 30:1148-1165.e7. [PMID: 37683602 DOI: 10.1016/j.stem.2023.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/24/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
Naive human pluripotent stem cells have the remarkable ability to self-organize into blastocyst-like structures ("blastoids") that model lineage segregation in the pre-implantation embryo. However, the extent to which blastoids can recapitulate the defining features of human post-implantation development remains unexplored. Here, we report that blastoids cultured on thick three-dimensional (3D) extracellular matrices capture hallmarks of early post-implantation development, including epiblast lumenogenesis, rapid expansion and diversification of trophoblast lineages, and robust invasion of extravillous trophoblast cells by day 14. Extended blastoid culture results in the localized activation of primitive streak marker TBXT and the emergence of embryonic germ layers by day 21. We also show that the modulation of WNT signaling alters the balance between epiblast and trophoblast fates in post-implantation blastoids. This work demonstrates that 3D-cultured blastoids offer a continuous and integrated in vitro model system of human embryonic and extraembryonic development from pre-implantation to early gastrulation stages.
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Affiliation(s)
- Rowan M Karvas
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph E Zemke
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Syed Shahzaib Ali
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric Upton
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eshan Sane
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura A Fischer
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chen Dong
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kyoung-Mi Park
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fei Wang
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kibeom Park
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Senyue Hao
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brian Chew
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brittany Meyer
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chao Zhou
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sabine Dietmann
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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13
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Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages. Mol Biol Evol 2023; 40:msad188. [PMID: 37739926 PMCID: PMC10516590 DOI: 10.1093/molbev/msad188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023] Open
Abstract
Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.
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Affiliation(s)
- Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego, CA, USA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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14
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Fu XX, Zhuo DH, Zhang YJ, Li YF, Liu X, Xing YY, Huang Y, Wang YF, Cheng T, Wang D, Chen SH, Chen YJ, Jiang GN, Lu FI, Feng Y, Huang X, Ma J, Liu W, Bai G, Xu PF. A spatiotemporal barrier formed by Follistatin is required for left-right patterning. Proc Natl Acad Sci U S A 2023; 120:e2219649120. [PMID: 37276408 PMCID: PMC10268237 DOI: 10.1073/pnas.2219649120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/25/2023] [Indexed: 06/07/2023] Open
Abstract
How left-right (LR) asymmetry emerges in a patterning field along the anterior-posterior axis remains an unresolved problem in developmental biology. Left-biased Nodal emanating from the LR organizer propagates from posterior to anterior (PA) and establishes the LR pattern of the whole embryo. However, little is known about the regulatory mechanism of the PA spread of Nodal and its asymmetric activation in the forebrain. Here, we identify bilaterally expressed Follistatin (Fst) as a regulator blocking the propagation of the zebrafish Nodal ortholog Southpaw (Spaw) in the right lateral plate mesoderm (LPM), and restricting Spaw transmission in the left LPM to facilitate the establishment of a robust LR asymmetric Nodal patterning. In addition, Fst inhibits the Activin-Nodal signaling pathway in the forebrain thus preventing Nodal activation prior to the arrival, at a later time, of Spaw emanating from the left LPM. This contributes to the orderly propagation of asymmetric Nodal activation along the PA axis. The LR regulation function of Fst is further confirmed in chick and frog embryos. Overall, our results suggest that a robust LR patterning emerges by counteracting a Fst barrier formed along the PA axis.
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Affiliation(s)
- Xin-Xin Fu
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Ding-Hao Zhuo
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Ying-Jie Zhang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Yun-Fei Li
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Xiang Liu
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Yan-Yi Xing
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorders, Hangzhou310058, China
| | - Ying Huang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Yi-Fan Wang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
- Precision Medicine Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117599, Singapore
| | - Tao Cheng
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Dan Wang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Si-Han Chen
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou310058, China
- Liangzhu Laboratory, Ministry of Education Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, Hangzhou311121, China
| | - Yi-Jian Chen
- Institute of Cell and Developmental Biology, Zhejiang University School of Life Sciences, Hangzhou310058, China
| | - Guan-Nan Jiang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Fu-I Lu
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - Yu Feng
- Department of Biophysics and Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Xiao Huang
- Institute of Cell and Developmental Biology, Zhejiang University School of Life Sciences, Hangzhou310058, China
| | - Jun Ma
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Wei Liu
- Department of Metabolic Medicine, International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu32200, China
| | - Ge Bai
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou310058, China
- Liangzhu Laboratory, Ministry of Education Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, Hangzhou311121, China
| | - Peng-Fei Xu
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
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15
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Čapek D, Safroshkin M, Morales-Navarrete H, Toulany N, Arutyunov G, Kurzbach A, Bihler J, Hagauer J, Kick S, Jones F, Jordan B, Müller P. EmbryoNet: using deep learning to link embryonic phenotypes to signaling pathways. Nat Methods 2023:10.1038/s41592-023-01873-4. [PMID: 37156842 DOI: 10.1038/s41592-023-01873-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/05/2023] [Indexed: 05/10/2023]
Abstract
Evolutionarily conserved signaling pathways are essential for early embryogenesis, and reducing or abolishing their activity leads to characteristic developmental defects. Classification of phenotypic defects can identify the underlying signaling mechanisms, but this requires expert knowledge and the classification schemes have not been standardized. Here we use a machine learning approach for automated phenotyping to train a deep convolutional neural network, EmbryoNet, to accurately identify zebrafish signaling mutants in an unbiased manner. Combined with a model of time-dependent developmental trajectories, this approach identifies and classifies with high precision phenotypic defects caused by loss of function of the seven major signaling pathways relevant for vertebrate development. Our classification algorithms have wide applications in developmental biology and robustly identify signaling defects in evolutionarily distant species. Furthermore, using automated phenotyping in high-throughput drug screens, we show that EmbryoNet can resolve the mechanism of action of pharmaceutical substances. As part of this work, we freely provide more than 2 million images that were used to train and test EmbryoNet.
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Affiliation(s)
- Daniel Čapek
- Systems Biology of Development, University of Konstanz, Konstanz, Germany
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | | | - Hernán Morales-Navarrete
- Systems Biology of Development, University of Konstanz, Konstanz, Germany
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- Centre for the Advanced Study of Collective Behaviour, Konstanz, Germany
| | - Nikan Toulany
- Systems Biology of Development, University of Konstanz, Konstanz, Germany
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | | | - Anica Kurzbach
- Systems Biology of Development, University of Konstanz, Konstanz, Germany
| | - Johanna Bihler
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Julia Hagauer
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Sebastian Kick
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Felicity Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Ben Jordan
- Systems Biology of Development, University of Konstanz, Konstanz, Germany
| | - Patrick Müller
- Systems Biology of Development, University of Konstanz, Konstanz, Germany.
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
- Centre for the Advanced Study of Collective Behaviour, Konstanz, Germany.
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16
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AI identifies developmental defects and drug mechanisms in embryos. Nat Methods 2023:10.1038/s41592-023-01872-5. [PMID: 37156845 DOI: 10.1038/s41592-023-01872-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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17
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Kocere A, Lalonde RL, Mosimann C, Burger A. Lateral thinking in syndromic congenital cardiovascular disease. Dis Model Mech 2023; 16:dmm049735. [PMID: 37125615 PMCID: PMC10184679 DOI: 10.1242/dmm.049735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Syndromic birth defects are rare diseases that can present with seemingly pleiotropic comorbidities. Prime examples are rare congenital heart and cardiovascular anomalies that can be accompanied by forelimb defects, kidney disorders and more. Whether such multi-organ defects share a developmental link remains a key question with relevance to the diagnosis, therapeutic intervention and long-term care of affected patients. The heart, endothelial and blood lineages develop together from the lateral plate mesoderm (LPM), which also harbors the progenitor cells for limb connective tissue, kidneys, mesothelia and smooth muscle. This developmental plasticity of the LPM, which founds on multi-lineage progenitor cells and shared transcription factor expression across different descendant lineages, has the potential to explain the seemingly disparate syndromic defects in rare congenital diseases. Combining patient genome-sequencing data with model organism studies has already provided a wealth of insights into complex LPM-associated birth defects, such as heart-hand syndromes. Here, we summarize developmental and known disease-causing mechanisms in early LPM patterning, address how defects in these processes drive multi-organ comorbidities, and outline how several cardiovascular and hematopoietic birth defects with complex comorbidities may be LPM-associated diseases. We also discuss strategies to integrate patient sequencing, data-aggregating resources and model organism studies to mechanistically decode congenital defects, including potentially LPM-associated orphan diseases. Eventually, linking complex congenital phenotypes to a common LPM origin provides a framework to discover developmental mechanisms and to anticipate comorbidities in congenital diseases affecting the cardiovascular system and beyond.
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Affiliation(s)
- Agnese Kocere
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
- Department of Molecular Life Science, University of Zurich, 8057 Zurich, Switzerland
| | - Robert L. Lalonde
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
| | - Christian Mosimann
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
| | - Alexa Burger
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, Aurora, CO 80045, USA
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18
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Cheng T, Xing YY, Liu C, Li YF, Huang Y, Liu X, Zhang YJ, Zhao GQ, Dong Y, Fu XX, Tian YM, Shu LP, Megason SG, Xu PF. Nodal coordinates the anterior-posterior patterning of germ layers and induces head formation in zebrafish explants. Cell Rep 2023; 42:112351. [PMID: 37018074 DOI: 10.1016/j.celrep.2023.112351] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 01/16/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Much progress has been made toward generating analogs of early embryos, such as gastruloids and embryoids, in vitro. However, methods for how to fully mimic the cell movements of gastrulation and coordinate germ-layer patterning to induce head formation are still lacking. Here, we show that a regional Nodal gradient applied to zebrafish animal pole explant can generate a structure that recapitulates the key cell movements of gastrulation. Using single-cell transcriptome and in situ hybridization analysis, we assess the dynamics of the cell fates and patterning of this structure. The mesendoderm differentiates into the anterior endoderm, prechordal plate, notochord, and tailbud-like cells along an anterior-posterior axis, and an anterior-posterior-patterned head-like structure (HLS) progressively forms during late gastrulation. Among 105 immediate Nodal targets, 14 genes contain axis-induction ability, and 5 of them induce a complete or partial head structure when overexpressed in the ventral side of zebrafish embryos.
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Affiliation(s)
- Tao Cheng
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan-Yi Xing
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorders, Hangzhou, Zhejiang, China
| | - Cong Liu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yun-Fei Li
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Huang
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiang Liu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying-Jie Zhang
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guo-Qin Zhao
- Department of Immunology, Guizhou Medical University, Guiyang 550004, China
| | - Yang Dong
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xin-Xin Fu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yi-Meng Tian
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Li-Ping Shu
- Department of Immunology, Guizhou Medical University, Guiyang 550004, China
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
| | - Peng-Fei Xu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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19
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Fishman L, Nechooshtan G, Erhard F, Regev A, Farrell JA, Rabani M. Single-cell temporal dynamics reveals the relative contributions of transcription and degradation to cell-type specific gene expression in zebrafish embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537620. [PMID: 37131717 PMCID: PMC10153228 DOI: 10.1101/2023.04.20.537620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the underlying regulation of mRNA transcription and degradation remains a challenge, especially within whole embryos with diverse cellular identities. Here, we collect temporal cellular transcriptomes of zebrafish embryos, and decompose them into their newly-transcribed (zygotic) and pre-existing (maternal) mRNA components by combining single-cell RNA-Seq and metabolic labeling. We introduce kinetic models capable of quantifying regulatory rates of mRNA transcription and degradation within individual cell types during their specification. These reveal different regulatory rates between thousands of genes, and sometimes between cell types, that shape spatio-temporal expression patterns. Transcription drives most cell-type restricted gene expression. However, selective retention of maternal transcripts helps to define the gene expression profiles of germ cells and enveloping layer cells, two of the earliest specified cell-types. Coordination between transcription and degradation restricts expression of maternal-zygotic genes to specific cell types or times, and allows the emergence of spatio-temporal patterns when overall mRNA levels are held relatively constant. Sequence-based analysis links differences in degradation to specific sequence motifs. Our study reveals mRNA transcription and degradation events that control embryonic gene expression, and provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jeffrey A. Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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20
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Mizoguchi T, Mikami S, Yatou M, Kondo Y, Omaru S, Kuwabara S, Okura W, Noda S, Tenno T, Hiroaki H, Itoh M. Small-Molecule-Mediated Suppression of BMP Signaling by Selective Inhibition of BMP1-Dependent Chordin Cleavage. Int J Mol Sci 2023; 24:4313. [PMID: 36901744 PMCID: PMC10001940 DOI: 10.3390/ijms24054313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
BMP signaling is critical for many biological processes. Therefore, small molecules that modulate BMP signaling are useful for elucidating the function of BMP signaling and treating BMP signaling-related diseases. Here, we performed a phenotypic screening in zebrafish to examine the in vivo effects of N-substituted-2-amino-benzoic acid analogs NPL1010 and NPL3008 and found that they affect BMP signaling-dependent dorsal-ventral (D-V) patterning and bone formation in zebrafish embryos. Furthermore, NPL1010 and NPL3008 suppressed BMP signaling upstream of BMP receptors. BMP1 cleaves Chordin, an antagonist of BMP, and negatively regulates BMP signaling. Docking simulations demonstrated that NPL1010 and NPL3008 bind BMP1. We found that NPL1010 and NPL3008 partially rescued the disruptions in the D-V phenotype caused by bmp1 overexpression and selectively inhibited BMP1-dependent Chordin cleavage. Therefore, NPL1010 and NPL3008 are potentially valuable inhibitors of BMP signaling that act through selective inhibition of Chordin cleavage.
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Affiliation(s)
- Takamasa Mizoguchi
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Shohei Mikami
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Mari Yatou
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Yui Kondo
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Shuhei Omaru
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Shuhei Kuwabara
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Wataru Okura
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Syouta Noda
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Aichi, Japan
| | - Takeshi Tenno
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Aichi, Japan
- BeCerllBar, LLC., Business Incubation Building, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
| | - Hidekazu Hiroaki
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Aichi, Japan
- BeCerllBar, LLC., Business Incubation Building, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8601, Aichi, Japan
- Department of Biological Sciences, Faculty of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Aichi, Japan
| | - Motoyuki Itoh
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
- Research Institute of Disaster Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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21
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Xiao Y, Chen J, Yang S, Sun H, Xie L, Li J, Jing N, Zhu X. Maternal mRNA deadenylation and allocation via Rbm14 condensates facilitate vertebrate blastula development. EMBO J 2023; 42:e111364. [PMID: 36477743 PMCID: PMC9890236 DOI: 10.15252/embj.2022111364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
Early embryonic development depends on proper utilization and clearance of maternal transcriptomes. How these processes are spatiotemporally regulated remains unclear. Here we show that nuclear RNA-binding protein Rbm14 and maternal mRNAs co-phase separate into cytoplasmic condensates to facilitate vertebrate blastula-to-gastrula development. In zebrafish, Rbm14 condensates were highly abundant in blastomeres and markedly reduced after prominent activation of zygotic transcription. They concentrated at spindle poles by associating with centrosomal γ-tubulin puncta and displayed mainly asymmetric divisions with a global symmetry across embryonic midline in 8- and 16-cell embryos. Their formation was dose-dependently stimulated by m6 A, but repressed by m5 C modification of the maternal mRNA. Furthermore, deadenylase Parn co-phase separated with these condensates, and this was required for deadenylation of the mRNAs in early blastomeres. Depletion of Rbm14 impaired embryonic cell differentiations and full activations of the zygotic genome in both zebrafish and mouse and resulted in developmental arrest at the blastula stage. Our results suggest that cytoplasmic Rbm14 condensate formation regulates early embryogenesis by facilitating deadenylation, protection, and mitotic allocation of m6 A-modified maternal mRNAs, and by releasing the poly(A)-less transcripts upon regulated disassembly to allow their re-polyadenylation and translation or clearance.
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Affiliation(s)
- Yue Xiao
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
| | - Jiehui Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Suming Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Honghua Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Lele Xie
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouChina
| | - Xueliang Zhu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
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22
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Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526059. [PMID: 36778215 PMCID: PMC9915506 DOI: 10.1101/2023.01.30.526059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 wild fish species that either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences (CONDELs) in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA , a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, s yngnathid, and synbranchid species with caudal fin reduction, and which alters caudal fin development when targeted by genome editing. Our study illustrates a general strategy for mapping phenotypes to genotypes across a tree of vertebrate species, and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes during 100 million years of fish evolution.
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Affiliation(s)
- Heidi I. Chen
- Department of Developmental Biology, Stanford University School of Medicine, CA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, CA
- Department of Biomedical Data Science, Stanford University School of Medicine, CA
- Department of Computer Science, Stanford University School of Engineering, CA
- Department of Pediatrics, Stanford University School of Medicine, CA
| | - David M. Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, CA
- Howard Hughes Medical Institute, Stanford University, CA
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23
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van Boxtel AL. Whole-Mount In Situ Hybridization for Detection of Migrating Zebrafish Endodermal Cells. Methods Mol Biol 2023; 2608:131-145. [PMID: 36653706 DOI: 10.1007/978-1-0716-2887-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
One of the most important events in early vertebrate development is the formation and positioning of the endoderm, the embryonic progenitor cell population that gives rise to the internal organs. Recent years have seen renewed interest in the mechanisms underlying the specification and migration of endodermal progenitor cells. The zebrafish is a well-established, accessible, and powerful model to study this cell population. Zebrafish endodermal cells are specified around 4 h after fertilization and subsequently migrate as evenly spaced single cells in a stereotypical manner in the next 6 h. Given the large numbers of fertilized eggs that can be obtained from a single breeding pair and the ease of chemical and genetic perturbations, the zebrafish is an excellent model to study mechanisms underlying endoderm specification and migration. An easy approach to visualizing and quantitating endodermal cells and their migratory routes is by whole-mount in situ hybridization (WISH) on fixed embryos, collected in time series. This chapter provides basic information on the organization and staging of the embryos, with an emphasis on the migrating endodermal cell population. In addition, optimized protocols for the isolation and fixation of staged embryos are provided as well as detailed probe synthesis and WISH protocols, specific for migrating endoderm. Finally, details are provided on how to approach these experiments quantitatively, and some common pitfalls are discussed.
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Affiliation(s)
- Antonius L van Boxtel
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
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24
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Wang B, Zhao Q, Gong X, Wang C, Bai Y, Wang H, Zhou J, Rong X. Transmembrane anterior posterior transformation 1 regulates BMP signaling and modulates the protein stability of SMAD1/5. J Biol Chem 2022; 298:102684. [PMID: 36370851 PMCID: PMC9763856 DOI: 10.1016/j.jbc.2022.102684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022] Open
Abstract
The bone morphogenetic protein (BMP) signaling pathway plays pivotal roles in various biological processes during embryogenesis and adult homeostasis. Transmembrane anterior posterior transformation 1 (TAPT1) is an evolutionarily conserved protein involved in murine axial skeletal patterning. Genetic defects in TAPT1 result in complex lethal osteochondrodysplasia. However, the specific cellular activity of TAPT1 is not clear. Herein, we report that TAPT1 inhibits BMP signaling and destabilizes the SMAD1/5 protein by facilitating its interaction with SMURF1 E3 ubiquitin ligase, which leads to SMAD1/5 proteasomal degradation. In addition, we found that the activation of BMP signaling facilitates the redistribution of TAPT1 and promotes its association with SMAD1. TAPT1-deficient murine C2C12 myoblasts or C3H/10T1/2 mesenchymal stem cells exhibit elevated SMAD1/5/9 protein levels, which amplifies BMP activation, in turn leading to a boost in the transdifferentiation or differentiation processing of these distinct TAPT1-deficient cell lines changing into mature osteoblasts. Furthermore, the enhancing effect of TAPT1 deficiency on osteogenic differentiation of C3H/10T1/2 cells was observed in an in vivo ectopic bone formation model. Importantly, a subset of TAPT1 mutations identified in humans with lethal skeletal dysplasia exhibited gain-of-function activity on SMAD1 protein levels. Thus, this finding elucidates the role of TAPT1 in the regulation of SMAD1/5 protein stability for controlling BMP signaling.
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Affiliation(s)
- Bo Wang
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Qian Zhao
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xiaoxia Gong
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Caixia Wang
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Yan Bai
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Hongying Wang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Jianfeng Zhou
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.
| | - Xiaozhi Rong
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.
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25
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Xing C, Zeng Z, Li Y, Gong B, Shen W, Shah R, Yan L, Du H, Meng A. Regulatory factor identification for nodal genes in zebrafish by causal inference. Front Cell Dev Biol 2022; 10:1047363. [DOI: 10.3389/fcell.2022.1047363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Activation of nodal genes is critical for mesoderm and endoderm induction. Our previous study reported that zebrafish nodal genes ndr1/squint and ndr2/cyclops are coordinately regulated by maternal Eomesa, Hwa-activated β-catenin (Hwa/β-catenin) signaling, and Nodal autoregulation (Nodal/Smad2) signaling. However, the exact contribution and underlying mechanisms are still elusive. Here, we applied “causal inference” to evaluate the causal between the independent and dependent variables, and we found that Hwa/β-catenin and Smad2 are the cause of ndr1 activation, while Eomesa is the cause of ndr2 activation. Mechanistically, the different cis-regulatory regions of ndr1 and ndr2 bound by Eomesa, β-catenin, and Smad2 were screened out via ChIP-qPCR and verified by the transgene constructs. The marginal GFP expression driven by ndr1 transgenesis could be diminished without both maternal Eomesa and Hwa/β-catenin, while Eomesa, not β-catenin, could bind and activate ndr2 demonstrated by ndr2 transgenesis. Thus, the distinct regulation of ndr1/ndr2 relies on different cis-regulatory regions.
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26
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Stock J, Kazmar T, Schlumm F, Hannezo E, Pauli A. A self-generated Toddler gradient guides mesodermal cell migration. SCIENCE ADVANCES 2022; 8:eadd2488. [PMID: 36103529 PMCID: PMC9473572 DOI: 10.1126/sciadv.add2488] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor-based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo.
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Affiliation(s)
- Jessica Stock
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Tomas Kazmar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Friederike Schlumm
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Edouard Hannezo
- Institute of Science and Technology Austria (IST), Klosterneuburg, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
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27
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Feng G, Sun Y. The Polycomb group gene rnf2 is essential for central and enteric neural system development in zebrafish. Front Neurosci 2022; 16:960149. [PMID: 36117635 PMCID: PMC9475114 DOI: 10.3389/fnins.2022.960149] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
The development of central nervous system (CNS) and enteric nervous system (ENS) is under precise and strict control in vertebrates. Whether and how the Polycomb repressive complex 1 (PRC1) is involved in it remain unclear. To investigate the role of PRC1 in the nervous system development, using CRISPR/Cas9 technology, we have generated mutant zebrafish lines for the rnf2 gene which encodes Ring1b, the enzymatic component of the PRC1 complex. We show that rnf2 loss of function leads to abnormal migration and differentiation of neural crest and neural precursor cells. rnf2 mutant embryos exhibit aganglionosis, in which the hindgut is devoid of neurons. In particular, the formation of 5-HT serotonin neurons and myelinating glial cells is defective. Furthermore, ectopic expression of ENS marker genes is observed in forebrain of rnf2 mutant embryos. These findings suggest that the rnf2 gene plays an important role in the migration and differentiation of neural precursor cells, and its absence leads to abnormal development of ENS and CNS in zebrafish.
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Affiliation(s)
- Gang Feng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Gang Feng,
| | - Yuhua Sun
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- Yuhua Sun,
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28
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Pang S, Gao Y, Wang Y, Yao X, Cao M, Liang Y, Song M, Jiang G. Tetrabromobisphenol A perturbs cell fate decisions via BMP signaling in the early embryonic development of zebrafish. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128512. [PMID: 35739651 DOI: 10.1016/j.jhazmat.2022.128512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/05/2022] [Accepted: 02/16/2022] [Indexed: 06/15/2023]
Abstract
Tetrabromobisphenol A (TBBPA) readily accumulates in the egg yolk of aquatic oviparous animals and is transferred to their embryos. Early embryogenesis is vital for organ formation and subsequent development. The developmental toxicity of TBBPA in aquatic animals has been extensively reported. However, few studies have assessed the toxic effects of TBBPA in the early embryonic development. In this work, we found that TBBPA perturbed cell fate decisions along the dorsal-ventral (DV) axis during gastrulation, further disrupting early organogenesis in the entire embryo. TBBPA exposure increased the number of embryonic cells that acquired a ventral cell fate, which formed epidermis, blood and heart tissues. In return, the number of embryonic cells that acquired a dorsal cell fate was greatly decreased, causing the TBBPA-exposed embryos to develop a small brain and small eyes. We revealed that TBBPA elevated the activity gradient of bone morphogenetic protein (BMP) signaling which is responsible for cell fate specification along the DV axis, with up-regulation of BMP ligands (bmp4, bmp7a) and target genes (szl) and promotion signal transduction through phosphorylation of Smad1/5. As the function of BMP signaling in embryogenesis is highly conserved among many vertebrates, these findings highlight the ecological and health risks of TBBPA.
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Affiliation(s)
- Shaochen Pang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China; Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yue Gao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanwu Wang
- School of Basic Medical Science, Wuhan University, Wuhan 430072, China
| | - Xinglei Yao
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Mengxi Cao
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Yong Liang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Maoyong Song
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China; Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guibin Jiang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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29
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Sfeir A, Fishell G, Schier AF, Dustin ML, Gan WB, Joyner A, Lehmann R, Ron D, Roth D, Talbot WS, Yelon D, Zychlinsky A. Basic science under threat: Lessons from the Skirball Institute. Cell 2022; 185:755-758. [DOI: 10.1016/j.cell.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
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30
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Hill CS. Establishment and interpretation of NODAL and BMP signaling gradients in early vertebrate development. Curr Top Dev Biol 2022; 149:311-340. [PMID: 35606059 DOI: 10.1016/bs.ctdb.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transforming growth factor β (TGF-β) family ligands play crucial roles in orchestrating early embryonic development. Most significantly, two family members, NODAL and BMP form signaling gradients and indeed in fish, frogs and sea urchins these two opposing gradients are sufficient to organize a complete embryonic axis. This review focuses on how these gradients are established and interpreted during early vertebrate development. The review highlights key principles that are emerging, in particular the importance of signaling duration as well as ligand concentration in both gradient generation and their interpretation. Feedforward and feedback loops involving other signaling pathways are also essential for providing spatial and temporal information downstream of the NODAL and BMP signaling pathways. Finally, new data suggest the existence of buffering mechanisms, whereby early signaling defects can be readily corrected downstream later in development, suggesting that signaling gradients do not have to be as precise as previously thought.
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Affiliation(s)
- Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, United Kingdom.
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31
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Yan Y, Wang Q. BMP Signaling: Lighting up the Way for Embryonic Dorsoventral Patterning. Front Cell Dev Biol 2022; 9:799772. [PMID: 35036406 PMCID: PMC8753366 DOI: 10.3389/fcell.2021.799772] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
One of the most significant events during early embryonic development is the establishment of a basic embryonic body plan, which is defined by anteroposterior, dorsoventral (DV), and left-right axes. It is well-known that the morphogen gradient created by BMP signaling activity is crucial for DV axis patterning across a diverse set of vertebrates. The regulation of BMP signaling during DV patterning has been strongly conserved across evolution. This is a remarkable regulatory and evolutionary feat, as the BMP gradient has been maintained despite the tremendous variation in embryonic size and shape across species. Interestingly, the embryonic DV axis exhibits robust stability, even in face of variations in BMP signaling. Multiple lines of genetic, molecular, and embryological evidence have suggested that numerous BMP signaling components and their attendant regulators act in concert to shape the developing DV axis. In this review, we summarize the current knowledge of the function and regulation of BMP signaling in DV patterning. Throughout, we focus specifically on popular model animals, such as Xenopus and zebrafish, highlighting the similarities and differences of the regulatory networks between species. We also review recent advances regarding the molecular nature of DV patterning, including the initiation of the DV axis, the formation of the BMP gradient, and the regulatory molecular mechanisms behind BMP signaling during the establishment of the DV axis. Collectively, this review will help clarify our current understanding of the molecular nature of DV axis formation.
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Affiliation(s)
- Yifang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Membrane Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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32
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Hao X, Wang Q, Hou J, Liu K, Feng B, Shao C. Temporal Transcriptome Analysis Reveals Dynamic Expression Profiles of Gametes and Embryonic Development in Japanese Flounder ( Paralichthys olivaceus). Genes (Basel) 2021; 12:genes12101561. [PMID: 34680958 PMCID: PMC8535655 DOI: 10.3390/genes12101561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022] Open
Abstract
The maternal-to-zygotic transition (MZT) is a crucial event in embryo development. While the features of the MZT across species are shared, the stage of this transition is different among species. We characterized MZT in a flatfish species, Japanese flounder (Paralichthys olivaceus). In this study, we analyzed the 551.57 GB transcriptome data of two types of gametes (sperms and eggs) and 10 embryo developmental stages in Japanese flounder. We identified 2512 maternal factor-related genes and found that most of those maternal factor-related genes expression decreased at the low blastula (LB) stage and remained silent in the subsequent embryonic development period. Meanwhile, we verified that the zygotic genome transcription might occur at the 128-cell stage and large-scale transcription began at the LB stage, which indicates the LB stage is the major wave zygotic genome activation (ZGA) occurs. In addition, we indicated that the Wnt signaling pathway, playing a diverse role in embryonic development, was involved in the ZGA and the axis formation. The results reported the list of the maternal genes in Japanese flounder and defined the stage of MZT, contributing to the understanding of the details of MZT during Japanese flounder embryonic development.
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Affiliation(s)
- Xiancai Hao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (Q.W.); (K.L.); (B.F.)
| | - Qian Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (Q.W.); (K.L.); (B.F.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jilun Hou
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China;
| | - Kaiqiang Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (Q.W.); (K.L.); (B.F.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Bo Feng
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (Q.W.); (K.L.); (B.F.)
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (Q.W.); (K.L.); (B.F.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Correspondence:
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33
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Choe CP, Choi SY, Kee Y, Kim MJ, Kim SH, Lee Y, Park HC, Ro H. Transgenic fluorescent zebrafish lines that have revolutionized biomedical research. Lab Anim Res 2021; 37:26. [PMID: 34496973 PMCID: PMC8424172 DOI: 10.1186/s42826-021-00103-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
Since its debut in the biomedical research fields in 1981, zebrafish have been used as a vertebrate model organism in more than 40,000 biomedical research studies. Especially useful are zebrafish lines expressing fluorescent proteins in a molecule, intracellular organelle, cell or tissue specific manner because they allow the visualization and tracking of molecules, intracellular organelles, cells or tissues of interest in real time and in vivo. In this review, we summarize representative transgenic fluorescent zebrafish lines that have revolutionized biomedical research on signal transduction, the craniofacial skeletal system, the hematopoietic system, the nervous system, the urogenital system, the digestive system and intracellular organelles.
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Affiliation(s)
- Chong Pyo Choe
- Division of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.,Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Min Jung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Seok-Hyung Kim
- Department of Marine Life Sciences and Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Yoonsung Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Hae-Chul Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan, 15355, Republic of Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
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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: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [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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Marelli F, Rurale G, Persani L. From Endoderm to Progenitors: An Update on the Early Steps of Thyroid Morphogenesis in the Zebrafish. Front Endocrinol (Lausanne) 2021; 12:664557. [PMID: 34149617 PMCID: PMC8213386 DOI: 10.3389/fendo.2021.664557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/14/2021] [Indexed: 12/24/2022] Open
Abstract
The mechanisms underlying thyroid gland development have a central interest in biology and this review is aimed to provide an update on the recent advancements on the early steps of thyroid differentiation that were obtained in the zebrafish, because this teleost fish revealed to be a suitable organism to study the early developmental stages. Physiologically, the thyroid precursors fate is delineated by the appearance among the endoderm cells of the foregut of a restricted cell population expressing specific transcription factors, including pax2a, nkx2.4b, and hhex. The committed thyroid primordium first appears as a thickening of the pharyngeal floor of the anterior endoderm, that subsequently detaches from the floor and migrates to its final location where it gives rise to the thyroid hormone-producing follicles. At variance with mammalian models, thyroid precursor differentiation in zebrafish occurs early during the developmental process before the dislocation to the eutopic positioning of thyroid follicles. Several pathways have been implicated in these early events and nowadays there is evidence of a complex crosstalk between intrinsic (coming from the endoderm and thyroid precursors) and extrinsic factors (coming from surrounding tissues, as the cardiac mesoderm) whose organization in time and space is probably required for the proper thyroid development. In particular, Notch, Shh, Fgf, Bmp, and Wnt signaling seems to be required for the commitment of endodermal cells to a thyroid fate at specific developmental windows of zebrafish embryo. Here, we summarize the recent findings produced in the various zebrafish experimental models with the aim to define a comprehensive picture of such complicated puzzle.
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Affiliation(s)
- Federica Marelli
- Dipartimento di Malattie Endocrine e del Metabolismo, IRCCS Istituto Auxologico Italiano IRCCS, Milan, Italy
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano - LITA, Segrate, Italy
| | - Giuditta Rurale
- Dipartimento di Malattie Endocrine e del Metabolismo, IRCCS Istituto Auxologico Italiano IRCCS, Milan, Italy
| | - Luca Persani
- Dipartimento di Malattie Endocrine e del Metabolismo, IRCCS Istituto Auxologico Italiano IRCCS, Milan, Italy
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano - LITA, Segrate, Italy
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Tuazon FB, Wang X, Andrade JL, Umulis D, Mullins MC. Proteolytic Restriction of Chordin Range Underlies BMP Gradient Formation. Cell Rep 2021; 32:108039. [PMID: 32814043 PMCID: PMC7731995 DOI: 10.1016/j.celrep.2020.108039] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 04/22/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
A fundamental question in developmental biology is how morphogens, such as bone morphogenetic protein (BMP), form precise signaling gradients to impart positional and functional identity to the cells of the early embryo. We combine rigorous mutant analyses with quantitative immunofluorescence to determine that the proteases Bmp1a and Tolloid spatially restrict the BMP antagonist Chordin in dorsoventral (DV) axial patterning of the early zebrafish gastrula. We show that maternally deposited Bmp1a plays an unexpected and non-redundant role in establishing the BMP signaling gradient, while the Bmp1a/Tolloid antagonist Sizzled is surprisingly dispensable. Combining computational modeling and in vivo analyses with an immobile Chordin construct, we demonstrate that long-range Chordin diffusion is not necessary for BMP gradient formation and DV patterning. Our data do not support a counter-gradient of Chordin and instead favor a Chordin sink, established by Bmp1a and Tolloid, as the primary mechanism that drives BMP gradient formation. The BMP morphogen generates a precise signaling gradient during axial patterning. In the zebrafish embryo, Tuazon et al. find that proteases Bmp1a/Tolloid are key to this process, preventing the long-range diffusion of the BMP antagonist, Chordin. By regionally restricting Chordin, Bmp1a/Tolloid establish the signaling sink that drives BMP gradient formation.
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Affiliation(s)
- Francesca B Tuazon
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xu Wang
- Department of Agriculture and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Jonathan Lee Andrade
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - David Umulis
- Department of Agriculture and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA.
| | - Mary C Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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37
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Montague TG, Rieth IJ, Axel R. Embryonic development of the camouflaging dwarf cuttlefish, Sepia bandensis. Dev Dyn 2021; 250:1688-1703. [PMID: 34028136 DOI: 10.1002/dvdy.375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The dwarf cuttlefish Sepia bandensis, a camouflaging cephalopod from the Indo-Pacific, is a promising new model organism for neuroscience, developmental biology, and evolutionary studies. Cuttlefish dynamically camouflage to their surroundings by altering the color, pattern, and texture of their skin. The skin's "pixels" (chromatophores) are controlled by motor neurons projecting from the brain. Thus, camouflage is a visible representation of neural activity. In addition to camouflage, the dwarf cuttlefish uses dynamic skin patterns for social communication. Despite more than 500 million years of evolutionary separation, cuttlefish and vertebrates converged to form limbs, camera-type eyes and a closed circulatory system. Moreover, cuttlefish have a striking ability to regenerate their limbs. Interrogation of these unique biological features will benefit from the development of a new set of tools. Dwarf cuttlefish reach sexual maturity in 4 months, they lay dozens of eggs over their 9-month lifespan, and the embryos develop to hatching in 1 month. RESULTS Here, we describe methods to culture dwarf cuttlefish embryos in vitro and define 25 stages of cuttlefish development. CONCLUSION This staging series serves as a foundation for future technologies that can be used to address a myriad of developmental, neurobiological, and evolutionary questions.
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Affiliation(s)
- Tessa G Montague
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, New York, USA.,Howard Hughes Medical Institute, Columbia University, New York, New York, USA
| | - Isabelle J Rieth
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, New York, USA
| | - Richard Axel
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, New York, USA.,Howard Hughes Medical Institute, Columbia University, New York, New York, USA
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38
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Torres-Paz J, Rétaux S. Pescoids and Chimeras to Probe Early Evo-Devo in the Fish Astyanax mexicanus. Front Cell Dev Biol 2021; 9:667296. [PMID: 33928092 PMCID: PMC8078105 DOI: 10.3389/fcell.2021.667296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/25/2021] [Indexed: 12/31/2022] Open
Abstract
The fish species Astyanax mexicanus with its sighted and blind eco-morphotypes has become an original model to challenge vertebrate developmental evolution. Recently, we demonstrated that phenotypic evolution can be impacted by early developmental events starting from the production of oocytes in the fish ovaries. A. mexicanus offers an amenable model to test the influence of maternal determinants on cell fate decisions during early development, yet the mechanisms by which the information contained in the eggs is translated into specific developmental programs remain obscure due to the lack of specific tools in this emergent model. Here we describe methods for the generation of pescoids from yolkless-blastoderm explants to test the influence of embryonic and extraembryonic tissues on cell fate decisions, as well as the production of chimeric embryos obtained by intermorph cell transplantations to probe cell autonomous or non-autonomous processes. We show that Astyanax pescoids have the potential to recapitulate the main ontogenetic events observed in intact embryos, including the internalization of mesodermal progenitors and eye development, as followed with zic:GFP reporter lines. In addition, intermorph cell grafts resulted in proper integration of exogenous cells into the embryonic tissues, with lineages becoming more restricted from mid-blastula to gastrula. The implementation of these approaches in A. mexicanus will bring new light on the cascades of events, from the maternal pre-patterning of the early embryo to the evolution of brain regionalization.
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Affiliation(s)
- Jorge Torres-Paz
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Gif-sur-Yvette, France
| | - Sylvie Rétaux
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Gif-sur-Yvette, France
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39
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Figiel DM, Elsayed R, Nelson AC. Investigating the molecular guts of endoderm formation using zebrafish. Brief Funct Genomics 2021:elab013. [PMID: 33754635 DOI: 10.1093/bfgp/elab013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
The vertebrate endoderm makes major contributions to the respiratory and gastrointestinal tracts and all associated organs. Zebrafish and humans share a high degree of genetic homology and strikingly similar endodermal organ systems. Combined with a multitude of experimental advantages, zebrafish are an attractive model organism to study endoderm development and disease. Recent functional genomics studies have shed considerable light on the gene regulatory programs governing early zebrafish endoderm development, while advances in biological and technological approaches stand to further revolutionize our ability to investigate endoderm formation, function and disease. Here, we discuss the present understanding of endoderm specification in zebrafish compared to other vertebrates, how current and emerging methods will allow refined and enhanced analysis of endoderm formation, and how integration with human data will allow modeling of the link between non-coding sequence variants and human disease.
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Affiliation(s)
- Daniela M Figiel
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
| | - Randa Elsayed
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
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40
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Klatt Shaw D, Mokalled MH. Efficient CRISPR/Cas9 mutagenesis for neurobehavioral screening in adult zebrafish. G3-GENES GENOMES GENETICS 2021; 11:6179145. [PMID: 33742663 PMCID: PMC8496216 DOI: 10.1093/g3journal/jkab089] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/07/2021] [Indexed: 12/22/2022]
Abstract
Adult zebrafish are widely used to interrogate mechanisms of disease development and tissue regeneration. Yet, the prospect of large-scale genetics in adult zebrafish has traditionally faced a host of biological and technical challenges, including inaccessibility of adult tissues to high-throughput phenotyping and the spatial and technical demands of adult husbandry. Here, we describe an experimental pipeline that combines high-efficiency CRISPR/Cas9 mutagenesis with functional phenotypic screening to identify genes required for spinal cord repair in adult zebrafish. Using CRISPR/Cas9 dual-guide ribonucleic proteins, we show selective and combinatorial mutagenesis of 17 genes at 28 target sites with efficiencies exceeding 85% in adult F0 “crispants”. We find that capillary electrophoresis is a reliable method to measure indel frequencies. Using a quantifiable behavioral assay, we identify seven single- or duplicate-gene crispants with reduced functional recovery after spinal cord injury. To rule out off-target effects, we generate germline mutations that recapitulate the crispant regeneration phenotypes. This study provides a platform that combines high-efficiency somatic mutagenesis with a functional phenotypic readout to perform medium- to large-scale genetic studies in adult zebrafish.
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Affiliation(s)
- Dana Klatt Shaw
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA.,Center of Regenerative Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA.,Center of Regenerative Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
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41
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Abstract
The transforming growth factor β (TGFβ) signaling family is evolutionarily conserved in metazoans. The signal transduction mechanisms of TGFβ family members have been expansively investigated and are well understood. During development and homeostasis, numerous TGFβ family members are expressed in various cell types with temporally changing levels, playing diverse roles in embryonic development, adult tissue homeostasis and human diseases by regulating cell proliferation, differentiation, adhesion, migration and apoptosis. Here, we discuss the molecular mechanisms underlying signal transduction and regulation of the TGFβ subfamily pathways, and then highlight their key functions in mesendoderm induction, dorsoventral patterning and laterality development, as well as in the formation of several representative tissues/organs.
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Affiliation(s)
- Shunji Jia
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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42
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Kemmler CL, Riemslagh FW, Moran HR, Mosimann C. From Stripes to a Beating Heart: Early Cardiac Development in Zebrafish. J Cardiovasc Dev Dis 2021; 8:17. [PMID: 33578943 PMCID: PMC7916704 DOI: 10.3390/jcdd8020017] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/18/2022] Open
Abstract
The heart is the first functional organ to form during vertebrate development. Congenital heart defects are the most common type of human birth defect, many originating as anomalies in early heart development. The zebrafish model provides an accessible vertebrate system to study early heart morphogenesis and to gain new insights into the mechanisms of congenital disease. Although composed of only two chambers compared with the four-chambered mammalian heart, the zebrafish heart integrates the core processes and cellular lineages central to cardiac development across vertebrates. The rapid, translucent development of zebrafish is amenable to in vivo imaging and genetic lineage tracing techniques, providing versatile tools to study heart field migration and myocardial progenitor addition and differentiation. Combining transgenic reporters with rapid genome engineering via CRISPR-Cas9 allows for functional testing of candidate genes associated with congenital heart defects and the discovery of molecular causes leading to observed phenotypes. Here, we summarize key insights gained through zebrafish studies into the early patterning of uncommitted lateral plate mesoderm into cardiac progenitors and their regulation. We review the central genetic mechanisms, available tools, and approaches for modeling congenital heart anomalies in the zebrafish as a representative vertebrate model.
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Affiliation(s)
| | | | | | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine and Children’s Hospital Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA; (C.L.K.); (F.W.R.); (H.R.M.)
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43
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Greenfeld H, Lin J, Mullins MC. The BMP signaling gradient is interpreted through concentration thresholds in dorsal-ventral axial patterning. PLoS Biol 2021; 19:e3001059. [PMID: 33481775 PMCID: PMC7857602 DOI: 10.1371/journal.pbio.3001059] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/03/2021] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
Bone Morphogenetic Protein (BMP) patterns the dorsal–ventral (DV) embryonic axis in all vertebrates, but it is unknown how cells along the DV axis interpret and translate the gradient of BMP signaling into differential gene activation that will give rise to distinct cell fates. To determine the mechanism of BMP morphogen interpretation in the zebrafish gastrula, we identified 57 genes that are directly activated by BMP signaling. By using Seurat analysis of single-cell RNA sequencing (scRNA-seq) data, we found that these genes are expressed in at least 3 distinct DV domains of the embryo. We distinguished between 3 models of BMP signal interpretation in which cells activate distinct gene expression through interpretation of thresholds of (1) the BMP signaling gradient slope; (2) the BMP signal duration; or (3) the level of BMP signal activation. We tested these 3 models using quantitative measurements of phosphorylated Smad5 (pSmad5) and by examining the spatial relationship between BMP signaling and activation of different target genes at single-cell resolution across the embryo. We found that BMP signaling gradient slope or BMP exposure duration did not account for the differential target gene expression domains. Instead, we show that cells respond to 3 distinct levels of BMP signaling activity to activate and position target gene expression. Together, we demonstrate that distinct pSmad5 threshold levels activate spatially distinct target genes to pattern the DV axis. This study tested three models of how a BMP morphogen gradient is translated into differential gene activation that specifies distinct cell fates, finding that BMP signal concentration thresholds, not gradient shape or signal duration, position three distinct gene activation domains.
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Affiliation(s)
- Hannah Greenfeld
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
| | - Jerome Lin
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
| | - Mary C. Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
- * E-mail:
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44
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Mignani L, Zizioli D, Borsani G, Monti E, Finazzi D. The Downregulation of c19orf12 Negatively Affects Neuronal and Musculature Development in Zebrafish Embryos. Front Cell Dev Biol 2021; 8:596069. [PMID: 33425903 PMCID: PMC7785858 DOI: 10.3389/fcell.2020.596069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial membrane Protein Associated Neurodegeneration (MPAN) is a rare genetic disorder due to mutations in C19orf12 gene. In most cases, the disorder is transmitted as an autosomal recessive trait and the main clinical features are progressive spastic para/tetraparesis, dystonia, motor axonal neuropathy, parkinsonisms, psychiatric symptoms, and optic atrophy. Besides iron accumulation in the globus pallidus and substantia nigra, the neuropathology shows features also observed in Parkinson’s Disease brains, such as α-synuclein-positive Lewy bodies and hyperphosphorylated tau. Mutations in the gene have been found in other neurodegenerative disorders, including PD, hereditary spastic paraplegia, pallido-pyramidal syndrome, and amyotrophic lateral sclerosis. The biological function of C19orf12 gene is poorly defined. In humans, it codes for two protein isoforms: the longer one is present in mitochondria, endoplasmic reticulum, and contact regions between mitochondria and ER. Mutations in the gene appear to be linked to defects in mitochondrial activity, lipid metabolism and autophagy/mitophagy. To increase the available tools for the investigation of MPAN pathogenesis, we generated a new animal model in zebrafish embryos. The zebrafish genome contains four co-orthologs of human C19orf12. One of them, located on chromosome 18, is expressed at higher levels at early stages of development. We downregulated its expression by microinjecting embryos with a specific ATG-blocking morpholino, and we analyzed embryonal development. Most embryos showed morphological defects such as unsettled brain morphology, with smaller head and eyes, reduced yolk extension, tilted and thinner tail. The severity of the defects progressively increased and all injected embryos died within 7 days post fertilization. Appropriate controls confirmed the specificity of the observed phenotype. Changes in the expression and distribution of neural markers documented a defective neuronal development, particularly evident in the eyes, the optic tectum, the midbrain-hindbrain boundary; Rohon Beard and dorsal root ganglia neurons were also affected. Phalloidin staining evidenced a significant perturbation of musculature formation that was associated with defective locomotor behavior. These data are consistent with the clinical features of MPAN and support the validity of the model to investigate the pathogenesis of the disease and evaluate molecules with potential therapeutic effect.
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Affiliation(s)
- Luca Mignani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Daniela Zizioli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giuseppe Borsani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Eugenio Monti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Dario Finazzi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.,Laboratory of Clinical Chemistry, Azienda Socio Sanitaria Territoriale (ASST) Spedali Civili di Brescia, Brescia, Italy
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45
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Isthmin1, a secreted signaling protein, acts downstream of diverse embryonic patterning centers in development. Cell Tissue Res 2020; 383:987-1002. [PMID: 33367974 PMCID: PMC7960586 DOI: 10.1007/s00441-020-03318-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/06/2020] [Indexed: 11/25/2022]
Abstract
Extracellular signals play essential roles during embryonic patterning by providing positional information in a concentration-dependent manner, and many such signals, like Wnt, fibroblast growth factor (FGF), Hedgehog (Hh), and retinoic acid, act by being secreted into the extracellular space, thereby triggering receptor-mediated responses in other cells. Isthmin1 (ism1) is a secreted protein whose gene expression pattern coincides with that of early dorsal determinants, nodal ligand genes like sqt and cyc, and with fgf8 during various phases of zebrafish development. Ism1 functions in early embryonic patterning and development are poorly understood; however, it has recently been shown to interact with nodal pathway genes to control organ asymmetry in chicken. Here, we show that misexpression of ism1 deletion constructs disrupts embryonic patterning in zebrafish and exhibits genetic interactions with both Fgf and nodal signaling. Unlike Fgf and nodal pathway mutants, CRISPR/Cas9-engineered ism1 mutants did not show obvious developmental defects. Further, in vivo single molecule fluorescence correlation spectroscopy (FCCS) showed that Ism1 diffuses freely in the extra-cellular space, with a diffusion coefficient similar to that of Fgf8a; however, our measurements do not support direct molecular interactions between Ism1 and either nodal ligands or Fgf8a in the developing zebrafish embryo. Together, data from gain- and loss-of-function experiments suggest that zebrafish Ism1 plays a complex role in regulating extracellular signals during early embryonic development.
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Kryvi H, Nordvik K, Fjelldal PG, Eilertsen M, Helvik JV, Støren EN, Long JH. Heads and tails: The notochord develops differently in the cranium and caudal fin of Atlantic Salmon (Salmo salar, L.). Anat Rec (Hoboken) 2020; 304:1629-1649. [PMID: 33155751 PMCID: PMC8359264 DOI: 10.1002/ar.24562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/27/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022]
Abstract
While it is well known that the notochord of bony fishes changes over developmental time, less is known about how it varies across different body regions. In the development of the Atlantic salmon, Salmo salar L., cranial and caudal ends of the notochord are overlaid by the formation of the bony elements of the neurocranium and caudal fin, respectively. To investigate, we describe how the notochord of the cranium and caudal fin changes from embryo to spawning adult, using light microscopy, SEM, TEM, dissection, and CT scanning. The differences are dramatic. In contrast to the abdominal and caudal regions, at the ends of the notochord vertebrae never develop. While the cranial notochord builds a tapering, unsegmented cone of chordal bone, the urostylic notochordal sheath never ossifies: adjacent, irregular bony elements form from the endoskeleton of the caudal fin. As development progresses, two previously undescribed processes occur. First, the bony cone of the cranial notochord, and its internal chordocytes, are degraded by chordoclasts, an undescribed function of the clastic cell type. Second, the sheath of the urostylic notochord creates transverse septae that partly traverse the lumen in an irregular pattern. By the adult stage, the cranial notochord is gone. In contrast, the urostylic notochord in adults is robust, reinforced with septae, covered by irregularly shaped pieces of cellular bone, and capped with an opistural cartilage that develops from the sheath of the urostylic notochord. A previously undescribed muscle, with its origin on the opistural cartilage, inserts on the lepidotrich ventral to it.
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Affiliation(s)
- Harald Kryvi
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Kari Nordvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | - Mariann Eilertsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Jon Vidar Helvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | - John H Long
- Department of Biology, Vassar College, Poughkeepsie, New York, USA
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47
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Rogers KW, ElGamacy M, Jordan BM, Müller P. Optogenetic investigation of BMP target gene expression diversity. eLife 2020; 9:58641. [PMID: 33174840 PMCID: PMC7728441 DOI: 10.7554/elife.58641] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
Signaling molecules activate distinct patterns of gene expression to coordinate embryogenesis, but how spatiotemporal expression diversity is generated is an open question. In zebrafish, a BMP signaling gradient patterns the dorsal-ventral axis. We systematically identified target genes responding to BMP and found that they have diverse spatiotemporal expression patterns. Transcriptional responses to optogenetically delivered high- and low-amplitude BMP signaling pulses indicate that spatiotemporal expression is not fully defined by different BMP signaling activation thresholds. Additionally, we observed negligible correlations between spatiotemporal expression and transcription kinetics for the majority of analyzed genes in response to BMP signaling pulses. In contrast, spatial differences between BMP target genes largely collapsed when FGF and Nodal signaling were inhibited. Our results suggest that, similar to other patterning systems, combinatorial signaling is likely to be a major driver of spatial diversity in BMP-dependent gene expression in zebrafish.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Mohammad ElGamacy
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.,Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.,Heliopolis Biotechnology Ltd, London, United Kingdom
| | - Benjamin M Jordan
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.,Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany
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48
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Breus O, Dickmeis T. Genetically encoded thiol redox-sensors in the zebrafish model: lessons for embryonic development and regeneration. Biol Chem 2020; 402:363-378. [PMID: 33021959 DOI: 10.1515/hsz-2020-0269] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022]
Abstract
Important roles for reactive oxygen species (ROS) and redox signaling in embryonic development and regenerative processes are increasingly recognized. However, it is difficult to obtain information on spatiotemporal dynamics of ROS production and signaling in vivo. The zebrafish is an excellent model for in vivo bioimaging and possesses a remarkable regenerative capacity upon tissue injury. Here, we review data obtained in this model system with genetically encoded redox-sensors targeting H2O2 and glutathione redox potential. We describe how such observations have prompted insight into regulation and downstream effects of redox alterations during tissue differentiation, morphogenesis and regeneration. We also discuss the properties of the different sensors and their consequences for the interpretation of in vivo imaging results. Finally, we highlight open questions and additional research fields that may benefit from further application of such sensor systems in zebrafish models of development, regeneration and disease.
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Affiliation(s)
- Oksana Breus
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344Eggenstein-Leopoldshafen, Germany
| | - Thomas Dickmeis
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344Eggenstein-Leopoldshafen, Germany
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49
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Weger M, Weger BD, Schink A, Takamiya M, Stegmaier J, Gobet C, Parisi A, Kobitski AY, Mertes J, Krone N, Strähle U, Nienhaus GU, Mikut R, Gachon F, Gut P, Dickmeis T. MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly. eLife 2020; 9:e57068. [PMID: 32969791 PMCID: PMC7515633 DOI: 10.7554/elife.57068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022] Open
Abstract
The glucose-sensing Mondo pathway regulates expression of metabolic genes in mammals. Here, we characterized its function in the zebrafish and revealed an unexpected role of this pathway in vertebrate embryonic development. We showed that knockdown of mondoa impaired the early morphogenetic movement of epiboly in zebrafish embryos and caused microtubule defects. Expression of genes in the terpenoid backbone and sterol biosynthesis pathways upstream of pregnenolone synthesis was coordinately downregulated in these embryos, including the most downregulated gene nsdhl. Loss of Nsdhl function likewise impaired epiboly, similar to MondoA loss of function. Both epiboly and microtubule defects were partially restored by pregnenolone treatment. Maternal-zygotic mutants of mondoa showed perturbed epiboly with low penetrance and compensatory changes in the expression of terpenoid/sterol/steroid metabolism genes. Collectively, our results show a novel role for MondoA in the regulation of early vertebrate development, connecting glucose, cholesterol and steroid hormone metabolism with early embryonic cell movements.
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Affiliation(s)
- Meltem Weger
- Institute of Biological and Chemical Systems – Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
- Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Benjamin D Weger
- Institute of Biological and Chemical Systems – Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
- Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
- Nestlé Institute of Health Sciences SA, EPFL Innovation ParkLausanneSwitzerland
| | - Andrea Schink
- Institute of Biological and Chemical Systems – Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
| | - Masanari Takamiya
- Institute of Biological and Chemical Systems – Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
| | - Johannes Stegmaier
- Institute for Automation and Applied Informatics, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
| | - Cédric Gobet
- Nestlé Institute of Health Sciences SA, EPFL Innovation ParkLausanneSwitzerland
| | - Alice Parisi
- Nestlé Institute of Health Sciences SA, EPFL Innovation ParkLausanneSwitzerland
| | - Andrei Yu Kobitski
- Institute of Biological and Chemical Systems – Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
- Institute of Applied Physics, Karlsruhe Institute of TechnologyKarlsruheGermany
| | - Jonas Mertes
- Institute of Applied Physics, Karlsruhe Institute of TechnologyKarlsruheGermany
| | - Nils Krone
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Uwe Strähle
- Institute of Biological and Chemical Systems – Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
| | - Gerd Ulrich Nienhaus
- Institute of Biological and Chemical Systems – Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
- Institute of Applied Physics, Karlsruhe Institute of TechnologyKarlsruheGermany
- Department of Physics, University of Illinois at Urbana-ChampaignUrbanaUnited States
- Institute of Nanotechnology, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
| | - Ralf Mikut
- Institute for Automation and Applied Informatics, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
| | - Frédéric Gachon
- Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
- Nestlé Institute of Health Sciences SA, EPFL Innovation ParkLausanneSwitzerland
| | - Philipp Gut
- Nestlé Institute of Health Sciences SA, EPFL Innovation ParkLausanneSwitzerland
| | - Thomas Dickmeis
- Institute of Biological and Chemical Systems – Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
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50
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Liu Y, Zhu Z, Ho IHT, Shi Y, Li J, Wang X, Chan MTV, Cheng CHK. Genetic Deletion of miR-430 Disrupts Maternal-Zygotic Transition and Embryonic Body Plan. Front Genet 2020; 11:853. [PMID: 32849832 PMCID: PMC7417628 DOI: 10.3389/fgene.2020.00853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022] Open
Abstract
MiR-430 is considered an important regulator during embryonic development, but genetic loss-of-function study is still lacking. Here we demonstrated that genetic deletion of the miR-430 cluster resulted in developmental defects in cell movement, germ layer specification, axis patterning and organ progenitor formation in zebrafish. Transcriptome analysis indicated that the maternally provided transcripts were not properly degraded whereas the zygotic genome expressed genes were not fully activated in the miR-430 mutants. We further found that a reciprocal regulatory loop exists between miR-430 and maternally provided transcripts: the maternally provided transcripts (Nanog, Dicer1, Dgcr8, and AGOs) are required for miR-430 biogenesis and function, whereas miR-430 is required for the clearance of these maternally provided transcripts. These data provide the first genetic evidence that miR-430 is required for maternal-zygotic transition and subsequent establishment of embryonic body plan.
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Affiliation(s)
- Yun Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Shenzhen Zelong Biological Technology Limited Cooperation, Shenzhen, China
| | - Zeyao Zhu
- Department of Anatomy, Histology and Developmental Biology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Idy H T Ho
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Anesthesia and Intensive Care, Prince of Wales Hospital, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yujian Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jianzhen Li
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Xia Wang
- Department of Anatomy, Histology and Developmental Biology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Matthew T V Chan
- Department of Anesthesia and Intensive Care, Prince of Wales Hospital, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Christopher H K Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
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