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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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2
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Niescierowicz K, Pryszcz L, Navarrete C, Tralle E, Sulej A, Abu Nahia K, Kasprzyk ME, Misztal K, Pateria A, Pakuła A, Bochtler M, Winata C. Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish. Nat Commun 2022; 13:5520. [PMID: 36127363 PMCID: PMC9489775 DOI: 10.1038/s41467-022-33260-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Adenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery reveals pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3'-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning are found to contain multiple editing sites. Adar knockdown or overexpression affect gene expression by 12 hpf. Analysis of adar-/- zygotic mutants further reveals that the previously described role of Adar in mammals in regulating the innate immune response is conserved in zebrafish. Our study therefore establishes distinct maternal and zygotic functions of RNA editing by Adar in embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes, and in the regulation of the innate immune response, respectively.
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Affiliation(s)
| | - Leszek Pryszcz
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Cristina Navarrete
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Eugeniusz Tralle
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Agata Sulej
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Karim Abu Nahia
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Marta Elżbieta Kasprzyk
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Misztal
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Abhishek Pateria
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Adrianna Pakuła
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland. .,Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland.
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
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3
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Houston DW, Elliott KL, Coppenrath K, Wlizla M, Horb ME. Maternal Wnt11b regulates cortical rotation during Xenopus axis formation: analysis of maternal-effect wnt11b mutants. Development 2022; 149:dev200552. [PMID: 35946588 PMCID: PMC9515810 DOI: 10.1242/dev.200552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/01/2022] [Indexed: 12/13/2022]
Abstract
Asymmetric signalling centres in the early embryo are essential for axis formation in vertebrates. These regions (e.g. amphibian dorsal morula, mammalian anterior visceral endoderm) require stabilised nuclear β-catenin, but the role of localised Wnt ligand signalling activity in their establishment remains unclear. In Xenopus, dorsal β-catenin is initiated by vegetal microtubule-mediated symmetry breaking in the fertilised egg, known as 'cortical rotation'. Localised wnt11b mRNA and ligand-independent activators of β-catenin have been implicated in dorsal β-catenin activation, but the extent to which each contributes to axis formation in this paradigm remains unclear. Here, we describe a CRISPR-mediated maternal-effect mutation in Xenopus laevis wnt11b.L. We find that wnt11b is maternally required for robust dorsal axis formation and for timely gastrulation, and zygotically for left-right asymmetry. Importantly, we show that vegetal microtubule assembly and cortical rotation are reduced in wnt11b mutant eggs. In addition, we show that activated Wnt coreceptor Lrp6 and Dishevelled lack behaviour consistent with roles in early β-catenin stabilisation, and that neither is regulated by Wnt11b. This work thus implicates Wnt11b in the distribution of putative dorsal determinants rather than in comprising the determinants themselves. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Douglas W. Houston
- Department of Biology, The University of Iowa, 257 BB, Iowa City, IA 52242-1324, USA
| | - Karen L. Elliott
- Department of Biology, The University of Iowa, 257 BB, Iowa City, IA 52242-1324, USA
| | - Kelsey Coppenrath
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Marcin Wlizla
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Marko E. Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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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: 7] [Impact Index Per Article: 3.5] [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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5
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Jones WD, Mullins MC. Cell signaling pathways controlling an axis organizing center in the zebrafish. Curr Top Dev Biol 2022; 150:149-209. [DOI: 10.1016/bs.ctdb.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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6
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Zhang B, Qin G, Qu L, Zhang Y, Li C, Cang C, Lin Q. Wnt8a is one of the candidate genes that play essential roles in the elongation of the seahorse prehensile tail. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:416-426. [PMID: 37073259 PMCID: PMC10077196 DOI: 10.1007/s42995-021-00099-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 01/08/2021] [Indexed: 05/03/2023]
Abstract
Seahorses are a hallmark of specialized morphological features due to their elongated prehensile tail. However, the underlying genomic grounds of seahorse tail development remain elusive. Herein, we evaluated the roles of essential genes from the Wnt gene family for the tail developmental process in the lined seahorse (Hippocampus erectus). Comparative genomic analysis revealed that the Wnt gene family is conserved in seahorses. The expression profiles and in situ hybridization suggested that Wnt5a, Wnt8a, and Wnt11 may participate in seahorse tail development. Like in other teleosts, Wnt5a and Wnt11 were found to regulate the development of the tail axial mesoderm and tail somitic mesoderm, respectively. However, a significantly extended expression period of Wnt8a during seahorse tail development was observed. Signaling pathway analysis further showed that Wnt8a up-regulated the expression of the tail axial mesoderm gene (Shh), while interaction analysis indicated that Wnt8a could promote the expression of Wnt11. In summary, our results indicate that the special extended expression period of Wnt8a might promote caudal tail axis formation, which contributes to the formation of the elongated tail of the seahorse. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00099-7.
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Affiliation(s)
- Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275 China
- Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510275 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275 China
- Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510275 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
| | - Lili Qu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026 China
| | - Yanhong Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275 China
- Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510275 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
| | - Chunyan Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275 China
- Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510275 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
| | - Chunlei Cang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026 China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510275 China
- Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510275 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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7
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Zhang C, Li J, Tarique I, Zhang Y, Lu T, Wang J, Chen A, Wen F, Zhang Z, Zhang Y, Shao M. A Time-Saving Strategy to Generate Double Maternal Mutants by an Oocyte-Specific Conditional Knockout System in Zebrafish. BIOLOGY 2021; 10:biology10080777. [PMID: 34440009 PMCID: PMC8389640 DOI: 10.3390/biology10080777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/29/2021] [Accepted: 08/14/2021] [Indexed: 12/23/2022]
Abstract
Simple Summary Maternally supplied mRNAs and proteins, termed maternal factors, are produced by over 14,000 coding genes in zebrafish. They play exclusive roles in controlling the formation of oocytes and the development of early embryos. These maternal factors can also compensate for the loss of function of its corresponding zygotic gene products. Thus, eliminating both maternal and zygotic gene products is essential to elucidate the functions of more than half of zebrafish genes. However, it is always challenging to inactivate maternal factors, because traditional genetic methods are either technically demanding or time-consuming. Our recent work established a rapid conditional knockout method to generate maternal or maternal and zygotic mutants in one fish generation. Here, we further test the feasibility of this approach to knock out two maternal genes with functional redundancy simultaneously. As a proof of principle, we successfully generated double maternal mutant embryos for dvl2 and dvl3a genes in three months for the first time. The cell movement defects in mutant embryos obtained by this approach mimic the genuine mutant embryos generated after fifteen months of time-consuming screening following the previously reported mosaic strategy. Therefore, this method has the potential to speed up the functional study of paralogous maternal genes. Abstract Maternal products are those mRNAs and proteins deposited during oogenesis, which play critical roles in controlling oocyte formation, fertilization, and early embryonic development. However, loss-of-function studies for these maternal factors are still lacking, mainly because of the prolonged period of transgenerational screening and technical barriers that prevent the generation of maternal (M) and maternal and zygotic (MZ) mutant embryos. By the transgenic expression of multiple sgRNAs targeting a single gene of interest in the background of a transgenic line Tg(zpc:zcas9) with oocyte-specific cas9 expression, we have successfully obtained maternal or maternal–zygotic mutant for single genes in F1 embryos. In this work, we tandemly connected a maternal GFP marker and eight sgRNA expression units to target dvl2 and dvl3a simultaneously and introduced this construct to the genome of Tg(zpc:zcas9) by meganuclease I-Sce I. As expected, we confirmed the existence of Mdvl2;Mdvl3a embryos with strong defective convergence and extension movement during gastrulation among outcrossed GFP positive F1 offspring. The MZdvl2;MZdvl3a embryos were also obtained by crossing the mutant carrying mosaic F0 female with dvl2+/−;dvl3a−/− male fish. This proof-of-principle thus highlights the potential of this conditional knockout strategy to circumvent the current difficulty in the study of genes with multiple functionally redundant paralogs.
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Affiliation(s)
- Chong Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Jiaguang Li
- Taishan College, Shandong University, Qingdao 266237, China; (J.L.); (Z.Z.)
| | - Imran Tarique
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Yizhuang Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Tong Lu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Jiasheng Wang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Aijun Chen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Fenfen Wen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Zhuoyu Zhang
- Taishan College, Shandong University, Qingdao 266237, China; (J.L.); (Z.Z.)
| | - Yanjun Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
| | - Ming Shao
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China; (C.Z.); (I.T.); (Y.Z.); (T.L.); (J.W.); (A.C.); (F.W.); (Y.Z.)
- Taishan College, Shandong University, Qingdao 266237, China; (J.L.); (Z.Z.)
- Correspondence:
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8
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Zhang C, Lu T, Zhang Y, Li J, Tarique I, Wen F, Chen A, Wang J, Zhang Z, Zhang Y, Shi DL, Shao M. Rapid generation of maternal mutants via oocyte transgenic expression of CRISPR-Cas9 and sgRNAs in zebrafish. SCIENCE ADVANCES 2021; 7:eabg4243. [PMID: 34362733 PMCID: PMC8346210 DOI: 10.1126/sciadv.abg4243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/21/2021] [Indexed: 05/08/2023]
Abstract
Maternal products are exclusive factors to drive oogenesis and early embryonic development. As disrupting maternal gene functions is either time-consuming or technically challenging, early developmental programs regulated by maternal factors remain mostly elusive. We provide a transgenic approach to inactivate maternal genes in zebrafish primary oocytes. By introducing three tandem single guide RNA (sgRNA) expression cassettes and a green fluorescent protein (GFP) reporter into Tg(zpc:zcas9) embryos, we efficiently obtained maternal nanog and ctnnb2 mutants among GFP-positive F1 offspring. Notably, most of these maternal mutants displayed either sgRNA site-spanning genomic deletions or unintended large deletions extending distantly from the sgRNA targets, suggesting a prominent deletion-prone tendency of genome editing in the oocyte. Thus, our method allows maternal gene knockout in the absence of viable and fertile homozygous mutant adults. This approach is particularly time-saving and can be applied for functional screening of maternal factors and generating genomic deletions in zebrafish.
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Affiliation(s)
- Chong Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Tong Lu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Yizhuang Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiaguang Li
- Shandong University Taishan College, Qingdao 266237, China
| | - Imran Tarique
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Fenfen Wen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Aijun Chen
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiasheng Wang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Zhuoyu Zhang
- Shandong University Taishan College, Qingdao 266237, China
| | - Yanjun Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - De-Li Shi
- Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China
- Developmental Biology Laboratory, CNRS-UMR7622, Institut de Biologie Paris-Seine, Sorbonne University, Paris 75005, France
| | - Ming Shao
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology and Key Laboratory for Experimental Teratology of the Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.
- Shandong University Taishan College, Qingdao 266237, China
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9
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Comparison of gene expression responses of zebrafish larvae to Vibrio parahaemolyticus infection by static immersion and caudal vein microinjection. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2019.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Gyimah E, Xu H, Dong X, Qiu X, Zhang Z, Bu Y, Akoto O. Developmental neurotoxicity of low concentrations of bisphenol A and S exposure in zebrafish. CHEMOSPHERE 2021; 262:128045. [PMID: 33182117 DOI: 10.1016/j.chemosphere.2020.128045] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
The vulnerability to environmental insults is heightened at early stages of development. However, the neurotoxic potential of bisphenol A (BPA) and bisphenol S (BPS) at developmental windows remains unclear. To investigate the mechanisms mediating the developmental neurotoxicity, zebrafish embryos were treated with 0.01, 0.03, 0.01, 0.3, 1 μM BPA/BPS. Also, we used Tg(HuC:GFP) zebrafish to investigate whether BPA/BPS could induce neuron development. The reduction in body length, and increased heart rate were significant in 0.3 and 1 μM BPA/BPS groups. The green fluorescence protein (GFP) intensity increased at 72 hpf and 120 hpf in Tg(HuC:GFP) larvae which was consistent with the increased mRNA expression of elval3 following BPS treatments, an indication of the plausible effect of BPS on embryonic neuron development. Additionally, BPA/BPS treatments elicited hyperactivity and reduced static time in zebrafish larvae, suggesting behavioral alterations. Moreover, qRT-PCR results showed that BPA and BPS could interfere with the normal expression of development-related genes vegfa, wnt8a, and mstn1 at the developmental stages. The expression of neurodevelopment-related genes (ngn1, elavl3, gfap, α1-tubulin, mbp, and gap43) were significantly upregulated in BPA and BPS treatments, except for the remarkable downregulation of mbp and gfap elicited by BPA at 48 (0.03 μM) and 120 hpf (0.3 μM) respectively; ngn1 at 48 hpf for 0.1 μM BPS. Overall, our results highlighted that embryonic exposure to low concentrations of BPA/BPS could be deleterious to the central nervous system development and elicit behavioral abnormalities in zebrafish at developmental stages.
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Affiliation(s)
- Eric Gyimah
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Hai Xu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Jiangsu College of Water Treatment Technology and Material Collaborative Innovation Center, Suzhou, 215009, China
| | - Xing Dong
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Xuchun Qiu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Zhen Zhang
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Jiangsu College of Water Treatment Technology and Material Collaborative Innovation Center, Suzhou, 215009, China
| | - Yuanqing Bu
- Nanjing Institute of Environmental Science, Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Ministry of Ecology and Environment, Nanjing, 210042, China.
| | - Osei Akoto
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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11
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A phospho-switch controls RNF43-mediated degradation of Wnt receptors to suppress tumorigenesis. Nat Commun 2020; 11:4586. [PMID: 32934222 PMCID: PMC7492264 DOI: 10.1038/s41467-020-18257-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
Frequent mutation of the tumour suppressor RNF43 is observed in many cancers, particularly colon malignancies. RNF43, an E3 ubiquitin ligase, negatively regulates Wnt signalling by inducing degradation of the Wnt receptor Frizzled. In this study, we discover that RNF43 activity requires phosphorylation at a triplet of conserved serines. This phospho-regulation of RNF43 is required for zebrafish development and growth of mouse intestinal organoids. Cancer-associated mutations that abrogate RNF43 phosphorylation cooperate with active Ras to promote tumorigenesis by abolishing the inhibitory function of RNF43 in Wnt signalling while maintaining its inhibitory function in p53 signalling. Our data suggest that RNF43 mutations cooperate with KRAS mutations to promote multi-step tumorigenesis via the Wnt-Ras-p53 axis in human colon cancers. Lastly, phosphomimetic substitutions of the serine trio restored the tumour suppressive activity of extracellular oncogenic mutants. Therefore, harnessing phospho-regulation of RNF43 might be a potential therapeutic strategy for tumours with RNF43 mutations.
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12
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He M, Zhang R, Jiao S, Zhang F, Ye D, Wang H, Sun Y. Nanog safeguards early embryogenesis against global activation of maternal β-catenin activity by interfering with TCF factors. PLoS Biol 2020; 18:e3000561. [PMID: 32702011 PMCID: PMC7402524 DOI: 10.1371/journal.pbio.3000561] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 08/04/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
Maternal β-catenin activity is essential and critical for dorsal induction and its dorsal activation has been thoroughly studied. However, how the maternal β-catenin activity is suppressed in the nondorsal cells remains poorly understood. Nanog is known to play a central role for maintenance of the pluripotency and maternal -zygotic transition (MZT). Here, we reveal a novel role of Nanog as a strong repressor of maternal β-catenin signaling to safeguard the embryo against hyperactivation of maternal β-catenin activity and hyperdorsalization. In zebrafish, knockdown of nanog at different levels led to either posteriorization or dorsalization, mimicking zygotic or maternal activation of Wnt/β-catenin activities, and the maternal zygotic mutant of nanog (MZnanog) showed strong activation of maternal β-catenin activity and hyperdorsalization. Although a constitutive activator-type Nanog (Vp16-Nanog, lacking the N terminal) perfectly rescued the MZT defects of MZnanog, it did not rescue the phenotypes resulting from β-catenin signaling activation. Mechanistically, the N terminal of Nanog directly interacts with T-cell factor (TCF) and interferes with the binding of β-catenin to TCF, thereby attenuating the transcriptional activity of β-catenin. Therefore, our study establishes a novel role for Nanog in repressing maternal β-catenin activity and demonstrates a transcriptional switch between β-catenin/TCF and Nanog/TCF complexes, which safeguards the embryo from global activation of maternal β-catenin activity. Maternal β-catenin activity induces the primary dorsal axis during early development, but how the activity is suppressed in the non-dorsal cells remains poorly understood. This study reveals Nanog as a strong repressor of nuclear β-catenin to safeguard embryogenesis against global activation of maternal β-catenin activity and hyper-dorsalization in zebrafish.
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Affiliation(s)
- Mudan He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ru Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shengbo Jiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fenghua Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ding Ye
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Houpeng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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13
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Moravec CE, Pelegri F. The role of the cytoskeleton in germ plasm aggregation and compaction in the zebrafish embryo. Curr Top Dev Biol 2020; 140:145-179. [PMID: 32591073 DOI: 10.1016/bs.ctdb.2020.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The transmission of genetic information from one generation to another is crucial for survival of animal species. This is accomplished by the induction of primordial germ cells (PGCs) that will eventually establish the germline. In some animals the germline is induced by signals in gastrula, whereas in others it is specified by inheritance of maternal determinants, known as germ plasm. In zebrafish, aggregation and compaction of maternally derived germ plasm during the first several embryonic cell cycles is essential for generation of PGCs. These processes are controlled by cellular functions associated with the cellular division apparatus. Ribonucleoparticles containing germ plasm components are bound to both the ends of astral microtubules and a dynamic F-actin network through a mechanism integrated with that which drives the cell division program. In this chapter we discuss the role that modifications of the cell division apparatus, including the cytoskeleton and cytoskeleton-associated proteins, play in the regulation of zebrafish germ plasm assembly.
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Affiliation(s)
- Cara E Moravec
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States.
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14
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Fuentes R, Tajer B, Kobayashi M, Pelliccia JL, Langdon Y, Abrams EW, Mullins MC. The maternal coordinate system: Molecular-genetics of embryonic axis formation and patterning in the zebrafish. Curr Top Dev Biol 2020; 140:341-389. [PMID: 32591080 DOI: 10.1016/bs.ctdb.2020.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Axis specification of the zebrafish embryo begins during oogenesis and relies on proper formation of well-defined cytoplasmic domains within the oocyte. Upon fertilization, maternally-regulated cytoplasmic flow and repositioning of dorsal determinants establish the coordinate system that will build the structure and developmental body plan of the embryo. Failure of specific genes that regulate the embryonic coordinate system leads to catastrophic loss of body structures. Here, we review the genetic principles of axis formation and discuss how maternal factors orchestrate axis patterning during zebrafish early embryogenesis. We focus on the molecular identity and functional contribution of genes controlling critical aspects of oogenesis, egg activation, blastula, and gastrula stages. We examine how polarized cytoplasmic domains form in the oocyte, which set off downstream events such as animal-vegetal polarity and germ line development. After gametes interact and form the zygote, cytoplasmic segregation drives the animal-directed reorganization of maternal determinants through calcium- and cell cycle-dependent signals. We also summarize how maternal genes control dorsoventral, anterior-posterior, mesendodermal, and left-right cell fate specification and how signaling pathways pattern these axes and tissues during early development to instruct the three-dimensional body plan. Advances in reverse genetics and phenotyping approaches in the zebrafish model are revealing positional patterning signatures at the single-cell level, thus enhancing our understanding of genotype-phenotype interactions in axis formation. Our emphasis is on the genetic interrogation of novel and specific maternal regulatory mechanisms of axis specification in the zebrafish.
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Affiliation(s)
- Ricardo Fuentes
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - Benjamin Tajer
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - Manami Kobayashi
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - Jose L Pelliccia
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | | | - Elliott W Abrams
- Department of Biology, Purchase College, State University of New York, Harrison, NY, United States
| | - Mary C Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States.
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15
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Green DG, Whitener AE, Mohanty S, Mistretta B, Gunaratne P, Yeh AT, Lekven AC. Wnt signaling regulates neural plate patterning in distinct temporal phases with dynamic transcriptional outputs. Dev Biol 2020; 462:152-164. [PMID: 32243887 DOI: 10.1016/j.ydbio.2020.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 02/28/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
The process that partitions the nascent vertebrate central nervous system into forebrain, midbrain, hindbrain, and spinal cord after neural induction is of fundamental interest in developmental biology, and is known to be dependent on Wnt/β-catenin signaling at multiple steps. Neural induction specifies neural ectoderm with forebrain character that is subsequently posteriorized by graded Wnt signaling: embryological and mutant analyses have shown that progressively higher levels of Wnt signaling induce progressively more posterior fates. However, the mechanistic link between Wnt signaling and the molecular subdivision of the neural ectoderm into distinct domains in the anteroposterior (AP) axis is still not clear. To better understand how Wnt mediates neural AP patterning, we performed a temporal dissection of neural patterning in response to manipulations of Wnt signaling in zebrafish. We show that Wnt-mediated neural patterning in zebrafish can be divided into three phases: (I) a primary AP patterning phase, which occurs during gastrulation, (II) a mes/r1 (mesencephalon-rhombomere 1) specification and refinement phase, which occurs immediately after gastrulation, and (III) a midbrain-hindbrain boundary (MHB) morphogenesis phase, which occurs during segmentation stages. A major outcome of these Wnt signaling phases is the specification of the major compartment divisions of the developing brain: first the MHB, then the diencephalic-mesencephalic boundary (DMB). The specification of these lineage divisions depends upon the dynamic changes of gene transcription in response to Wnt signaling, which we show primarily involves transcriptional repression or indirect activation. We show that otx2b is directly repressed by Wnt signaling during primary AP patterning, but becomes resistant to Wnt-mediated repression during late gastrulation. Also during late gastrulation, Wnt signaling becomes both necessary and sufficient for expression of wnt8b, en2a, and her5 in mes/r1. We suggest that the change in otx2b response to Wnt regulation enables a transition to the mes/r1 phase of Wnt-mediated patterning, as it ensures that Wnts expressed in the midbrain and MHB do not suppress midbrain identity, and consequently reinforce formation of the DMB. These findings integrate important temporal elements into our spatial understanding of Wnt-mediated neural patterning and may serve as an important basis for a better understanding of neural patterning defects that have implications in human health.
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Affiliation(s)
- David G Green
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Amy E Whitener
- Department of Biology, Texas A&M University, College Station, TX, 77843-3258, USA
| | - Saurav Mohanty
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Brandon Mistretta
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Preethi Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Alvin T Yeh
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77843-3120, USA
| | - Arne C Lekven
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.
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16
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Abstract
Soon after fertilization the zebrafish embryo generates the pool of cells that will give rise to the germline and the three somatic germ layers of the embryo (ectoderm, mesoderm and endoderm). As the basic body plan of the vertebrate embryo emerges, evolutionarily conserved developmental signaling pathways, including Bmp, Nodal, Wnt, and Fgf, direct the nearly totipotent cells of the early embryo to adopt gene expression profiles and patterns of cell behavior specific to their eventual fates. Several decades of molecular genetics research in zebrafish has yielded significant insight into the maternal and zygotic contributions and mechanisms that pattern this vertebrate embryo. This new understanding is the product of advances in genetic manipulations and imaging technologies that have allowed the field to probe the cellular, molecular and biophysical aspects underlying early patterning. The current state of the field indicates that patterning is governed by the integration of key signaling pathways and physical interactions between cells, rather than a patterning system in which distinct pathways are deployed to specify a particular cell fate. This chapter focuses on recent advances in our understanding of the genetic and molecular control of the events that impart cell identity and initiate the patterning of tissues that are prerequisites for or concurrent with movements of gastrulation.
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Affiliation(s)
- Florence L Marlow
- Icahn School of Medicine Mount Sinai Department of Cell, Developmental and Regenerative Biology, New York, NY, United States.
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17
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Leerberg DM, Hopton RE, Draper BW. Fibroblast Growth Factor Receptors Function Redundantly During Zebrafish Embryonic Development. Genetics 2019; 212:1301-1319. [PMID: 31175226 PMCID: PMC6707458 DOI: 10.1534/genetics.119.302345] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/29/2019] [Indexed: 01/08/2023] Open
Abstract
Fibroblast growth factor (Fgf) signaling regulates many processes during development. In most cases, one tissue layer secretes an Fgf ligand that binds and activates an Fgf receptor (Fgfr) expressed by a neighboring tissue. Although studies have identified the roles of specific Fgf ligands during development, less is known about the requirements for the receptors. We have generated null mutations in each of the five fgfr genes in zebrafish. Considering the diverse requirements for Fgf signaling throughout development, and that null mutations in the mouse Fgfr1 and Fgfr2 genes are embryonic lethal, it was surprising that all zebrafish homozygous mutants are viable and fertile, with no discernable embryonic defect. Instead, we find that multiple receptors are involved in coordinating most Fgf-dependent developmental processes. For example, mutations in the ligand fgf8a cause loss of the midbrain-hindbrain boundary, whereas, in the fgfr mutants, this phenotype is seen only in embryos that are triple mutant for fgfr1a;fgfr1b;fgfr2, but not in any single or double mutant combinations. We show that this apparent fgfr redundancy is also seen during the development of several other tissues, including posterior mesoderm, pectoral fins, viscerocranium, and neurocranium. These data are an essential step toward defining the specific Fgfrs that function with particular Fgf ligands to regulate important developmental processes in zebrafish.
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Affiliation(s)
- Dena M Leerberg
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Rachel E Hopton
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Bruce W Draper
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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18
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Integrated Analysis of miRNA and mRNA Expression Profiles Reveals Functional miRNA-Targets in Development Testes of Small Tail Han Sheep. G3-GENES GENOMES GENETICS 2019; 9:523-533. [PMID: 30559255 PMCID: PMC6385976 DOI: 10.1534/g3.118.200947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Small Tail Han Sheep is a highly valued local breed in China because of their precocity, perennial estrus, and high fecundity. The average annual lambing rate of ewes is as high as 180–270%, the semen of ram has characteristics of high yield, high density, and good motility. To reveal the key miRNAs and miRNA-targets underlying testis development and spermatogenesis in male Small Tail Han Sheep, integrated analysis of miRNA and mRNA expression profiles in 2-, 6-, and 12-month-old testes was performed by RNA-seq technology and bioinformatics methods. The results showed that total of 153 known sheep miRNAs and 2712 novel miRNAs were obtained in 2-,6 - and 12-month-old Small Tail Han Sheep testes; 5, 1, and 4 differentially expressed (DE) known sheep miRNAs, and 132, 105, and 24 DE novel miRNAs were identified in 2- vs. 6-, 6- vs. 12-, and 2- vs. 12-month-old testes, respectively. We combined miRNA results of this study and the mRNA results obtained in our previous study to predict the target mRNAs of DE known sheep miRNAs; 131, 10, and 15 target mRNAs of DE known sheep miRNAs and 76, 1, and 11 DE miRNA–targets were identified in the three groups, respectively. GO and KEGG analyses showed that: in 2- vs. 6-month-olds, the target genes of DE known sheep miRNAs were involved in 100 biological processes and 11 signaling pathways; in 6- vs. 12-month-olds, the target genes of DE known sheep miRNAs were involved in 4 biological processes; and in 2- vs. 12-month-olds, the target genes of DE known sheep miRNAs were involved in 17 biological processes and 4 signaling pathways. Three miR–target regulatory networks were constructed based on these DE miRNA–targets. The key miRNA-Targets involved in testis development and spermatogenesis were screened. 6 known sheep miRNAs and 6 novel miRNAs were selected to validate the accuracy of miRNA sequencing data by qRT-PCR. The binding sites of oar-miR-379-5p with WNT8A was validated by a dual luciferase reporter gene detection system.
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19
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Yan L, Chen J, Zhu X, Sun J, Wu X, Shen W, Zhang W, Tao Q, Meng A. Maternal Huluwa dictates the embryonic body axis through β-catenin in vertebrates. Science 2018; 362:362/6417/eaat1045. [DOI: 10.1126/science.aat1045] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/27/2018] [Indexed: 12/26/2022]
Abstract
The vertebrate body is formed by cell movements and shape change during embryogenesis. It remains undetermined which maternal signals govern the formation of the dorsal organizer and the body axis. We found that maternal depletion of huluwa, a previously unnamed gene, causes loss of the dorsal organizer, the head, and the body axis in zebrafish and Xenopus embryos. Huluwa protein is found on the plasma membrane of blastomeres in the future dorsal region in early zebrafish blastulas. Huluwa has strong dorsalizing and secondary axis–inducing activities, which require β-catenin but can function independent of Wnt ligand/receptor signaling. Mechanistically, Huluwa binds to and promotes the tankyrase-mediated degradation of Axin. Therefore, maternal Huluwa is an essential determinant of the dorsal organizer and body axis in vertebrate embryos.
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20
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Mutational analysis of dishevelled genes in zebrafish reveals distinct functions in embryonic patterning and gastrulation cell movements. PLoS Genet 2018; 14:e1007551. [PMID: 30080849 PMCID: PMC6095615 DOI: 10.1371/journal.pgen.1007551] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 08/16/2018] [Accepted: 07/10/2018] [Indexed: 12/31/2022] Open
Abstract
Wnt signaling plays critical roles in dorsoventral fate specification and anteroposterior patterning, as well as in morphogenetic cell movements. Dishevelled proteins, or Dvls, mediate the activation of Wnt/ß-catenin and Wnt/planar cell polarity pathways. There are at least three highly conserved Dvl proteins in vertebrates, but the implication of each Dvl in key early developmental processes remains poorly understood. In this study, we use genome-editing approach to generate different combinations of maternal and zygotic dvl mutants in zebrafish, and examine their functions during early development. Maternal transcripts for dvl2 and dvl3a are most abundantly expressed, whereas the transcript levels of other dvl genes are negligible. Phenotypic and molecular analyses show that early dorsal fate specification is not affected in maternal and zygotic dvl2 and dvl3a double mutants, suggesting that the two proteins may be dispensable for the activation of maternal Wnt/ß-catenin signaling. Interestingly, convergence and extension movements and anteroposterior patterning require both maternal and the zygotic functions of Dvl2 and Dvl3a, but these processes are more sensitive to Dvl2 dosage. Zygotic dvl2 and dvl3a double mutants display mild axis extension defect with correct anteroposterior patterning. However, maternal and zygotic double mutants exhibit most strongly impaired convergence and extension movements, severe trunk and posterior deficiencies, and frequent occurrence of cyclopia and craniofacial defects. Our results suggest that Dvl2 and Dvl3a products are required for the activation of zygotic Wnt/ß-catenin signaling and Wnt/planar cell polarity pathway, and regulate zygotic developmental processes in a dosage-dependent manner. This work provides insight into the mechanisms of Dvl-mediated Wnt signaling pathways during early vertebrate development. The embryogenesis of most animals is first supported by maternal gene products accumulated in the oocyte, and then by the expression of genes from the zygote. In all vertebrates, there are at least three Dishevelled (Dvl) proteins, which play critical roles in normal development and human diseases. They are both maternally and zygotically expressed, and can activate the ß-catenin-dependent Wnt pathway that regulates gene expression and cell fate, and the ß-catenin-independent Wnt pathway that orchestrates cell movements. In zebrafish embryo, Dvl2 and Dvl3a are most abundant, but their functions are not fully understood. We find that maternally and zygotically expressed Dvl2 plays a predominant role in the elongation of the anteroposterior axis, and the expression of genes involved in the development of the posterior region. Dvl3a cooperates with Dvl2 in these processes. Analyses after loss-of-function of these genes indicate that deficiency of maternal and zygotic Dvl2 and Dvl3a results in embryos with cyclopia, craniofacial defects, and severe abnormality in the trunk and posterior regions. Many human birth defects and other diseases, like cancer, are attributed to the dysfunction of the Wnt pathways. Our results help to understand the mechanisms of Dvl-mediated Wnt pathway activation, and the causes of developmental disorders.
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21
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Winata CL, Korzh V. The translational regulation of maternal mRNAs in time and space. FEBS Lett 2018; 592:3007-3023. [PMID: 29972882 PMCID: PMC6175449 DOI: 10.1002/1873-3468.13183] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/29/2018] [Accepted: 06/29/2018] [Indexed: 12/16/2022]
Abstract
Since their discovery, the study of maternal mRNAs has led to the identification of mechanisms underlying their spatiotemporal regulation within the context of oogenesis and early embryogenesis. Following synthesis in the oocyte, maternal mRNAs are translationally silenced and sequestered into storage in cytoplasmic granules. At the same time, their unique distribution patterns throughout the oocyte and embryo are tightly controlled and connected to their functions in downstream embryonic processes. At certain points in oogenesis and early embryogenesis, maternal mRNAs are translationally activated to perform their functions in a timely manner. The cytoplasmic polyadenylation machinery is responsible for the translational activation of maternal mRNAs, and its role in initiating the maternal to zygotic transition events has recently come to light. Here, we summarize the current knowledge on maternal mRNA regulation, with particular focus on cytoplasmic polyadenylation as a mechanism for translational regulation.
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Affiliation(s)
- Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, Poland.,Max-Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, Poland
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