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England SJ, Campbell PC, Banerjee S, Bates RL, Grieb G, Fancher WF, Lewis KE. Transcriptional regulators with broad expression in the zebrafish spinal cord. Dev Dyn 2024. [PMID: 38850245 DOI: 10.1002/dvdy.717] [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: 01/23/2024] [Revised: 04/12/2024] [Accepted: 05/15/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND The spinal cord is a crucial part of the vertebrate CNS, controlling movements and receiving and processing sensory information from the trunk and limbs. However, there is much we do not know about how this essential organ develops. Here, we describe expression of 21 transcription factors and one transcriptional regulator in zebrafish spinal cord. RESULTS We analyzed the expression of aurkb, foxb1a, foxb1b, her8a, homeza, ivns1abpb, mybl2b, myt1a, nr2f1b, onecut1, sall1a, sall3a, sall3b, sall4, sox2, sox19b, sp8b, tsc22d1, wdhd1, zfhx3b, znf804a, and znf1032 in wild-type and MIB E3 ubiquitin protein ligase 1 zebrafish embryos. While all of these genes are broadly expressed in spinal cord, they have distinct expression patterns from one another. Some are predominantly expressed in progenitor domains, and others in subsets of post-mitotic cells. Given the conservation of spinal cord development, and the transcription factors and transcriptional regulators that orchestrate it, we expect that these genes will have similar spinal cord expression patterns in other vertebrates, including mammals and humans. CONCLUSIONS Our data identify 22 different transcriptional regulators that are strong candidates for playing different roles in spinal cord development. For several of these genes, this is the first published description of their spinal cord expression.
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Affiliation(s)
| | - Paul C Campbell
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, New York, USA
| | - Richard L Bates
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, Syracuse, New York, USA
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England SJ, Campbell PC, Banerjee S, Bates RL, Grieb G, Fancher WF, Lewis KE. Transcriptional Regulators with Broad Expression in the Zebrafish Spinal Cord. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580357. [PMID: 38405913 PMCID: PMC10888778 DOI: 10.1101/2024.02.14.580357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background The spinal cord is a crucial part of the vertebrate CNS, controlling movements and receiving and processing sensory information from the trunk and limbs. However, there is much we do not know about how this essential organ develops. Here, we describe expression of 21 transcription factors and one transcriptional regulator in zebrafish spinal cord. Results We analyzed the expression of aurkb, foxb1a, foxb1b, her8a, homeza, ivns1abpb, mybl2b, myt1a, nr2f1b, onecut1, sall1a, sall3a, sall3b, sall4, sox2, sox19b, sp8b, tsc22d1, wdhd1, zfhx3b, znf804a, and znf1032 in wild-type and MIB E3 ubiquitin protein ligase 1 zebrafish embryos. While all of these genes are broadly expressed in spinal cord, they have distinct expression patterns from one another. Some are predominantly expressed in progenitor domains, and others in subsets of post-mitotic cells. Given the conservation of spinal cord development, and the transcription factors and transcriptional regulators that orchestrate it, we expect that these genes will have similar spinal cord expression patterns in other vertebrates, including mammals and humans. Conclusions Our data identify 22 different transcriptional regulators that are strong candidates for playing different roles in spinal cord development. For several of these genes, this is the first published description of their spinal cord expression.
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Affiliation(s)
- Samantha J. England
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Paul C. Campbell
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, NY 13045, USA
| | - Richard L. Bates
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - William F. Fancher
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Katharine E. Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
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Chong-Morrison V, Mayes S, Simões FC, Senanayake U, Carroll DS, Riley PR, Wilson SW, Sauka-Spengler T. Ac/Ds transposition for CRISPR/dCas9-SID4x epigenome modulation in zebrafish. Biol Open 2023; 12:bio059995. [PMID: 37367831 PMCID: PMC10320716 DOI: 10.1242/bio.059995] [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: 05/03/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Due to its genetic amenability coupled with advances in genome editing, zebrafish is an excellent model to examine the function of (epi)genomic elements. Here, we repurposed the Ac/Ds maize transposition system to efficiently characterise zebrafish cis-regulated elements, also known as enhancers, in F0-microinjected embryos. We further used the system to stably express guide RNAs enabling CRISPR/dCas9-interference (CRISPRi) perturbation of enhancers without disrupting the underlying genetic sequence. In addition, we probed the phenomenon of antisense transcription at two neural crest gene loci. Our study highlights the utility of Ac/Ds transposition as a new tool for transient epigenome modulation in zebrafish.
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Affiliation(s)
- Vanessa Chong-Morrison
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Sarah Mayes
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Filipa C. Simões
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
- University of Oxford, Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, Oxford OX3 7DQ, UK
| | - Upeka Senanayake
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Dervla S. Carroll
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Paul R. Riley
- University of Oxford, Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, Oxford OX3 7DQ, UK
| | - Stephen W. Wilson
- University College London, Department of Cell & Developmental Biology, London WC1E 6BT, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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Parvez S, Brandt ZJ, Peterson RT. Large-scale F0 CRISPR screens in vivo using MIC-Drop. Nat Protoc 2023; 18:1841-1865. [PMID: 37069311 PMCID: PMC10419324 DOI: 10.1038/s41596-023-00821-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 04/19/2023]
Abstract
The zebrafish is a powerful model system for studying animal development, for modeling genetic diseases, and for large-scale in vivo functional genetics. Because of its ease of use and its high efficiency in targeted gene perturbation, CRISPR-Cas9 has recently gained prominence as the tool of choice for genetic manipulation in zebrafish. However, scaling up the technique for high-throughput in vivo functional genetics has been a challenge. We recently developed a method, Multiplexed Intermixed CRISPR Droplets (MIC-Drop), that makes large-scale CRISPR screening in zebrafish possible. Here, we outline the step-by-step protocol for performing functional genetic screens in zebrafish by using MIC-Drop. MIC-Drop uses multiplexed single-guide RNAs to generate biallelic mutations in injected zebrafish embryos, allowing genetic screens to be performed in F0 animals. Combining microfluidics and DNA barcoding enables simultaneous targeting of tens to hundreds of genes from a single injection needle, while also enabling retrospective and rapid identification of the genotype responsible for an observed phenotype. The primary target audiences for MIC-Drop are developmental biologists, zebrafish geneticists, and researchers interested in performing in vivo functional genetic screens in a vertebrate model system. MIC-Drop will also prove useful in the hands of chemical biologists seeking to identify targets of small molecules that cause phenotypic changes in zebrafish. By using MIC-Drop, a typical screen of 100 genes can be conducted within 2-3 weeks by a single user.
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Affiliation(s)
- Saba Parvez
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Zachary J Brandt
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Randall T Peterson
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
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5
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Cao S, Dong Z, Dong X, Jia W, Zhou F, Zhao Q. Zebrafish sox2 Is Required for the Swim Bladder Inflation by Controlling the Swim-Up Behavior. Zebrafish 2023; 20:10-18. [PMID: 36795618 PMCID: PMC9968866 DOI: 10.1089/zeb.2022.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
The swim bladder functions to maintain the fish balance at a certain position under water. Although the motoneuron-dependent swim-up behavior is important for swim bladder inflation, the underlying molecular mechanism remains largely unknown. We generated a sox2 KO zebrafish using TALEN and found that the posterior chamber of the swim bladder was uninflated. The tail flick and the swim-up behavior were absent in the mutant zebrafish embryos and the behavior could not be accomplished. As the tail flick behavior is absent, the mutant larvae therefore cannot reach the water surface to gulp air, ultimately leading to the uninflation of the swim bladder. To understand the mechanism underlying the swim-up defects, we crossed the sox2 null allele in the background of Tg(huc:eGFP) and Tg(hb9:GFP). The deficiency of sox2 in zebrafish resulted in abnormal motoneuron axons in the regions of trunk, tail, and swim bladder. To identify the downstream target gene of sox2 to control the motor neuron development, we performed RNA sequencing on the transcriber of mutant embryos versus wild type embryos and found that the axon guidance pathway was abnormal in the mutant embryos. RT-PCR demonstrated that the expression of sema3bl, ntn1b, and robo2 were decreased in the mutants.
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Affiliation(s)
- Shasha Cao
- Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang, China
| | - Zhangji Dong
- The MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Xiaohua Dong
- The MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Wenshuang Jia
- The MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Fuyou Zhou
- Anyang Tumor Hospital, The Affiliated Anyang Tumor Hospital of Henan University of Science and Technology, Anyang, China
| | - Qingshun Zhao
- The MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
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6
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Henke K, Farmer DT, Niu X, Kraus JM, Galloway JL, Youngstrom DW. Genetically engineered zebrafish as models of skeletal development and regeneration. Bone 2023; 167:116611. [PMID: 36395960 PMCID: PMC11080330 DOI: 10.1016/j.bone.2022.116611] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Zebrafish (Danio rerio) are aquatic vertebrates with significant homology to their terrestrial counterparts. While zebrafish have a centuries-long track record in developmental and regenerative biology, their utility has grown exponentially with the onset of modern genetics. This is exemplified in studies focused on skeletal development and repair. Herein, the numerous contributions of zebrafish to our understanding of the basic science of cartilage, bone, tendon/ligament, and other skeletal tissues are described, with a particular focus on applications to development and regeneration. We summarize the genetic strengths that have made the zebrafish a powerful model to understand skeletal biology. We also highlight the large body of existing tools and techniques available to understand skeletal development and repair in the zebrafish and introduce emerging methods that will aid in novel discoveries in skeletal biology. Finally, we review the unique contributions of zebrafish to our understanding of regeneration and highlight diverse routes of repair in different contexts of injury. We conclude that zebrafish will continue to fill a niche of increasing breadth and depth in the study of basic cellular mechanisms of skeletal biology.
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Affiliation(s)
- Katrin Henke
- Department of Orthopaedics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - D'Juan T Farmer
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA.
| | - Xubo Niu
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Jessica M Kraus
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel W Youngstrom
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
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Normal embryonic development and neonatal digit regeneration in mice overexpressing a stem cell factor, Sall4. PLoS One 2022; 17:e0267273. [PMID: 35482646 PMCID: PMC9049339 DOI: 10.1371/journal.pone.0267273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/05/2022] [Indexed: 01/29/2023] Open
Abstract
Sall4 encodes a transcription factor and is known to participate in the pluripotency network of embryonic stem cells. Sall4 expression is known to be high in early stage post-implantation mouse embryos. During early post-gastrulation stages, Sall4 is highly expressed in the tail bud and distal limb buds, where progenitor cells are maintained in an undifferentiated status. The expression of Sall4 is rapidly downregulated during embryonic development. We previously demonstrated that Sall4 is required for limb and posterior axial skeleton development by conditional deletion of Sall4 in the T (Brachyury) lineage. To gain insight into Sall4 functions in embryonic development and postnatal digit regeneration, we genetically overexpressed Sall4 in the mesodermal lineage by the TCre transgene and a novel knockin allele of Rosa26-loxP-stop-loxP-Sall4. In significant contrast to severe defects by Sall4 loss of function reported in previous studies, overexpression of Sall4 resulted in normal morphology and pattern in embryos and neonates. The length of limb long bones showed subtle reduction in Sall4-overexpression mice. It is known that the digit tip of neonatal mice has level-specific regenerative ability after experimental amputation. We observed Sall4 expression in the digit tip by using a sensitive Sall4-LacZ knock-in reporter expression. Sall4 overexpression did not alter the regenerative ability of the terminal phalange that normally regenerates after amputation. Moreover, Sall4 overexpression did not confer regenerative ability to the second phalange that normally does not regenerate after amputation. These genetic experiments show that overexpression of Sall4 does not alter the development of the appendicular and axial skeleton, or neonatal digit regeneration. The results suggest that Sall4 acts as a permissive factor rather than playing an instructive role.
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8
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VPS28 regulates brain vasculature by controlling neuronal VEGF trafficking through extracellular vesicle secretion. iScience 2022; 25:104042. [PMID: 35330682 PMCID: PMC8938284 DOI: 10.1016/j.isci.2022.104042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/27/2022] [Accepted: 03/04/2022] [Indexed: 11/21/2022] Open
Abstract
Extracellular vesicles (EVs) participate in intercellular communication and contribute to the angiogenesis. However, the understanding of the mechanisms underlying EVs secretion by neurons and their action on the vascular system of the central nervous system (CNS) remain rudimentary. Here, we show that vacuolar protein sorting 28 (Vps28) is essential for the sprouting of brain central arteries (CtAs) and for the integrity of blood-brain barrier (BBB) in zebrafish. Disruption of neuron-enriched Vps28 significantly decreased EVs secretion by regulating the formation of intracellular multivesicular bodies (MVBs). EVs derived from zebrafish embryos or mouse cortical neurons partially rescued the brain vasculature defect and brain leakage. Further investigations revealed that neuronal EVs containing vascular endothelial growth factor A (VEGF-A) are key regulators in neurovascular communication. Our results indicate that Vps28 acts as an intercellular endosomal regulator mediating the secretion of neuronal EVs, which in turn communicate with endothelial cells to mediate angiogenesis through VEGF-A trafficking. Vps28 is highly expressed in neurons and involved in the secretion of neuronal EVs Vps28, as a subunit of ESCRT-1 complexes, participates in the formation of MVB Vps28 plays an important role in VEGFA transport and promotes neurovascular communication
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9
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Yuikawa T, Ikeda M, Tsuda S, Saito S, Yamasu K. Involvement of Oct4-type transcription factor Pou5f3 in posterior spinal cord formation in zebrafish embryos. Dev Growth Differ 2021; 63:306-322. [PMID: 34331767 DOI: 10.1111/dgd.12742] [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: 05/30/2021] [Revised: 07/13/2021] [Accepted: 07/27/2021] [Indexed: 12/21/2022]
Abstract
In vertebrate embryogenesis, elongation of the posterior body is driven by de novo production of the axial and paraxial mesoderm as well as the neural tube at the posterior end. This process is presumed to depend on the stem cell-like population in the tail bud region, but the details of the gene regulatory network involved are unknown. Previous studies suggested the involvement of pou5f3, an Oct4-type POU gene in zebrafish, in axial elongation. In the present study, we first found that pou5f3 is expressed mainly in the dorsal region of the tail bud immediately after gastrulation, and that this expression is restricted to the posterior-most region of the elongating neural tube during somitogenesis. This pou5f3 expression was complementary to the broad expression of sox3 in the neural tube, and formed a sharp boundary with specific expression of tbxta (orthologue of mammalian T/Brachyury) in the tail bud, implicating pou5f3 in the specification of tail bud-derived cells toward neural differentiation in the spinal cord. When pou5f3 was functionally impaired after gastrulation by induction of a dominant-interfering pou5f3 mutant gene (en-pou5f3), trunk and tail elongation were markedly disturbed at distinct positions along the axis depending on the stage. This finding showed involvement of pou5f3 in de novo generation of the body from the tail bud. Conditional functional abrogation also showed that pou5f3 downregulates mesoderm-forming genes but promotes neural development by activating neurogenesis genes around the tail bud. These results suggest that pou5f3 is involved in formation of the posterior spinal cord.
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Affiliation(s)
- Tatsuya Yuikawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Japan
| | - Masaaki Ikeda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Japan
| | - Sachiko Tsuda
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Japan
| | - Shinji Saito
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Japan
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10
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Fricke T, Smalakyte D, Lapinski M, Pateria A, Weige C, Pastor M, Kolano A, Winata C, Siksnys V, Tamulaitis G, Bochtler M. Targeted RNA Knockdown by a Type III CRISPR-Cas Complex in Zebrafish. CRISPR J 2020; 3:299-313. [PMID: 32833532 PMCID: PMC7469701 DOI: 10.1089/crispr.2020.0032] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA interference is a powerful experimental tool for RNA knockdown, but not all organisms are amenable. Here, we provide a proof of principle demonstration that a type III Csm effector complex can be used for programmable mRNA transcript degradation in eukaryotes. In zebrafish, Streptococcus thermophilus Csm complex (StCsm) proved effective for knockdown of maternally expressed EGFP in germ cells of Tg(ddx4:ddx4-EGFP) fish. It also led to significant, albeit less drastic, fluorescence reduction at one day postfertilization in Tg(myl7:GFP) and Tg(fli1:EGFP) fish that express EGFP zygotically. StCsm targeted against the endogenous tdgf1 elicited the characteristic one-eyed phenotype with greater than 50% penetrance, and hence with similar efficiency to morpholino-mediated knockdown. We conclude that Csm-mediated knockdown is very efficient for maternal transcripts and can also be used for mixed maternal/early zygotic and early zygotic transcripts, in some cases reaching comparable efficiency to morpholino-based knockdown without significant off-target effects.
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Affiliation(s)
- Thomas Fricke
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Dalia Smalakyte
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Maciej Lapinski
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Abhishek Pateria
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Charles Weige
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michal Pastor
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Agnieszka Kolano
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | | | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
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11
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Zhang Q, Liang D, Yue Y, He L, Li N, Jiang D, Hu P, Zhao Q. Axenfeld-Rieger syndrome-associated mutants of the transcription factor FOXC1 abnormally regulate NKX2-5 in model zebrafish embryos. J Biol Chem 2020; 295:11902-11913. [PMID: 32631953 DOI: 10.1074/jbc.ra120.013287] [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: 02/29/2020] [Revised: 07/04/2020] [Indexed: 12/25/2022] Open
Abstract
FOXC1 is a member of the forkhead family of transcription factors, and whose function is poorly understood. A variety of FOXC1 mutants have been identified in patients diagnosed with the autosomal dominant disease Axenfeld-Rieger syndrome, which is mainly characterized by abnormal development of the eyes, particularly those who also have accompanying congenital heart defects (CHD). However, the role of FOXC1 in CHD, and how these mutations might impact FOXC1 function, remains elusive. Our previous work provided one clue to possible function, demonstrating that zebrafish foxc1a, an orthologue of human FOXC1 essential for heart development, directly regulates the expression of nkx2.5, encoding a transcriptional regulator of cardiac progenitor cells. Abnormal expression of Nkx2-5 leads to CHD in mice and is also associated with CHD patients. Whether this link extends to the human system, however, requires investigation. In this study, we demonstrate that FOXC1 does regulate human NKX2-5 expression in a dose-dependent manner via direct binding to its proximal promoter. A comparison of FOXC1 mutant function in the rat cardiac cell line H9c2 and zebrafish embryos suggested that the zebrafish embryos might serve as a more representative model system than the H9c2 cells. Finally, we noted that three of the Axenfeld-Rieger syndrome FOXC1 mutations tested increased, whereas a fourth repressed the expression of NKX2-5 These results imply that mutant FOXC1s might play etiological roles in CHD by abnormally regulating NKX2-5 in the patients. And zebrafish embryos can serve as a useful in vivo platform for rapidly evaluating disease-causing roles of mutated genes.
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Affiliation(s)
- Qinxin Zhang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Dong Liang
- Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yunyun Yue
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Luqingqing He
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Nan Li
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Dongya Jiang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Qingshun Zhao
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
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12
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Inomata C, Yuikawa T, Nakayama-Sadakiyo Y, Kobayashi K, Ikeda M, Chiba M, Konishi C, Ishioka A, Tsuda S, Yamasu K. Involvement of an Oct4-related PouV gene, pou5f3/pou2, in neurogenesis in the early neural plate of zebrafish embryos. Dev Biol 2020; 457:30-42. [DOI: 10.1016/j.ydbio.2019.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 01/03/2023]
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13
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Gao T, Li J, Li N, Gao Y, Yu L, Zhuang S, Zhao Y, Dong X. lncrps25 play an essential role in motor neuron development through controlling the expression of olig2 in zebrafish. J Cell Physiol 2019; 235:3485-3496. [PMID: 31549395 DOI: 10.1002/jcp.29237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022]
Abstract
lncrps25 is an intergenic long noncoding RNA (lncRNA), which is location close to rps25 (ribosomal protein S25) gene, is reported share high conserved sequence with NREP (neuronal regeneration-related protein) 3'-untranslated region. The function and mechanism of most of the lncRNA in embryo development remain largely unknown. In zebrafish, lncrps25 is widely expressed in the early embryonic stage and spinal cord during development. Morpholino (MO) knockdown of zebrafish lncrps25 exhibit locomotor behavior defects, caused by abnormal development of motor neurons. In addition, the defect of swimming ability and motor neurons could be recovery by microinject with lncrps25 RNA in lncrps25 morphants. By performing RNA sequencing and quantitative real-time polymerase chain reaction, we found that olig2 (oligodendrocyte transcription factor 2) messenger RNA (mRNA) was downregulated in lncrps25 morphants. Moreover, overexpression of olig2 mRNA in lncrps25 morphants partially rescued motor neurons development. Taken together, these results indicate that lncrps25 plays an essential role in the development of motor neurons in zebrafish.
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Affiliation(s)
- Tianheng Gao
- College of Oceanography, Hohai University, Nanjing, China
| | - Jingyun Li
- Nanjing Maternal and Child Health Medical Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Nan Li
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Yan Gao
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Lingling Yu
- Department of Pediatric, Jingjiang People's Hospital Affiliated to Yangzhou University, Jingjiang, China
| | - Sisi Zhuang
- Nanjing Maternal and Child Health Medical Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China.,Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Yingmin Zhao
- Department of Pediatric, Jingjiang People's Hospital Affiliated to Yangzhou University, Jingjiang, China
| | - Xiaohua Dong
- Department of Pediatric, Jingjiang People's Hospital Affiliated to Yangzhou University, Jingjiang, China
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14
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Liu K, Petree C, Requena T, Varshney P, Varshney GK. Expanding the CRISPR Toolbox in Zebrafish for Studying Development and Disease. Front Cell Dev Biol 2019; 7:13. [PMID: 30886848 PMCID: PMC6409501 DOI: 10.3389/fcell.2019.00013] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/24/2019] [Indexed: 12/13/2022] Open
Abstract
The study of model organisms has revolutionized our understanding of the mechanisms underlying normal development, adult homeostasis, and human disease. Much of what we know about gene function in model organisms (and its application to humans) has come from gene knockouts: the ability to show analogous phenotypes upon gene inactivation in animal models. The zebrafish (Danio rerio) has become a popular model organism for many reasons, including the fact that it is amenable to various forms of genetic manipulation. The RNA-guided CRISPR/Cas9-mediated targeted mutagenesis approaches have provided powerful tools to manipulate the genome toward developing new disease models and understanding the pathophysiology of human diseases. CRISPR-based approaches are being used for the generation of both knockout and knock-in alleles, and also for applications including transcriptional modulation, epigenome editing, live imaging of the genome, and lineage tracing. Currently, substantial effort is being made to improve the specificity of Cas9, and to expand the target coverage of the Cas9 enzymes. Novel types of naturally occurring CRISPR systems [Cas12a (Cpf1); engineered variants of Cas9, such as xCas9 and SpCas9-NG], are being studied and applied to genome editing. Since the majority of pathogenic mutations are single point mutations, development of base editors to convert C:G to T:A or A:T to G:C has further strengthened the CRISPR toolbox. In this review, we provide an overview of the increasing number of novel CRISPR-based tools and approaches, including lineage tracing and base editing.
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Affiliation(s)
| | | | | | | | - Gaurav K. Varshney
- Functional and Chemical Genomics Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
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15
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Li J, Zhao Y, He L, Huang Y, Yang X, Yu L, Zhao Q, Dong X. Znfl1s are essential for patterning the anterior-posterior axis of zebrafish posterior hindbrain by acting as direct target genes of retinoic acid. Mech Dev 2018; 155:27-33. [PMID: 30472261 DOI: 10.1016/j.mod.2018.11.001] [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: 08/21/2018] [Revised: 10/29/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
Abstract
RA (retinoic acid) signaling is essential for the patterning the hindbrain of vertebrates. Although hundreds of potential RA targets genes are identified, the ones other than hox genes playing roles in patterning anterior-posterior axis of hindbrain by mediating RA signaling remains largely unknown. Previously, we reported that znfl1s play essential roles in the formation of posterior neuroectoderm in zebrafish embryos. Here, we revealed that znfl1s play a critical role in patterning the posterior axis of hindbrain by maintaining the homeostasis of RA signaling in zebrafish embryos. Knocking down znfl1s shortened the length of the posterior hindbrain in a similar way of reducing RA signaling in zebrafish embryos and the defective posterior hindbrain was effectively rescued by elevating RA signaling. By performing mutagenesis assays and chromatin immunoprecipitation assays on the promoter of znfl1s, we demonstrated that znfl1s are direct target genes of RA to mediate RA signaling through a functional DR1 RA response element. Taken together, our results showed that Znfl1s are essential for patterning the anterior-posterior axis development of posterior hindbrain by acting as direct target genes of RA signaling.
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Affiliation(s)
- Jingyun Li
- Maternal and Child Health Medical Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yingmin Zhao
- Department of Pediatric, Jingjiang People's Hospital Affiliated to Yangzhou University, Jingjiang 214500, China
| | - Luqingqing He
- Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Yun Huang
- Department of Pediatric, Jingjiang People's Hospital Affiliated to Yangzhou University, Jingjiang 214500, China
| | - Xiaojing Yang
- Department of Pediatric, Jingjiang People's Hospital Affiliated to Yangzhou University, Jingjiang 214500, China
| | - Lingling Yu
- Department of Pediatric, Jingjiang People's Hospital Affiliated to Yangzhou University, Jingjiang 214500, China
| | - Qingshun Zhao
- Model Animal Research Center, Nanjing University, Nanjing 210061, China.
| | - Xiaohua Dong
- Department of Pediatric, Jingjiang People's Hospital Affiliated to Yangzhou University, Jingjiang 214500, China.
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16
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Li J, Gao F, Zhao Y, He L, Huang Y, Yang X, Zhou Y, Yu L, Zhao Q, Dong X. Zebrafish
znfl1s
regulate left‐right asymmetry patterning through controlling the expression of
fgfr1a. J Cell Physiol 2018; 234:1987-1995. [PMID: 30317609 DOI: 10.1002/jcp.27564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/14/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Jingyun Li
- Maternal and Child Health Medical InstituteWomen’s Hospital of Nanjing Medical University
| | - Feng Gao
- Department of PediatricJingjiang People's Hospital Affiliated to Yangzhou UniversityJingjiang, Jiangsu China
| | - Yingmin Zhao
- Department of PediatricJingjiang People's Hospital Affiliated to Yangzhou UniversityJingjiang, Jiangsu China
| | - Luqingqing He
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing UniversityNanjing China
| | - Yun Huang
- Department of PediatricJingjiang People's Hospital Affiliated to Yangzhou UniversityJingjiang, Jiangsu China
| | - Xiaojing Yang
- Department of PediatricJingjiang People's Hospital Affiliated to Yangzhou UniversityJingjiang, Jiangsu China
| | - Yahui Zhou
- Maternal and Child Health Medical InstituteWomen’s Hospital of Nanjing Medical University
| | - Lingling Yu
- Department of PediatricJingjiang People's Hospital Affiliated to Yangzhou UniversityJingjiang, Jiangsu China
| | - Qingshun Zhao
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing UniversityNanjing China
| | - Xiaohua Dong
- Department of PediatricJingjiang People's Hospital Affiliated to Yangzhou UniversityJingjiang, Jiangsu China
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