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Tufan T, Comertpay G, Villani A, Nelson GM, Terekhova M, Kelley S, Zakharov P, Ellison RM, Shpynov O, Raymond M, Sun J, Chen Y, Bockelmann E, Stremska M, Peterson LW, Boeckaerts L, Goldman SR, Etchegaray JI, Artyomov MN, Peri F, Ravichandran KS. Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release. Nature 2024; 628:408-415. [PMID: 38480883 DOI: 10.1038/s41586-024-07172-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/07/2024] [Indexed: 03/18/2024]
Abstract
During development, inflammation or tissue injury, macrophages may successively engulf and process multiple apoptotic corpses via efferocytosis to achieve tissue homeostasis1. How macrophages may rapidly adapt their transcription to achieve continuous corpse uptake is incompletely understood. Transcriptional pause/release is an evolutionarily conserved mechanism, in which RNA polymerase (Pol) II initiates transcription for 20-60 nucleotides, is paused for minutes to hours and is then released to make full-length mRNA2. Here we show that macrophages, within minutes of corpse encounter, use transcriptional pause/release to unleash a rapid transcriptional response. For human and mouse macrophages, the Pol II pause/release was required for continuous efferocytosis in vitro and in vivo. Interestingly, blocking Pol II pause/release did not impede Fc receptor-mediated phagocytosis, yeast uptake or bacterial phagocytosis. Integration of data from three genomic approaches-precision nuclear run-on sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-seq)-on efferocytic macrophages at different time points revealed that Pol II pause/release controls expression of select transcription factors and downstream target genes. Mechanistic studies on transcription factor EGR3, prominently regulated by pause/release, uncovered EGR3-related reprogramming of other macrophage genes involved in cytoskeleton and corpse processing. Using lysosomal probes and a new genetic fluorescent reporter, we identify a role for pause/release in phagosome acidification during efferocytosis. Furthermore, microglia from egr3-deficient zebrafish embryos displayed reduced phagocytosis of apoptotic neurons and fewer maturing phagosomes, supporting defective corpse processing. Collectively, these data indicate that macrophages use Pol II pause/release as a mechanism to rapidly alter their transcriptional programs for efficient processing of the ingested apoptotic corpses and for successive efferocytosis.
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Affiliation(s)
- Turan Tufan
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gamze Comertpay
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ambra Villani
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Geoffrey M Nelson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Marina Terekhova
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Shannon Kelley
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Pavel Zakharov
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rochelle M Ellison
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Oleg Shpynov
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- JetBrains Research, Munich, Germany
| | - Michael Raymond
- Department of Neuroscience and MIC, University of Virginia, Charlottesville, VA, USA
| | - Jerry Sun
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yitan Chen
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Enno Bockelmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Marta Stremska
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lance W Peterson
- Department of Pediatrics, Division of Rheumatology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Laura Boeckaerts
- Unit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research and the Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Seth R Goldman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - J Iker Etchegaray
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Francesca Peri
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Kodi S Ravichandran
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Neuroscience and MIC, University of Virginia, Charlottesville, VA, USA.
- Unit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research and the Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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2
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Briski O, La Motta GE, Ratner LD, Allegroni FA, Pillado S, Álvarez G, Gutierrez B, Tarragona L, Zaccagnini A, Acerbo M, Ciampi C, Fernández-Martin R, Salamone DF. Comparison of ICSI, IVF, and in vivo derived embryos to produce CRISPR-Cas9 gene-edited pigs for xenotransplantation. Theriogenology 2024; 220:43-55. [PMID: 38471390 DOI: 10.1016/j.theriogenology.2024.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
Genome editing in pigs for xenotransplantation has seen significant advances in recent years. This study compared three methodologies to generate gene-edited embryos, including co-injection of sperm together with the CRISPR-Cas9 system into oocytes, named ICSI-MGE (mediated gene editing); microinjection of CRISPR-Cas9 components into oocytes followed by in vitro fertilization (IVF), and microinjection of in vivo fertilized zygotes with the CRISPR-Cas9 system. Our goal was to knock-out (KO) porcine genes involved in the biosynthesis of xenoantigens responsible for the hyperacute rejection of interspecific xenografts, namely GGTA1, CMAH, and β4GalNT2. Additionally, we attempted to KO the growth hormone receptor (GHR) gene with the aim of limiting the growth of porcine organs to a size that is physiologically suitable for human transplantation. Embryo development, pregnancy, and gene editing rates were evaluated. We found an efficient mutation of the GGTA1 gene following ICSI-MGE, comparable to the results obtained through the microinjection of oocytes followed by IVF. ICSI-MGE also showed higher rates of biallelic mutations compared to the other techniques. Five healthy piglets were born from in vivo-derived embryos, all of them exhibiting biallelic mutations in the GGTA1 gene, with three displaying mutations in the GHR gene. No mutations were observed in the CMAH and β4GalNT2 genes. In conclusion, in vitro methodologies showed high rates of gene-edited embryos. Specifically, ICSI-MGE proved to be an efficient technique for obtaining homozygous biallelic mutated embryos. Lastly, only live births were obtained from in vivo-derived embryos showing efficient multiple gene editing for GGTA1 and GHR.
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Affiliation(s)
- Olinda Briski
- CONICET-Universidad de Buenos Aires - Instituto de Investigaciones en Producción Animal (INPA), Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina; Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Gastón Emilio La Motta
- CONICET-Universidad de Buenos Aires - Instituto de Investigaciones en Producción Animal (INPA), Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina
| | - Laura Daniela Ratner
- CONICET-Universidad de Buenos Aires - Instituto de Investigaciones en Producción Animal (INPA), Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina; Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Federico Andrés Allegroni
- Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Santiago Pillado
- Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Guadalupe Álvarez
- Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Betiana Gutierrez
- Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Lisa Tarragona
- Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Andrea Zaccagnini
- Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Marcelo Acerbo
- Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Carla Ciampi
- CONICET-Universidad de Buenos Aires - Instituto de Investigaciones en Producción Animal (INPA), Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina; Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina
| | - Rafael Fernández-Martin
- CONICET-Universidad de Buenos Aires - Instituto de Investigaciones en Producción Animal (INPA), Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina; Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina.
| | - Daniel Felipe Salamone
- CONICET-Universidad de Buenos Aires - Instituto de Investigaciones en Producción Animal (INPA), Ciudad Autónoma de Buenos Aires, C1425FQB, Argentina; Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1417DSE, Argentina.
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Patton BK, Madadi S, Briley SM, Ahmed AA, Pangas SA. Sumoylation regulates functional properties of the oocyte transcription factors SOHLH1 and NOBOX. FASEB J 2023; 37:e22747. [PMID: 36607631 PMCID: PMC10129296 DOI: 10.1096/fj.202201481r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023]
Abstract
SOHLH1 and NOBOX are oocyte-expressed transcription factors with critical roles in ovary development and fertility. In mice, Sohlh1 and Nobox are essential for fertility through their regulation of the oocyte transcriptional network and cross-talk to somatic cells. Sumoylation is a posttranslational modification that regulates transcription factor function, and we previously showed that mouse oocytes deficient for sumoylation had an altered transcriptional landscape that included significant changes in NOBOX target genes. Here, we show that mouse SOHLH1 is modified by SUMO2/3 at lysine 345 and mutation of this residue alters SOHLH1 nuclear to cytoplasmic localization. In NOBOX, we identify a non-consensus SUMO site, K97, that eliminates NOBOX mono-SUMO2/3 conjugation, while a point mutation at K125 had no effect on NOBOX sumoylation. However, NOBOXK97R/K125R double mutants showed loss of mono-SUMO2/3 and altered higher molecular weight modifications, suggesting cooperation between these lysine's. NOBOXK97R and NOBOXK97R/K125R differentially regulated NOBOX promoter targets, with increased activity on the Gdf9 promoter, but no effect on the Pou5f1 promoter. These data implicate sumoylation as a novel regulatory mechanism for SOHLH1 and NOBOX, which may prove useful in refining their roles during oogenesis as well as their function during reprogramming to generate de novo germ cells.
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Affiliation(s)
- Bethany K. Patton
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Surabhi Madadi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Rice University, Houston, TX 77005
| | - Shawn M. Briley
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Avery A. Ahmed
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030
| | - Stephanie A. Pangas
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030
- Graduate Program in Development, Disease Models & Therapeutics, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030
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The tissue-specificity associated region and motif of an emx2 downstream enhancer CNE2.04 in zebrafish. Gene Expr Patterns 2022; 45:119269. [PMID: 35970322 DOI: 10.1016/j.gep.2022.119269] [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: 03/31/2022] [Revised: 07/04/2022] [Accepted: 07/29/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Expression level of EMX2 plays an important role in the development of nervous system and cancers. CNE2.04, a conserved enhancer downstream of emx2, drives fluorescent protein expression in the similar pattern of emx2. METHODS CNE2.04 truncated or motif-mutated transgenic reporter plasmids were constructed and injected into the zebrafish fertilized egg with Tol2 mRNA at the unicellular stage of zebrafish eggs. The green fluorescence expression patterns were observed at 24, 48, and 72 hpf, and the fluorescence rates of different tissues were counted at 48 hpf. RESULTS Compared to CNE2.04, CNE2.04-R400 had comparable enhancer activity, while the tissue specificity of CNE2.04-L400 was obviously changed. Motif CCCCTC mutation obviously changed the enhancer activity, while motif CCGCTC mutations also changed it. CONCLUSION Due to their correlation with tissue specificity, CNE2.04-R400 is associated with the tissue-specificity of CNE2.04, and motif CCCCTC plays an important role in the enhancer activity of CNE2.04.
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Effects of the timing of electroporation during in vitro maturation on triple gene editing in porcine embryos using CRISPR/Cas9 system. Vet Anim Sci 2022; 16:100241. [PMID: 35265771 PMCID: PMC8899406 DOI: 10.1016/j.vas.2022.100241] [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] [Indexed: 12/04/2022] Open
Abstract
Mosaicism is a serious problem for genome editing during embryogenesis. We hypothesized that genome-editing before in vitro fertilization can increase its efficiency. We introduced CRISPR/Cas9 system into oocytes during in vitro maturation using electroporation. Gene editing efficiency in matured oocytes was comparable with that in fertilized zygotes. Matured oocytes are suggested as functional material accepting gene editing application.
Mosaicism, including alleles comprising both wild-type and mutant, is a serious problem for gene modification by gene editing using electroporation. One-step generation of F0 pigs with completely desired gene modifications saves cost and time, but the major obstacles have been mosaic mutations. We hypothesized that the timing of electroporation prior to in vitro fertilization (IVF) can increase the rates of biallelic mutation for multiple gene knockout as the permeability of mature oocytes is greater than that of zygotes. Hence, we determined whether the timing of electroporation during in vitro maturation (IVM) culture enhances triple gene editing in the resulting blastocysts. Three gRNAs targeting KDR, PDX1, and SALL1 were simultaneously introduced into the oocytes that had been incubated for 40, 42, and 44 h from the start of the IVM culture. Electroporation with three gRNAs at 40 h and 42 h during IVM culture decreased the blastocyst formation rates and did not improve the mutation rates and target number of biallelic mutations in the resulting blastocysts. The blastocyst formation rate, mutation rates, and target numbers in the resulting blastocysts from oocytes treated by electroporation at 44 h of IVM culture were similar to those of control zygotes electroporated at 13 h after the initiation of IVF. In conclusion, multiple gene editing efficiency in the resulting blastocysts was comparable between oocytes electroporated before and after the fertilization, indicating that oocytes with completed maturation time may allow better functioning of materials accepting gene editing application.
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Shi DL. Circumventing Zygotic Lethality to Generate Maternal Mutants in Zebrafish. BIOLOGY 2022; 11:102. [PMID: 35053100 PMCID: PMC8773025 DOI: 10.3390/biology11010102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 11/16/2022]
Abstract
Maternal gene products accumulated during oogenesis are essential for supporting early developmental processes in both invertebrates and vertebrates. Therefore, understanding their regulatory functions should provide insights into the maternal control of embryogenesis. The CRISPR/Cas9 genome editing technology has provided a powerful tool for creating genetic mutations to study gene functions and developing disease models to identify new therapeutics. However, many maternal genes are also essential after zygotic genome activation; as a result, loss of their zygotic functions often leads to lethality or sterility, thus preventing the generation of maternal mutants by classical crossing between zygotic homozygous mutant adult animals. Although several approaches, such as the rescue of mutant phenotypes through an injection of the wild-type mRNA, germ-line replacement, and the generation of genetically mosaic females, have been developed to overcome this difficulty, they are often technically challenging and time-consuming or inappropriate for many genes that are essential for late developmental events or for germ-line formation. Recently, a method based on the oocyte transgenic expression of CRISPR/Cas9 and guide RNAs has been designed to eliminate maternal gene products in zebrafish. This approach introduces several tandem guide RNA expression cassettes and a GFP reporter into transgenic embryos expressing Cas9 to create biallelic mutations and inactivate genes of interest specifically in the developing oocytes. It is particularly accessible and allows for the elimination of maternal gene products in one fish generation. By further improving its efficiency, this method can be used for the systematic characterization of maternal-effect genes.
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Affiliation(s)
- De-Li Shi
- Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China;
- Laboratory of Developmental Biology, CNRS-UMR7622, Institut de Biologie Paris-Seine, Sorbonne University, 75005 Paris, France
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Wu X, Zhang H, Zhang B, Zhang Y, Wang Q, Shen W, Wu X, Li L, Xia W, Nakamura R, Liu B, Liu F, Takeda H, Meng A, Xie W. Methylome inheritance and enhancer dememorization reset an epigenetic gate safeguarding embryonic programs. SCIENCE ADVANCES 2021; 7:eabl3858. [PMID: 34936444 PMCID: PMC8694617 DOI: 10.1126/sciadv.abl3858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/10/2021] [Indexed: 05/31/2023]
Abstract
Marked epigenetic reprogramming is essential to convert terminally differentiated gametes to totipotent embryos. It remains puzzling why postfertilization global DNA reprogramming occurs in mammals but not in nonmammalian vertebrates. In zebrafish, global methylome inheritance is however accompanied by extensive enhancer “dememorization” as they become fully methylated. By depleting maternal dnmt1 using oocyte microinjection, we eliminated DNA methylation in early embryos, which died around gastrulation with severe differentiation defects. Notably, methylation deficiency leads to derepression of adult tissue–specific genes and CG-rich enhancers, which acquire ectopic transcription factor binding and, unexpectedly, histone H3 lysine 4 trimethylation (H3K4me3). By contrast, embryonic enhancers are generally CG-poor and evade DNA methylation repression. Hence, global DNA hypermethylation inheritance coupled with enhancer dememorization installs an epigenetic gate that safeguards embryonic programs and ensures temporally ordered gene expression. We propose that “enhancer dememorization” underlies and unifies distinct epigenetic reprogramming modes in early development between mammals and nonmammals.
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Affiliation(s)
- Xiaotong Wu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongmei Zhang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bingjie Zhang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu Zhang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiuyan Wang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xi Wu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lijia Li
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weikun Xia
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Bofeng Liu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, University of Chinese Academy of Science, Beijing, China
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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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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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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10
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Zhang L, Chen L, Chen J, Shen W, Meng A. Mini-III RNase-based dual-color system for in vivo mRNA tracking. Development 2020; 147:dev.190728. [PMID: 33093152 PMCID: PMC7725608 DOI: 10.1242/dev.190728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/15/2020] [Indexed: 11/25/2022]
Abstract
Mini-III RNase (mR3), a member of RNase III endonuclease family, can bind to and cleave double-stranded RNAs (dsRNAs). Inactive mR3 protein without the α5β-α6 loop loses the dsRNA cleavage activity, but retains dsRNA binding activity. Here, we establish an inactive mR3-based non-engineered mR3/dsRNA system for RNA tracking in zebrafish embryos. In vitro binding experiments show that inactive Staphylococcus epidermidis mR3 (dSmR3) protein possesses the highest binding affinity with dsRNAs among mR3s from other related species, and its binding property is retained in zebrafish embryos. Combined with a fluorescein-labeled antisense RNA probe recognizing the target mRNAs, dSmR3 tagged with a nuclear localization sequence and a fluorescent protein could allow visualization of the dynamics of endogenous target mRNAs. The dSmR3/antisense probe dual-color system provides a new approach for tracking non-engineered RNAs in real-time, which will help understand how endogenous RNAs dynamically move during embryonic development. Summary: A fluorescent antisense probe and the inactive form of Staphylococcus epidermidis Mini-III RNase with a fluorescent tag may be used together to visualize endogenous mRNAs in zebrafish embryos.
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Affiliation(s)
- Lin Zhang
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Luxi Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jing Chen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
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11
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Ye M, Chen Y. Zebrafish as an emerging model to study gonad development. Comput Struct Biotechnol J 2020; 18:2373-2380. [PMID: 32994895 PMCID: PMC7498840 DOI: 10.1016/j.csbj.2020.08.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 01/24/2023] Open
Abstract
The zebrafish (Danio rerio) has emerged as a popular model organism in developmental biology and pharmacogenetics due to its attribute of pathway conservation. Coupled with the availability of robust genetic and transgenic tools, transparent embryos and rapid larval development, studies of zebrafish allow detailed cellular analysis of many dynamic processes. In recent decades, the cellular and molecular mechanisms involved in the process of gonad development have been the subject of intense research using zebrafish models. In this mini-review, we give a brief overview of these studies, and highlight the essential genes involved in sex determination and gonad development in zebrafish.
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Affiliation(s)
- Mengling Ye
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Ye Chen
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, China
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12
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Su X, Chen W, Cai Q, Liang P, Chen Y, Cong P, Huang J. Production of non-mosaic genome edited porcine embryos by injection of CRISPR/Cas9 into germinal vesicle oocytes. J Genet Genomics 2019; 46:335-342. [PMID: 31378649 DOI: 10.1016/j.jgg.2019.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/16/2019] [Accepted: 07/04/2019] [Indexed: 12/26/2022]
Abstract
Genetically modified pigs represent a great promise for generating models of human diseases and producing new breeds. Generation of genetically edited pigs using somatic cell nuclear transfer (SCNT) or zygote cytoplasmic microinjection is a tedious process due to the low developmental rate or mosaicism of the founder (F0). Herein, we developed a method termed germinal vesicle oocyte gene editing (GVGE) to produce non-mosaic porcine embryos by editing maternal alleles during the GV to MⅡ transition. Injection of Cas9 mRNA and X-linked Dmd gene-specific gRNA into GV oocytes did not affect their developmental potential. The MⅡ oocytes edited during in vitro maturation (IVM) could develop into blastocysts after parthenogenetic activation (PA) or in vitro fertilization (IVF). Genotyping results indicated that the maternal gene X-linked Dmd could be efficiently edited during oocyte maturation. Up to 81.3% of the edited IVF embryos were non-mosaic Dmd gene mutant embryos. In conclusion, GVGE might be a valuable method for the generation of non-mosaic maternal allele edited F0 embryos in a short simple step.
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Affiliation(s)
- Xiaohu Su
- Key Laboratory of Reproductive Medicine of Guangdong Province, First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qingqing Cai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Puping Liang
- Key Laboratory of Reproductive Medicine of Guangdong Province, First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yaosheng Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Peiqing Cong
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Junjiu Huang
- Key Laboratory of Reproductive Medicine of Guangdong Province, First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; Key Laboratory of Reproductive Medicine of Guangdong Province, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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13
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Zhang B, Wu X, Zhang W, Shen W, Sun Q, Liu K, Zhang Y, Wang Q, Li Y, Meng A, Xie W. Widespread Enhancer Dememorization and Promoter Priming during Parental-to-Zygotic Transition. Mol Cell 2019; 72:673-686.e6. [PMID: 30444999 DOI: 10.1016/j.molcel.2018.10.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/25/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022]
Abstract
The epigenome plays critical roles in controlling gene expression and development. However, how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show that parental-to-zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory, starting with methylating gametic enhancers. Surprisingly, this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4-cell stage, and zygotic enhancers are not activated until around zygotic genome activation (ZGA). By contrast, many promoters remain hypomethylated and, unexpectedly, acquire histone acetylation before ZGA at as early as the 4-cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally, such reprogramming is largely driven by maternal factors, with zygotic products mainly contributing to embryonic enhancer activation. These data reveal widespread enhancer dememorization and promoter priming during parental-to-zygotic transition.
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Affiliation(s)
- Bingjie Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaotong Wu
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenhao Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weimin Shen
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qingrui Sun
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kaili Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuanyuan Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anming Meng
- Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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14
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Zhang X, Jia S, Chen Z, Chong YL, Xie H, Feng D, Wu X, Song DZ, Roy S, Zhao C. Cilia-driven cerebrospinal fluid flow directs expression of urotensin neuropeptides to straighten the vertebrate body axis. Nat Genet 2018; 50:1666-1673. [DOI: 10.1038/s41588-018-0260-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/21/2018] [Indexed: 01/27/2023]
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