Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish

Advances in imaging and cell-labeling techniques have greatly enhanced our understanding of developmental and neurobiological processes. Among vertebrates, zebrafish is uniquely suited for in vivo imaging owing to its small size and optical translucency. However, distinguishing and following cells over extended time periods remains difficult. Previous studies have demonstrated that Cre recombinase-mediated recombination can lead to combinatorial expression of spectrally distinct fluorescent proteins (RFP, YFP and CFP) in neighboring cells, creating a ‘Brainbow’ of colors. The random combination of fluorescent proteins provides a way to distinguish adjacent cells, visualize cellular interactions and perform lineage analyses. Here, we describe Zebrabow (Zebrafish Brainbow) tools for in vivo multicolor imaging in zebrafish. First, we show that the broadly expressed ubi:Zebrabow line provides diverse color profiles that can be optimized by modulating Cre activity. Second, we find that colors are inherited equally among daughter cells and remain stable throughout embryonic and larval stages. Third, we show that UAS:Zebrabow lines can be used in combination with Gal4 to generate broad or tissue-specific expression patterns and facilitate tracing of axonal processes. Fourth, we demonstrate that Zebrabow can be used for long-term lineage analysis. Using the cornea as a model system, we provide evidence that embryonic corneal epithelial clones are replaced by large, wedge-shaped clones formed by centripetal expansion of cells from the peripheral cornea. The Zebrabow tool set presented here provides a resource for next-generation color-based anatomical and lineage analyses in zebrafish.

[1]  W. Guido,et al.  ClearT: a detergent- and solvent-free clearing method for neuronal and non-neuronal tissue , 2013, Development.

[2]  M. Brand,et al.  Comparative aspects of adult neural stem cell activity in vertebrates , 2013, Development Genes and Evolution.

[3]  Jeff W. Lichtman,et al.  Developmental Bias in Cleavage-Stage Mouse Blastomeres , 2013, Current Biology.

[4]  Jan Huisken,et al.  Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope , 2012, Development.

[5]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[6]  A. Schier,et al.  Bivalent histone modifications in early embryogenesis. , 2012, Current opinion in cell biology.

[7]  K. Poss,et al.  Clonally dominant cardiomyocytes direct heart morphogenesis , 2012, Nature.

[8]  Chi-Bin Chien,et al.  Crowding induces live cell extrusion to maintain homeostatic cell numbers in epithelia , 2012, Nature.

[9]  Michael Brand,et al.  Adult neurogenesis and brain regeneration in zebrafish , 2012, Developmental neurobiology.

[10]  A. Schier,et al.  Robo2 determines subtype-specific axonal projections of trigeminal sensory neurons , 2012, Development.

[11]  P. Witten,et al.  The mechanism of cartilage subdivision in the reorganization of the zebrafish pectoral fin endoskeleton. , 2011, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[12]  Atsushi Miyawaki,et al.  Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain , 2011, Nature Neuroscience.

[13]  M. Buckingham,et al.  Tracing cells for tracking cell lineage and clonal behavior. , 2011, Developmental cell.

[14]  J. Livet,et al.  Generating and imaging multicolor Brainbow mice. , 2011, Cold Spring Harbor protocols.

[15]  J. Rosenblatt,et al.  Live imaging of cell extrusion from the epidermis of developing zebrafish. , 2011, Journal of visualized experiments : JoVE.

[16]  Stephen L. Johnson,et al.  Fate restriction in the growing and regenerating zebrafish fin. , 2011, Developmental cell.

[17]  M. Goll,et al.  Transgenerational analysis of transcriptional silencing in zebrafish. , 2011, Developmental biology.

[18]  L. Zon,et al.  Ubiquitous transgene expression and Cre-based recombination driven by the ubiquitin promoter in zebrafish , 2011, Development.

[19]  Ethan K. Scott,et al.  Filtering of Visual Information in the Tectum by an Identified Neural Circuit , 2010, Science.

[20]  Hans Clevers,et al.  Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells , 2010, Cell.

[21]  N. Di Girolamo,et al.  Corneal stem cells and their origins: significance in developmental biology. , 2010, Stem cells and development.

[22]  David R. Liu,et al.  Potent Delivery of Functional Proteins into Mammalian Cells in Vitro and in Vivo Using a Supercharged Protein , 2010, ACS chemical biology.

[23]  H. Okamoto,et al.  Characterization of neural stem cells and their progeny in the adult zebrafish optic tectum. , 2010, Developmental biology.

[24]  Ryan M. Anderson,et al.  Primary contribution to zebrafish heart regeneration by gata4+ cardiomyocytes , 2010, Nature.

[25]  S. Tseng,et al.  Location of corneal epithelial stem cells , 2010, Nature.

[26]  D. Wakefield,et al.  Stem Cell Activity in the Developing Human Cornea , 2009, Stem cells.

[27]  Ethan K. Scott,et al.  The cellular architecture of the larval zebrafish tectum , as revealed by Gal 4 enhancer trap lines , 2022 .

[28]  M. Wullimann,et al.  Secondary neurogenesis and telencephalic organization in zebrafish and mice: a brief review. , 2009, Integrative zoology.

[29]  J. Kaslin,et al.  Temporally-Controlled Site-Specific Recombination in Zebrafish , 2009, PloS one.

[30]  Christopher Dunsby,et al.  Optically sectioned imaging by oblique plane microscopy , 2008, European Conference on Biomedical Optics.

[31]  Philipp J. Keller,et al.  Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy , 2008, Science.

[32]  Y. Barrandon,et al.  Oligopotent stem cells are distributed throughout the mammalian ocular surface , 2008, Nature.

[33]  Michael Z. Lin,et al.  Improving the photostability of bright monomeric orange and red fluorescent proteins , 2008, Nature Methods.

[34]  J. Livet,et al.  A technicolour approach to the connectome , 2008, Nature Reviews Neuroscience.

[35]  N. Trede,et al.  Method for isolation of PCR-ready genomic DNA from zebrafish tissues. , 2007, BioTechniques.

[36]  R. W. Draft,et al.  Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system , 2007, Nature.

[37]  Julio D Amigo,et al.  Gateway compatible vectors for analysis of gene function in the zebrafish , 2007, Developmental dynamics : an official publication of the American Association of Anatomists.

[38]  Melissa Hardy,et al.  The Tol2kit: A multisite gateway‐based construction kit for Tol2 transposon transgenesis constructs , 2007, Developmental dynamics : an official publication of the American Association of Anatomists.

[39]  D. Stainier,et al.  Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM). , 2007, Optics letters.

[40]  Herwig Baier,et al.  Targeting neural circuitry in zebrafish using GAL4 enhancer trapping , 2007, Nature Methods.

[41]  R. Yee,et al.  The zebrafish cornea: structure and development. , 2006, Investigative ophthalmology & visual science.

[42]  K. Hatta,et al.  Cell tracking using a photoconvertible fluorescent protein , 2006, Nature Protocols.

[43]  R. Lansford,et al.  Four-color, 4-D time-lapse confocal imaging of chick embryos. , 2006, BioTechniques.

[44]  Ali Shilatifard,et al.  Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. , 2006, Annual review of biochemistry.

[45]  R. Köster,et al.  Multicolor in vivo time‐lapse imaging at cellular resolution by stereomicroscopy , 2006, Developmental dynamics : an official publication of the American Association of Anatomists.

[46]  Nathan C Shaner,et al.  A guide to choosing fluorescent proteins , 2005, Nature Methods.

[47]  F. Gage,et al.  Proliferation, migration, neuronal differentiation, and long‐term survival of new cells in the adult zebrafish brain , 2005, The Journal of comparative neurology.

[48]  B. Link,et al.  Morphogenesis of the anterior segment in the zebrafish eye , 2005, BMC Developmental Biology.

[49]  Alexander F. Schier,et al.  Repulsive Interactions Shape the Morphologies and Functional Arrangement of Zebrafish Peripheral Sensory Arbors , 2005, Current Biology.

[50]  S. Tseng,et al.  Corneal epithelial stem cells at the limbus: looking at some old problems from a new angle. , 2004, Experimental eye research.

[51]  T. Nagasaki,et al.  Centripetal movement of corneal epithelial cells in the normal adult mouse. , 2003, Investigative ophthalmology & visual science.

[52]  M. Wullimann,et al.  Anatomy of neurogenesis in the early zebrafish brain. , 2003, Brain research. Developmental brain research.

[53]  J. Joly,et al.  I-SceI meganuclease mediates highly efficient transgenesis in fish , 2002, Mechanisms of Development.

[54]  B. Dhillon,et al.  Clonal analysis of patterns of growth, stem cell activity, and cell movement during the development and maintenance of the murine corneal epithelium , 2002, Developmental dynamics : an official publication of the American Association of Anatomists.

[55]  S. Fraser,et al.  Tracing transgene expression in living zebrafish embryos. , 2001, Developmental biology.

[56]  C. Kimmel,et al.  Stages of embryonic development of the zebrafish , 1995, Developmental dynamics : an official publication of the American Association of Anatomists.

[57]  J. Zieske,et al.  Localization of corneal epithelial stem cells in the developing rat. , 1992, Investigative ophthalmology & visual science.

[58]  C. Cepko,et al.  Widespread dispersion of neuronal clones across functional regions of the cerebral cortex. , 1992, Science.

[59]  C. Kimmel,et al.  Cell lineage of zebrafish blastomeres. III. Clonal analyses of the blastula and gastrula stages. , 1985, Developmental biology.

[60]  C. Kimmel,et al.  Cell lineage of zebrafish blastomeres. I. Cleavage pattern and cytoplasmic bridges between cells. , 1985, Developmental biology.

[61]  F. Watt,et al.  Lineage Tracing , 2012, Cell.

[62]  J. Livet,et al.  Multicolor Brainbow imaging in zebrafish. , 2011, Cold Spring Harbor protocols.

[63]  S. Remy,et al.  Analysis by quantitative PCR of zygosity in genetically modified organisms. , 2010, Methods in molecular biology.

[64]  K. Kawakami,et al.  Transient and stable transgenesis using tol2 transposon vectors. , 2009, Methods in molecular biology.

[65]  S. Megason,et al.  In toto imaging of embryogenesis with confocal time-lapse microscopy. , 2009, Methods in molecular biology.

[66]  K. Kawakami Transgenesis and gene trap methods in zebrafish by using the Tol2 transposable element. , 2004, Methods in cell biology.

[67]  M. Westerfield The zebrafish book : a guide for the laboratory use of zebrafish (Danio rerio) , 1995 .

[68]  J. Sanes,et al.  Neurons and glia arise from a common progenitor in chicken optic tectum: demonstration with two retroviruses and cell type-specific antibodies. , 1990, Proceedings of the National Academy of Sciences of the United States of America.