Journal ArticleDOI
High-resolution in situ hybridization to whole-mount zebrafish embryos
Christine Thisse,Bernard Thisse +1 more
TLDR
This protocol describes ISH of digoxigenin-labeled antisense RNA probes to whole-mount zebrafish embryos and uses conditions that favor specific hybridization to complementary mRNA sequences in the tissue(s) expressing the corresponding gene.Abstract:
The in situ hybridization (ISH) technique allows the sites of expression of particular genes to be detected. This protocol describes ISH of digoxigenin-labeled antisense RNA probes to whole-mount zebrafish embryos. In our method, PCR-amplified sequence of a gene of interest is used as a template for the synthesis of an antisense RNA probe, which is labeled with digoxigenin-linked nucleotides. Embryos are fixed and permeabilized before being soaked in the digoxigenin-labeled probe. We use conditions that favor specific hybridization to complementary mRNA sequences in the tissue(s) expressing the corresponding gene. After washing away excess probe, hybrids are detected by immunohistochemistry using an alkaline phosphatase-conjugated antibody against digoxigenin and a chromogenic substrate. The whole procedure takes only 3 days and, because ISH conditions are the same for each probe tested, allows high throughput analysis of zebrafish gene expression during embryogenesis.read more
Citations
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Journal ArticleDOI
Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution
Igor Ulitsky,Alena Shkumatava,Alena Shkumatava,Calvin H. Jan,Calvin H. Jan,Hazel Sive,David P. Bartel,David P. Bartel +7 more
TL;DR: This study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that linc RNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation.
Journal ArticleDOI
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
Andrea Pauli,Eivind Valen,Michael F. Lin,Manuel Garber,Nadine L. Vastenhouw,Joshua Z. Levin,Lin Fan,Albin Sandelin,John L. Rinn,Aviv Regev,Alexander F. Schier +10 more
TL;DR: This study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies.
Journal ArticleDOI
Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust
Harry M. T. Choi,Maayan Schwarzkopf,Mark E. Fornace,Aneesh Acharya,Georgios Artavanis,Johannes Stegmaier,Johannes Stegmaier,Johannes Stegmaier,Alexandre Cunha,Niles A. Pierce,Niles A. Pierce +10 more
TL;DR: Third-generation in situ HCR v3.0 exploits automatic background suppression to enable multiplexed quantitative mRNA imaging and flow cytometry with dramatically enhanced performance and ease of use.
Journal ArticleDOI
Toddler: an embryonic signal that promotes cell movement via Apelin receptors.
Andrea Pauli,Megan L Norris,Eivind Valen,Guo-Liang Chew,James A. Gagnon,Steven Zimmerman,Andrew D. Mitchell,Jiao Ma,Julien Dubrulle,Deepak Reyon,Shengdar Q. Tsai,J. Keith Joung,J. Keith Joung,Alan Saghatelian,Alexander F. Schier +14 more
TL;DR: Toddler is an essential, short, conserved embryonic signal that promotes cell migration during zebrafish gastrulation and helps explain previous genetic studies that found a broader requirement for APJ/Apelin receptors than for Apelin, and may be one of several uncharacterized embryonic signals.
Journal ArticleDOI
Lyn is a redox sensor that mediates leukocyte wound attraction in vivo
TL;DR: This work identifies the Src family kinase (SFK) Lyn as a redox sensor that mediates initial neutrophil recruitment to wounds in zebrafish larvae and identifies a single cysteine residue, C466, as being responsible for direct oxidation-mediated activation of Lyn.
References
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Journal ArticleDOI
Structure of the zebrafish snail1 gene and its expression in wild-type, spadetail and no tail mutant embryos
TL;DR: The work presented here suggests that snail1 is involved in morphogenetic events during gastrulation, somitogenesis and development of the cephalic neural crest, and that no tail may act as a positive regulator of snail1.
Journal ArticleDOI
Cloning of the zebrafish krox-20 gene (krx-20) and its expression during hindbrain development
Elli Oxtoby,Trevor Jowett +1 more
TL;DR: It is established that expression of the zebrafish gene (krx-20) first appears at 100% epiboly as a single anterior domain of the prospective neuroepithelium, followed very soon after by a second more posterior domain.
Journal ArticleDOI
The protein product of the zebrafish homologue of the mouse T gene is expressed in nuclei of the germ ring and the notochord of the early embryo.
TL;DR: The cloning and sequencing of the T gene in the zebrafish is reported and the nuclear localization of the protein product is shown, indicating high levels of expression are maintained throughout early development in the notochord.
Journal ArticleDOI
Synexpression groups in eukaryotes.
Christof Niehrs,Nicolas Pollet +1 more
TL;DR: Global expression analysis has shown that the highly coordinate expression of genes functioning in common processes is also a widespread phenomenon in eukaryotes, and sets of co-regulated genes show a striking parallel to the operon, and may be a key determinant facilitating evolutionary change leading to animal diversity.
Journal ArticleDOI
The Zebrafish Information Network: the zebrafish model organism database
Judy Sprague,Leyla Bayraktaroglu,Dave Clements,Tom Conlin,David Fashena,Ken Frazer,Melissa A. Haendel,Douglas G. Howe,Prita Mani,Sridhar Ramachandran,Kevin Schaper,Erik Segerdell,Peiran Song,Brock Sprunger,Sierra Taylor,Ceri E. Van Slyke,Monte Westerfield +16 more
TL;DR: The Zebrafish Information Network (ZFIN) provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community resources such as meeting announcements and contact information.