Genes. Genome editing technologies have been employed in zebrafish for retinal studies. 1.2.4 Zebrafish photoreceptor-specific genes edited to model human retinal pathologies. ; Published by Cold Spring Harbor Laboratory Press. Our data suggest that there are roughly 1,400 embryonic-essential genes in the … Author to whom correspondence should be addressed. The statements, opinions and data contained in the journal, © 1996-2021 MDPI (Basel, Switzerland) unless otherwise stated. USA.gov. HHS See this image and copyright information in PMC. Would you like email updates of new search results? COVID-19 is an emerging, rapidly evolving situation. National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error, Collaborators, The zebrafish (Danio rerio) is a freshwater fish belonging to the minnow family of the order Cypriniformes.Native to South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (and thus often called a "tropical fish" although both tropical and subtropical).. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. The present invention relates to a zebrafish HuC promoter with its 5′-flanking region which directs the neuron-specific expression of structural genes, a transgenic animal that shows the neuron-specific expression of GFP (green fluorescence protein) under the regulation of the HuC promoter, and a method for screening neurogenesis mutants in zebrafish by use of the transgenic animal. © 2020 Sun et al. Although real-time reverse transcription PCR (QPCR), normalized to an internal reference ("housekeeping") gene, is a frequently used method for quantifying gene expression changes in zebrafish, many commonly used housekeeping genes are known to vary with experimental conditions. Scientists for some time have known that specific genes pair up on the same chromosome and appear together or "co-express" in cells and tissues. https://doi.org/10.3390/genes10030230, Wasilewska I, Gupta RK, Palchevska O, Kuźnicki J. Neuron , 2020; DOI: 10.1016/j.neuron.2020.12.003 Cite This Page : Meanwhile, by high-throughput bioinformatics analysis, we found that sequence features play pivotal roles in effective gRNA targeting at specific genes of interest, while the success rate of gene targeting positively correlates with GC content of the target sites. Thus, the expression pattern of zp genes varies among fish species. However, it is not clear whether this is the case for all teleost species. The Zebrafish Gene Collection (ZGC) is an NIH initiative that supports the production of cDNA libraries, clones and sequences to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. doi: 10.1128/mSphere.00340-16. We used this dataset to engineer transgenic driver lines, enabling specific experimental access to … Comparison of Various Nuclear Localization Signal-Fused Cas9 Proteins and. You seem to have javascript disabled. (, Distribution of nucleotide motifs in the 12-nt seed region of all the tested target sites. The zebrafish cloche (clo) mutation affects the earliest known step in differentiation of blood and endothelial cells in vertebrates. NIH Based on quantitative real-time polymerase chain reaction arrays, we estimated the relative mRNA levels in the brain of CaTK genes at two developmental stages. ( A ) Whole-mount…, Phenotypic comparison between klf3 mutants…, Phenotypic comparison between klf3 mutants and morphants. This site needs JavaScript to work properly. Research using the zebrafish model has experienced a rapid growth in recent years. The zebrafish has emerged as a robust alternative xenograft model but, like mice, lack specific cytokines that mimic the microenvironment found in human patients. In both 5 dpf larvae and adult zebrafish, the highest relative expression was observed for, This is an open access article distributed under the, Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. In contrast, carp, goldfish, and zebrafish have only ovary-specific zp genes [4, 19– 22, 26]. Owing to the teleost-specific genome duplication (Postlethwait et al., 1998), each of the CNVs encompass at least one gene that has more than one zebrafish ortholog, with five CNVs with three or fewer genes with duplicates and three CNVs with five or more genes with duplicates. See further details. Front Cell Dev Biol. | https://doi.org/10.3390/genes10030230, Subscribe to receive issue release notifications and newsletters from MDPI journals, You can make submissions to other journals. ECR distribution near the zebrafish notch1b locus in the updated assembly. Methods Mol Biol. In fact, 70% of human genes are found in zebrafish. Using single-cell transcriptomics, we systematically classified RGCs in adult and larval zebrafish, thereby identifying marker genes for >30 mature types and several developmental intermediates. Altogether, this work has generated the first chromosome-wide collection of zebrafish genetic mutants by the CRISPR/Cas9 technology, which will serve as a valuable resource for the community, and our bioinformatics analysis also provides some useful guidance to design gene-specific gRNAs for successful gene editing. ( a ) Categorization of gene expression patterns of 493 EST assemblies. Identification of Zebrafish Calcium Toolkit Genes and Their Expression in the Brain. Furthermore, we tried to identify the underlying mechanisms leading to distinct phenotypes between genetic mutants and antisense morpholino-mediated knockdown embryos. Moreover, we found that nearly one-fourth of all mutants are related to human diseases, and several representative CRISPR/Cas9-generated mutants are described here. Genome editing by the well-established CRISPR/Cas9 technology has greatly facilitated our understanding of many biological processes. Scientists for some time have known that specific genes pair up on the same chromosome and appear together or "co-express" in cells and tissues. Our dedicated information section provides allows you to learn more about MDPI. zebrafish; calcium toolkit; calcium homeostasis; calcium signaling; neurons; brain; bioinformatics; RNA-sequencing; gene ontology; RT-PCR, Help us to further improve by taking part in this short 5 minute survey, H3K27me3 Depletion during Differentiation Promotes Myogenic Transcription in Porcine Satellite Cells, Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices. (. Raterman ST, Metz JR, Wagener FADTG, Von den Hoff JW. Zebrafish Models of Craniofacial Malformations: Interactions of Environmental Factors. Multiple requests from the same IP address are counted as one view. We isolated 525 mutants, representing lesions in ≈390 different genes, and we cloned the majority of these. Zebrafish genetics provides strong evidence that overall levels of Gata4/5/6 are critical during early cardiogenesis rather than unique specific functions for each gene, in a much more rigorous manner than can be obtained using morphant models. The text part introduces the molecular expression patterns that we have selected to illustrate specific neurogenetic processes such as lateral inhibition among neural stem cells (notch), proliferation (PCNA, BrdU), determination (basic helix-loop-helix genes neurogenin/neurod), and differentiation (Hu, GABA) during zebrafish secondary neurogenesis. Please note that many of the page functionalities won't work as expected without javascript enabled. 2020 Nov 16;8:600926. doi: 10.3389/fcell.2020.600926. 2020 Jun 26;295(26):8846-8856. doi: 10.1074/jbc.RA119.012043. GC-content distribution in the 12-nt seed sequence of all the tested target sites…, Distribution of nucleotide motifs in the 12-nt seed region of all the tested…, Characterization of plrg1 mutant generated…, Characterization of plrg1 mutant generated by the CRISPR/Cas9 system. Annotation demonstrated that 10 of the 18 genes in this cluster represented known zebrafish endothelial cell markers, such as tie1, flt4, kdr, fli1, dusp5, or mical-l2. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK). 2017;149:111-132. doi: 10.1016/bs.pmbts.2017.05.003. eCollection 2020. Compared with the lineage-specific genes identified in plants [36, 43, 44], the number of lineage-specific genes within zebrafish is significantly lower, which may reflect the basic difference between animals and plants, considering the likely small number of lineage-specific genes identified in primate and insects [40, 41]. Yu T, Kuang H, Chen J, Lin X, Wu Y, Chen K, Zhang M, Zhang W, Wen Z. J Biol Chem. Affiliations, GC-content distribution in the 12-nt seed sequence of all the tested target sites (including 1086 positive sites and 1191 negative sites). Wasilewska, I.; Gupta, R.K.; Palchevska, O.; Kuźnicki, J. Identification of Zebrafish Calcium Toolkit Genes and Their Expression in the Brain. Get the latest public health information from CDC: https://www.coronavirus.gov, Get the latest research information from NIH: https://www.nih.gov/coronavirus, Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. 2019; 10(3):230. 2017 Jan 18;2(1):e00340-16. ( A ) WISH showing the…, NLM Genes are shown as blue rectangles, and the orientation of arrows indicates the translational initiation sites of genes. Using RNA-sequencing, we then evaluated the expression of these genes in the adult zebrafish brain and found 380 hits that belonged to the CaTK. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. The ECRs located near the notch1b gene are indicated by red lines. CRISPR/Cas9-Based Genome Editing of Transcription Factor Genes in Marchantia polymorpha. Please let us know what you think of our products and services. We completed a large insertional mutagenesis screen in zebrafish to identify genes essential for embryonic and early larval development. Please enable it to take advantage of the complete set of features! 8, 45, 46, 52-54 However, several novel vascular zebrafish genes, for instance eltd1, aqp1, erg, mrc1, and yrk, were additionally identified. The zebrafish orthologue of human phenylalanine hydroxylase ( PAH ) (Hs.325404) was expressed in the developing CNS and pnd at 18 ( b - d ) and 24 ( e and f ) hpf embryos (arrowheads). The cascade of genes induced after amputation or injury, leading to restoration of the lost fin structures, include those responsible for wound healing, blastema formation, tissue outgrowth, … However, only a few studies have investigated calcium homeostasis and signaling in zebrafish neurons, and little is known about the proteins that are involved in these processes. By contrast, slc2a1b, one of two duplicated zebrafish genes that encodes the GLUT1 glucose transporter, as well as other blood-brain barrier markers, such as solute carrier family 7 member 5 (slc7a5; Boado et al., 1999), were significantly enriched in kdrl pos cells using RefSeq, but not Ens95 (Figure 1A,B, Figure 1—source data 2). To examine whether these orthologs of Bach1 are involved in the liver‐specific induction of hmox1a, knockdown analyses were carried out using morpholino oligonucleotides (MOs). Here, we performed a systematic knockout of all the genes (1333) on Chromosome 1 in zebrafish, successfully mutated 1029 genes, and generated 1039 germline-transmissible alleles corresponding to 636 genes. Zebrafish and humans share 70% of the same genes. 8,45,46,52-54 However, several novel vascular zebrafish genes, for instance eltd1, aqp1, erg, mrc1, and yrk, were additionally identified. 2019. Annotation demonstrated that 10 of the 18 genes in this cluster represented known zebrafish endothelial cell markers, such as tie1, flt4, kdr, fli1, dusp5, or mical-l2. Using RNA-sequencing, we then evaluated the expression of these genes in the adult zebrafish brain and found 380 hits that belonged to the CaTK. However, it quickly became a priority to be able to disrupt the function of specific genes in a targeted way. Altogether, this work has generated the first chromosome-wide collection of zebrafish genetic mutants by the CRISPR/Cas9 technology, which will serve as a valuable resource for the community, and our bioinformatics analysis also provides some useful guidance to design gene-specific gRNAs for successful gene editing. Xenograft models are invaluable tools in establishing the current paradigms of hematopoiesis and leukemogenesis. mSphere. We use cookies on our website to ensure you get the best experience. The zebrafish was originally chosen as a model with forward genetics in mind and has been used successfully in countless genetic screens. | Here we describe 315 mutants and the corresponding genes. All resources generated by the ZGC are publicly accessible to the biomedical research community. However, a complete whole-genome knockout for any species or model organism has rarely been achieved. Methods Enzymol. The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK). Zebrafish eggs are fertilized and develop outside of the mother’s body making visualization with high resolution imaging easier for researchers. 2018 Mar 2;8(3):823-831. doi: 10.1534/g3.117.300359. | A molecular catalog of neuronal cell types in the zebrafish retina helps to understand how visual stimuli are transformed into behavior. “We can see exactly what’s happening while it’s happening in zebrafish providing us with insight for human embryonic development,” says Zinani. CRISPR/Cas9-Enabled Multiplex Genome Editing and Its Application. Recently, it has been reported that medaka and fugu have both liver-specific zp genes (choriogenins) and oocyte-specific zp genes . Clipboard, Search History, and several other advanced features are temporarily unavailable. The zebrafish has become an ideal model organism for the study of vertebrate embryogenesis. Using RNA-Seq expression profiles, the 31,901 Ensembl release 92 zebrafish genes were classified (see File S1) at 20 SS into categories of ‘S’kin genes vs. ‘N’onskin genes, and at each of 52 and 72 hpf into categories of ‘P’eriderm-preferred genes, ‘B’asal-preferred genes, ‘G’eneral skin genes, and ‘N’onskin genes. Validation of differentially expressed known protein coding genes in cardiac chambers using qRT-PCR and whole mount in situhybridization. In Jagadeeswaran’s research, recently published in Scientific Reports , he used zebrafish to develop a “piggyback” knockdown method that can knockdown six genes simultaneously. G3 (Bethesda). Here, we describe a protocol for identifying two types of transcription-activating CREs-core promoters and enhancers-of zebrafish photoreceptor type-specific genes. Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior. those of the individual authors and contributors and not of the publisher and the editor(s). MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. In the zebrafish genome, there are two Bach1 homologue genes, bach1a and bach1b, which are located on chromosomes 15 and 10, respectively. Moreover, zebrafish have two eyes, a mouth, brain, spinal cord, intestine, pancreas, liver, bile ducts, kidney, esophagus, heart, ear, nose, muscle, blood, bone, cartilage, and teeth. Tripartite-motif family protein 35-28 regulates microglia development by preventing necrotic death of microglial precursors in zebrafish. Find support for a specific problem on the support section of our website. "Identification of Zebrafish Calcium Toolkit Genes and Their Expression in the Brain" Genes 10, no. 2014;546:377-413. doi: 10.1016/B978-0-12-801185-0.00018-0. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Epub 2020 May 12. Received: 28 February 2019 / Accepted: 13 March 2019 / Published: 18 March 2019, Zebrafish are well-suited for in vivo calcium imaging because of the transparency of their larvae and the ability to express calcium probes in various cell subtypes. The zebrafish caudal fin constitutes an important model for studying the molecular basis of tissue regeneration. This model organism has been used extensively to study brain development, neuronal function, and network activity. In humans, at least 10% of genes … The statements, opinions and data contained in the journals are solely (A) Representative examples of zebrafish genes exhibiting tissue-specific expression by WISH. Genes 2019, 10, 230. We established clo/gata1-GFP transgenic line with erythroid-specific green fluorescent protein (GFP) expression, which allowed differentiation of clo and wild-type siblings at the midsomitogenesis stages before morphologically visible phenotypes appeared. The horizontal line at the middle indicates the studied range of the DNA sequence. eCollection 2017 Jan-Feb. Prog Mol Biol Transl Sci. The transparency and accessibility of zebrafish embryos allow for a variety of detailed manipulations and phenotypic analyses, while its small size, fecundity, and ease of maintenance have helped to establish it as a powerful genetic International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland, Postgraduate School of Molecular Medicine, Warsaw Medical University, 61 Żwirki i Wigury St., 02-091 Warsaw, Poland. 2018;1830:109-126. doi: 10.1007/978-1-4939-8657-6_7. https://doi.org/10.3390/genes10030230, Wasilewska, Iga; Gupta, Rishikesh K.; Palchevska, Oksana; Kuźnicki, Jacek. Other highly expressed genes in the zebrafish bulbus arteriosus included fibulin 5(fbln5), elastin b(elnb) and regulator of G-protein signalling 5a(rgs5a) [74]. Methodologies previously available to knockdown genes in zebrafish were expensive, time consuming and required researchers to target genes individually. 3: 230. 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