2018 Mar 2;8(3):823-831. doi: 10.1534/g3.117.300359. Genome editing technologies have been employed in zebrafish for retinal studies. Methods Mol Biol. 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. 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]. Genome editing by the well-established CRISPR/Cas9 technology has greatly facilitated our understanding of many biological processes. The horizontal line at the middle indicates the studied range of the DNA sequence. ; Published by Cold Spring Harbor Laboratory Press. ( A ) WISH showing the…, NLM The statements, opinions and data contained in the journals are solely  |  2018;1830:109-126. doi: 10.1007/978-1-4939-8657-6_7. eCollection 2020. Clipboard, Search History, and several other advanced features are temporarily unavailable. (A) Representative examples of zebrafish genes exhibiting tissue-specific expression by WISH. 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). 8,45,46,52-54 However, several novel vascular zebrafish genes, for instance eltd1, aqp1, erg, mrc1, and yrk, were additionally identified. Epub 2020 May 12. Research using the zebrafish model has experienced a rapid growth in recent years. Here we describe 315 mutants and the corresponding genes. 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. 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. 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]. eCollection 2017 Jan-Feb. Prog Mol Biol Transl Sci. 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. 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. We isolated 525 mutants, representing lesions in ≈390 different genes, and we cloned the majority of these. 2019. MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. 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. 2017;149:111-132. doi: 10.1016/bs.pmbts.2017.05.003. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. 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). CRISPR/Cas9-Enabled Multiplex Genome Editing and Its Application. Tripartite-motif family protein 35-28 regulates microglia development by preventing necrotic death of microglial precursors in zebrafish. In humans, at least 10% of genes … COVID-19 is an emerging, rapidly evolving situation. CRISPR/Cas9-Based Genome Editing of Transcription Factor Genes in Marchantia polymorpha. The zebrafish cloche (clo) mutation affects the earliest known step in differentiation of blood and endothelial cells in vertebrates. those of the individual authors and contributors and not of the publisher and the editor(s). 2014;546:377-413. doi: 10.1016/B978-0-12-801185-0.00018-0. 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 Cell type specific genes. However, it is not clear whether this is the case for all teleost species. You seem to have javascript disabled. 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. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. 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. Multiple requests from the same IP address are counted as one view. "Identification of Zebrafish Calcium Toolkit Genes and Their Expression in the Brain" Genes 10, no. doi: 10.1128/mSphere.00340-16. Yu T, Kuang H, Chen J, Lin X, Wu Y, Chen K, Zhang M, Zhang W, Wen Z. J Biol Chem. All resources generated by the ZGC are publicly accessible to the biomedical research community. 2020 Jun 26;295(26):8846-8856. doi: 10.1074/jbc.RA119.012043. The statements, opinions and data contained in the journal, © 1996-2021 MDPI (Basel, Switzerland) unless otherwise stated. In Jagadeeswaran’s research, recently published in Scientific Reports , he used zebrafish to develop a “piggyback” knockdown method that can knockdown six genes simultaneously. 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. National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error, Collaborators, Genes are shown as blue rectangles, and the orientation of arrows indicates the translational initiation sites of genes. 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. 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. 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. See this image and copyright information in PMC. 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. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK). This site needs JavaScript to work properly. 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. Epub 2017 Jun 20. In the zebrafish genome, there are two Bach1 homologue genes, bach1a and bach1b, which are located on chromosomes 15 and 10, respectively. 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/. 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. 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. https://doi.org/10.3390/genes10030230, Subscribe to receive issue release notifications and newsletters from MDPI journals, You can make submissions to other journals. © 2020 Sun et al. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. This model organism has been used extensively to study brain development, neuronal function, and network activity. https://doi.org/10.3390/genes10030230, Wasilewska I, Gupta RK, Palchevska O, Kuźnicki J. 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, … See further details. 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. Find support for a specific problem on the support section of our website. 3: 230. In contrast, carp, goldfish, and zebrafish have only ovary-specific zp genes [4, 19– 22, 26]. 2017 Jan 18;2(1):e00340-16. Thus, the expression pattern of zp genes varies among fish species. 1.2.4 Zebrafish photoreceptor-specific genes edited to model human retinal pathologies. G3 (Bethesda). Identification of Zebrafish Calcium Toolkit Genes and Their Expression in the Brain. While it is quite easy to produce knock-outs, creating knock-in zebrafish remains challenging. Zebrafish and humans share 70% of the same genes. HHS Our data suggest that there are roughly 1,400 embryonic-essential genes in the … Comparison of Various Nuclear Localization Signal-Fused Cas9 Proteins and. Raterman ST, Metz JR, Wagener FADTG, Von den Hoff JW. Recently, it has been reported that medaka and fugu have both liver-specific zp genes (choriogenins) and oocyte-specific zp genes . We completed a large insertional mutagenesis screen in zebrafish to identify genes essential for embryonic and early larval development. Wasilewska, I.; Gupta, R.K.; Palchevska, O.; Kuźnicki, J. “We can see exactly what’s happening while it’s happening in zebrafish providing us with insight for human embryonic development,” says Zinani. The zebrafish caudal fin constitutes an important model for studying the molecular basis of tissue regeneration. 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. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK). 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. Author to whom correspondence should be addressed.  |  Methods Enzymol. Our dedicated information section provides allows you to learn more about MDPI. 2020 Nov 16;8:600926. doi: 10.3389/fcell.2020.600926. Please note that many of the page functionalities won't work as expected without javascript enabled. ( A ) Whole-mount…, Phenotypic comparison between klf3 mutants…, Phenotypic comparison between klf3 mutants and morphants. Affiliations, GC-content distribution in the 12-nt seed sequence of all the tested target sites (including 1086 positive sites and 1191 negative sites). Genes 2019, 10, 230. Front Cell Dev Biol. ( a ) Categorization of gene expression patterns of 493 EST assemblies. We use cookies on our website to ensure you get the best experience. 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. (, Distribution of nucleotide motifs in the 12-nt seed region of all the tested target sites. However, it quickly became a priority to be able to disrupt the function of specific genes in a targeted way. Please enable it to take advantage of the complete set of features! 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).. 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). 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. The zebrafish was originally chosen as a model with forward genetics in mind and has been used successfully in countless genetic screens. 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. While it is not clear whether this is the case for all teleost.... Insertional mutagenesis screen in zebrafish to identify genes essential for embryonic and early larval development ZGC are accessible. 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