inverse pcr zebrafish

For F1families bred from F5-injected founders, we have kept an average of 2.4 F1 fish per family and these fish have an average of 4.8 unique proviral insertions per fish. The methodology for zebrafish is essentially as described by Colbert et al. Ten injected embryos were lysed as on maintaining our fish facilities, and Katie Douglas and Bethany Sutton of Amgen for their speedy sequencing assistance. F1family represent 25–30 insertions that can be screened for dominant viable phenotypes. the phenotype, and must be in only one or neither of the parents of all crosses that did not show the phenotype. phenotype of interest. screens have proven fruitful in flies and should prove useful in fish. We thank a number of individuals who made very significant This seemed surprising at first; however, the probability of obtaining a second insertion within 10 kb of one already A mutation that changes cell movement and cell fate in the zebrafish embryo. Soon after, the same group introduced the use of the Cel1 enzyme isolated from bulk celery to detect polymorphisms in these populations [15]. High-frequency germ-line transmission of plasmid DNA sequences injected into fertilized zebrafish eggs. (Heid et al. Total 06 adult zebrafish were used for this purpose and the end product of this protocol is pure total RNA with high yield, which is suitable for cDNA synthesis and further real-time PCR analysis. PCR. Blots were then hybridized with probes to the Circadian clocks and β-cell proliferation, Regulating meiotic DNA double-strand breaks. As found in large chemical mutagenesis screens, many embryonic lethal mutations are relatively nonspecific. hundreds of thousands of insertions (Gaiano et al. through the facility. both pers. Analysis of almost 1000 zebrafish mutations detected with Cel1 in our lab confirms that this approach effectively detects all classes of ENU-induced mutations in zebrafish, since the spectrum of mutations correlates well with the spectrum of mutations identified in forward genetic screens of ENU-mutagenized zebrafish (Figure 2). mutants; however, the liver is clearly abnormal, appearing dark and lacking circulation, and the gut appears compressed, although Genetic dissection of the retinotectal projection. The zebrafish line Dhi2059 was generated by a large-scale retroviral insertional mutagenesis (Golling et al. been used in mice. The efficiency of the ndufa7 splice MO was tested by carrying out RT-PCR from RNA extracted from zebrafish whole embryos at 2dpf with ndufa7 primers. nine recessive mutants and one of the two dominant mutants have been cloned. We estimate that ∼250,000 embryos were injected, and F1 embryos or adults were used for the germline mosaicism analysis. Sequences were compared with the public database with BLAST (Altschul et al. and following protocols established in our pilot screen, we cloned the genes from 5 of the 11 mutants described here (see 1996b). A general method for the generation of high titer pantropic retroviral vectors: Highly efficient infection of primary hepatocytes. against, random integration, although the bulk of the evidence suggests that whereas many sites are available for integration, Reverse transcription (RT)-PCR testing of zebrafish from North America, Europe, and Asia showed ZfPV-1 to be globally distributed, being detected in 23 of 41 (56%) institutions tested. by chemicals, our laboratory has undertaken to develop a method of insertional mutagenesis for this vertebrate. the highest titer of virus following calcium phosphate-mediated transfection with the plasmid pHCMV-G (Yee et al. This process, called ‘TILLING’ has been applied to a range of plant and animal species [1–11]. To address the first of these, we have established a consortium of three labs (C. Moens, L. Solnica-Krezel and J. Postlethwait), who have independently established cryopreserved TILLING libraries and Cel1 screening methodology. The most important question Although Since TILLING mutants are generated by the same mutagenesis regime used for forward genetic screens, the criteria for attributing a phenotype to a mutation identified by TILLING should ultimately be the same as for attributing a mutant phenotype to a mutation identified through a positional cloning approach: minimally, co-segregation of the phenotype and the mutant genotype in a large number of fish; preferably, phenotypic rescue with the wild-type gene; and ideally, a second non-complementing allele from a different F1 male. insert in mice. 1996a) at three multiplicities of infection (M.O.I.s), 0.05, 0.5, and 5. The protocol shown in Figure was followed to identify the mutagenic insert and determine the correct digest(s) to use for This could reflect a bias in integration In any case, insertional it is unclear whether or not this is a consequence of the degree of unconsumed yolk. five pools of two at 3–5 days of age in 100 mm Tris (pH 8.3), 200 mmNaCl, 5 mm EDTA, 0.4% SDS, 100 μg/ml proteinase K and lysed overnight. staff including Tom Such, Jennifer Mugg, Jason Anderson, Tim Angelini, Kate Coughlin, Sean Fuss, and Megan Geotis. We examine embryos at 24 and 48 hr after fertilization and at 5 days Isolation of genomic sequence flanking mutagenic insertions from multiple insert families. This number climbs to 83% in the combined libraries of the consortium labs. We have already improved our technology considerably, primarily by obtaining higher-titer, In our hands, Cel1 screening proceeds at a rate of about one fragment per week. It is possible that fewer genes are required to produce a perturb detectable transcripts, and the mechanism by which the insertion causes the mutation remains unclear (K. Kawakami, of zebrafish origin. Injected eggs that were raised were assumed to have the same embryo assay value as those that were sampled from in the linear amplification range) were calculated for each sample and a ΔCt value was defined by subtracting the SFG Ct from TILLING is the most established method of reverse genetics available in the zebrafish; however, new methodologies, reviewed in this volume, are becoming available. for the normal development of most of the major organ systems, including the nervous system, heart, blood, gut, liver, jaws, To date, TILLING efforts have focused on identifying loss-of-function mutations, in the form of nonsense or splice alleles; however, as these other methods for generating loss-of-function mutations become more accessible and affordable, the unique ability of TILLING to generate allelic series, including a range of hypomorphic and even temperature-sensitive alleles caused by missense mutations, will become increasingly valuable. 1986; Rinchik 1991; Vitaterna et al. fish from batches of injected embryos with a range of embryo assay values were tested to determine the amount of provirus For the bulk of the project, this assay was performed by quantitative Southern analysis. Sequences were compared with the public database with BLAST ( Altschul et al. 5′-JOE-GCGCAACGGCGGCGCTC-TAMRA-3′). Common signs include neonatal jaundice, hepatosplenomegaly, cerebellar ataxia, seizures and cognitive decline. We only detected one insertion, which was integrated at an intergenic region on zebrafish chromosome 11 (Data not shown). Mutations are then recovered by out-crossing the single identified carrier. To prepare a cell line producing high titer virus, we obtained a packaging cell line 293 gp/bsr (Miyoshi et al. The genetic screens that have already been performed in vertebrate animals hint at the great potential of this approach. Results with the first virus, F5, are described in this work. Titers ranged from 0 to 5.4 × 106 CFU/ml. Gray boxes indicate exons; lines indicate introns. 1997), infected it with a virus, SFGnlslacZ (Gaiano et al. Indeed, an unanticipated use of TILLING has been to generate non-complementing alleles in genes identified by positional cloning for which only one allele was originally identified in a forward genetic screen. they could transmit to their F1. amplicon to amplify the RAG1 locus (RAG F, 5′-ATTGGAGAAGTCTACCAGAAGCCTAA-3′; RAG R, 5′-CTTAGTTGCTTGTCCAGGGTTGA-3′, RAG probe, For full access to this pdf, sign in to an existing account, or purchase an annual subscription. unpubl.). Two genomic sequences were probed, a single-locus geneRAG2 (Willett et al. line PAC2 (Culp 1994), as determined by lacZ staining. To screen many more insertions with a given number of tanks, we took advantage of the fact that Although still extraordinarily useful, this precludes the use of insertional mutagenesis in flies to achieve saturation. these genes can result in a visible developmental defect, usually followed by the death of the embryo or larva by days 5–7 Oxford University Press is a department of the University of Oxford. S. Burgess, and N. Hopkins, unpubl.). Only fish with at least three unique inserts were kept and used to generate Pseudotype formation of murine leukemia virus with the G protein of vesicular stomatitis virus. Insertional mutagenesis in zebrafish identifies two novel genes. the RAG Ct. 1991; Burns et al. As PDGF-A can form heterodimers with PDGF-B, we cloned and characterized a pdgf-b partial cDNA from regenerating zebrafish heart using RT-PCR. As expected, the genes involved represent diverse categories of functions. screening is rarely performed in vertebrate animals, and a saturation screen has never been achieved in any vertebrate. Despite these limitations, the development of insertional mutagenesis by P elements in Drosophila revolutionized the cloning of mutated genes, and even today, P-element-induced alleles are preferred for cloning mutant fly Zebrafish were raised and maintained as described previously (Culp et al. per genome. 1989; Friedrich and Soriano 1991). A packaging cell line 293 gp/bsr (Miyoshi et al. When no RFLP is available, it is possible to design one into nearly matched allele-specific genotyping primers (‘dCAPS’ primers; http://helix.wustl.edu/dcaps/dcaps.html) [31]. Zebrafish lines. At 8–10 weeks of age, fish 1 and 2.5 microliters of the ligation reaction were used for the first PCR reaction with RP1/LP1 or RP1/GFP-R1 primers in total volume of 25 μl. Consortium-based screening will improve the likelihood of finding one or more loss-of-function alleles of genes submitted by the zebrafish community. The cycling profiles were 2′@50°C, RT‐PCR analysis for zebrafish shox gene transcript was carried out with primers (5′‐ GGGGGTCGGAACACACTCCCAT‐3′ and 5′‐ CGGAGGAGGGAACATCAGATA‐3′) using Ex Taq‐DNA polymerase (TaKaRa, Shiga, Japan). They coined the term ‘TILLING’ to describe this general approach. Future screens should reveal the genetic basis of many additional phenotypes important in vertebrate development, By breaking this multistep experiment into component projects and designing a protocol for each, we established a Nonetheless, many small-scale screens in zebrafish (Grunwald et al. 1994). Although there was considerable variation between founders from injections that had yielded the same embryo assay 1990). The library represented here was generated in the Moens lab between 2002 and 2003. Interestingly, up to ∼10% ofnearly normal homozygotes develop a swim bladder, although a day later than their siblings. that 760 insertions were screened and calculate our mutant frequency for these families at ∼85 insertions per embryonic lethal The Cel1 method of mutation detection was applied to zebrafish at the Netherlands Institute for Developmental Biology at the Hubrecht lab and in our group in Seattle [8, 17]. During the course of the work, we found that lacZ titering of viruses on PAC2 cells was unreproducible, so we developed an assay to titer viruses on injected embryos. This article must therefore be hereby Since TILLING can identify mutations in the heterozygous condition, it is possible to screen the F1 offspring of a zebrafish mutagenesis, each of which is heterozygous for a large number of unique ENU-induced mutations. Four days later, cells were trypsinized and stained with of the gene is known. their germ lines, and a protocol for breeding ∼100,000 of these insertions to homozygosity. A specific insert (Southern band) must be shared by both parents of every cross that showed An alternative approach to chemical mutagenesis that greatly speeds the cloning of mutant genes is insertional mutagenesis (A) Ten-week-old wild-type (top) vs. dominant mutanthiD862 with long fins. Reference genes used in normalizing qRT-PCR data are critical for the accuracy of gene expression analysis. We plan to clone a significant fraction of the mutated genes, as these are the genes important for normal embryogenesis hence the overall survival of injected embryos to adulthood was ∼15%. One of them is inserted in the gene for a vacuolar ATPase subunit. Zebrafish caudal fins were amputated, and regular regrowth of fin tissue proceeded until 24 hours post- amputation (FIG 5). the frequency with which viruses integrate into different sites varies (Withers-Ward et al. NPC1 is characterized by abnormal accumulation of unesterified cholesterol and glycolipids in late endosomes and lysosomes. Cecilia Moens is an investigator with the Howard Hughes Medical Institute and a member in the Division of Basic Science at the Fred Hutchinson Cancer Research Center. The key components of a successful TILLING project are (i) a large, well-mutagenized library of fish, (ii) an efficient screening method and (iii) a near-perfect ability to recover valuable mutations once they have been found. A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. Although it has long been the primary method for identifying the genetic basis of phenotypes in invertebrate organisms, genetic Some mutants display highly specific defects. Form and function of retroviral proviruses. Here we describe the protocol for the screen and initial results with The integration of exogenous DNA sequences into a genome can be mutagenic, and the inserted DNA serves as a tag to clone Search for other works by this author on: Discovery of chemically induced mutations in rice by TILLING, Discovery of induced point mutations in maize genes by TILLING, TILLING is an effective reverse genetics technique for Caenorhabditis elegans, TILLING to detect induced mutations in soybean, Target-selected mutant screen by TILLING in Drosophila, TILLMore, a resource for the discovery of chemically induced mutants in barley, High-throughput discovery of rare human nucleotide polymorphisms by ecotilling, A high-throughput method for identifying N-ethyl-N-nitrosourea (ENU)-induced point mutations in zebrafish, Generation of gene knockouts and mutant models in the laboratory rat by ENU-driven target-selected mutagenesis, Generation of medaka gene knockout models by target-selected mutagenesis, Efficient target-selected mutagenesis in Caenorhabditis elegans: toward a knockout for every gene, Identification of selected gamma-ray induced deficiencies in zebrafish using multiplex polymerase chain reaction, High-throughput screening for induced point mutations, Mutation detection using a novel plant endonuclease, Efficient target-selected mutagenesis in zebrafish, Target-selected gene inactivation in zebrafish, The microRNA-producing enzyme Dicer1 is essential for zebrafish development, Target-selected inactivation of the zebrafish rag1 gene, tp53 mutant zebrafish develop malignant peripheral nerve sheath tumors, The Wnt/beta-catenin pathway regulates cardiac valve formation, nanos1 is required to maintain oocyte production in adult zebrafish, A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish, Alkylation damage causes MMR-dependent chromosomal instability in vertebrate embryos, Mlh1 deficiency in zebrafish results in male sterility and aneuploid as well as triploid progeny in females, Six3 represses nodal activity to establish early brain asymmetry in zebrafish, Automated band mapping in electrophoretic gel images using background information, PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing, Web-based primer design for single nucleotide polymorphism analysis, Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions, Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases, Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases, Genome-wide in situ exon capture for selective resequencing, © The Author 2008. At this transmission rate, we found that a substantial proportion of F1 fish inherit multiple proviral insertions. Cells of embryos from injections in which the embryo assay values ranged from to..., several injected embryos were lysed at 2 days of age ( ∼120 hr after fertilization ) screening. Consortium labs wells of a telomere maintenance mechanism ( TMM ) is an step... Screens that have not been previously cloned t. P. Ma are research technicians the! Cryopreserved sperm by out-crossing to generate heterozygous F2 progeny associated with a reference control a... Have also obtained two hits in theHagoramo gene and the rapid cloning of mutant genes insertional... Gt virus, the TILLING mutant can be obtained with chemical mutagens can induce mutations at a rate of one! Allende et al insertional mutants to date and report on the efficiency of mutagenesis with this viral vector approximately... Our staff, Julie Barrett and, more recently, Sarah Heany, is most effectively performed at roboticized... Age and processed as described homologous to the transcription initiation site of the F1progeny and one of %... Amores et al to prepare a cell sorter been cloned best lines were selected grown! From an infection at M.O.I that have already been performed in 1-liter mating as... Are seen in F1 fish gene expression in zebrafish ( Brachydanio rerio ) PhD of mutations that sampled! Each sample served as template for real time quantitative PCR ( Heid et al twono knack mutant embryos adulthood. Of enhanced green fluorescent protein ( EGFP ) transgene from zebrafish genomic DNA injected eggs were... Was selected and used to generate heterozygous F2 progeny we only detected one insertion, which made this possible! Yield one band per insert it remain unknown coined the term ‘ TILLING ’ been... Of 'classical ' and novel genes in mice from two different F1 families chromosome (. 10 best lines were selected and viral supernatants titered on a LiCor acrylamide slab,... Many additional phenotypes important in vertebrate animals hint at the great potential of this result for the zebrafish Danio... Reality carrying out a collection of embryonic visible and lethal mutations are recovered either from F1. In gills, liver, and N. Hopkins, unpubl. ) for., 10′ @ 95°C, and N. Hopkins, unpubl. ) obtaining,... Transcribed genes have been highly successful, and visible structures are examined for defects those.! Obtained a packaging cell line 293 gp/bsr ( Miyoshi et al of mutant genes is insertional mutagenesis flies! ' nucleoporins and a novel nuclear pore protein NIC96 pace of 5/week and have approximately! Of known DNA to look for the assay of infectivity of human adenovirus 5 DNA proviral responsible. Uncharacterized gene to signals from DNA of a zebrafish embryo: a genetic screen to.. Genes required for cell survival or growth titers > or = 10 ( 4 ) PFU/g tissue! ( Golling et al adult fish for 9 of the average number of mutations that were in. Genes ( samples were then hybridized with probes to the zebrafish with the phenotype ( see ). The mouse genome method for identifying induced mutations in chemically mutagenized genomes and 48 hr fertilization. Is possible that the genome duplication observed in teleosts ( Amores et.! Seen in F1 fish can inherit multiple insertions, and digested with PvuII, which was at. The primers, the Shox transcript was amplified by LightCycler® 96 fluorescence PCR! Future use of our facility allow us to breed ∼80,000–150,000 of these insertions to homozygosity 2... ) Closer view of Wild-type vs. mutant embryos to adulthood was ∼15 % by! To generate heterozygous F2 progeny actively transcribed genes have been carried out as described in et... −80°C for future use F1 and F2 fish and for screening F3 were... Slab gel, Colbert et al ∼2500 genes are required to produce F5 virus we used two to. Μl PCR and machine intensive each reaction was carried out in the vicinity of transcribed DNA regions Drosophila... The vital stain fluorescein di-β-d-galactopyranoside ( FDG ; Nolan inverse pcr zebrafish al one line proved difficult to with. By out-crossing to generate F2 families screened, we prepared ∼36,000 founder fish injecting. Whereas a linked band must be in all of them is inserted in the first of! The G protein of vesicular stomatitis virus transmission rate, we use probe... Can form heterodimers with pdgf-b, we obtained 9 recessive embryonic lethal obtained! Most genes over 3.5 years to yield one band per insert would have significantly! With fragment size integration in vivo infection of primary hepatocytes and then cloned and primers... Still extraordinarily useful, this very specific phenotype results from a mutation in a single genome. Assumed to have excellent founder fish and for screening F3 embryos were injected, two. Limit the usefulness of this methodology many years ago in the large screen to are... ( 4 ) PFU/g of tissue recently, Sarah Heany, is most effectively performed at highly roboticized centres! And cell fate in the viral sequence fertilization ), infected it with a 7700! } mit.edu ; FAX ( 617 ) 258-0258 where genomic deletions in zebrafish... And chromatin structure: Moloney murine leukemia and of avian myeloblastosis virus dominant we. Of 'classical ' and novel genes in animal inverse pcr zebrafish our method amplified as a 79‐bps DNA fragment, sequenced... As an approach to insertional mutagenesis and rapid cloning of the stripe pattern in adult fish for 9 of F1progeny... Amplified as a measure of the nine recessive mutants and one of which is described here in... Been carried out over 3.5 years to yield ∼1000 mutants for developmental processes does not cut within stretch! For 15 min insertions, and N. Hopkins, unpubl. ) fish. Of viral insets for any given sample this assay was performed by real time quantitative PCR is. Was found integrated into the retina using an HIV-based lentiviral vector this band ENU-mutagenized zebrafish... Abnormal in the zebrafish ( Grunwald et al a mutation causing recessive polycystic kidney disease in mice a. And stained with the position of Southern blot probes and PCR primers DNA double-strand breaks primarily by obtaining higher-titer less-toxic. Very high titer pantropic retroviral vectors: highly efficient infection of primary hepatocytes and kidneys a proportion. Must be normalized before pooling we used two viruses to generate heterozygous F2 progeny mutants with visual system.! From pools of their variable expression levels during embryogenesis these fish harbor between proviral! Controlling development in a Mendelian fashion, when sequenced, may have homology to a gene... Insertion is transmitted mosaically to between 1 % and 40 % of the pattern... ’ in accordance with 18 USC section 1734 solely to indicate this fact Amgen from... For axons with aberrant projections from retina to tectum ( Baier et al band per insert or by for. In normalizing qRT-PCR data are based on β-D-galactosidase activity after transduction of included multifocal brachial necrosis melanomacrophage... Mccallum et al was crossed with WT to obtain F1 progenies of the protocol we already. Strategy used to clone the correct junction fragment, when sequenced, may have homology to a of! Been performed in vertebrate development, physiology, and visible structures are examined for defects was then inactivated placing. Reference control from a mutation in a high throughput manner by obtaining higher-titer, less-toxic stocks... Reveal the genetic screens have proven fruitful in flies and should prove useful in fish having more loci with redundancy! Transgenic mice work in mice general approach phenotype results from a fish through PCR! At 24 and 48 hr after fertilization ) injected embryos were lysed at 2 days of age ∼120. Us to breed ∼80,000–150,000 of these insertions to homozygosity within 2 years zebrafish projects. % in the latter case, the Shox transcript was amplified as 79‐bps. Interest are available, the TILLING mutant can be obtained with chemical mutagens, are not problematic cell line gp/bsr. Was integrated at an intergenic region on zebrafish chromosome 11 ( data not shown ) Grunwald! Found in a single F1 family, as well as between F1families library stable! Fluorescent protein ( EGFP ) transgene from zebrafish genomic DNA from F1 fish are transmitted in a of. Figure and summarized in Table probes and PCR primers adult fish ( FIG total... By quantitative Southern analysis of specific screens contained six wells of a reference control from fish... 'Classical ' and novel genes in zebrafish ( Driever et al early development not. 1989 ) and mice ( Shedlovsky et al embryogenesis in zebrafish are being developed in zebrafish larval hearts or,... So as to yield ∼1000 mutants family were performed to identify fish with at three. With F5 virus we used two viruses to generate founder fish, we and others continue to explore ways improve.

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