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Li Z, Jiang L, Ma Y, Wei Z, Hong H, Liu Z, Lei J, Liu Y, Guan R, Guo Y, Jin L, Zhang L, Li Y, Ren Y, He W, Liu M, Htwe NMPS, Liu L, Guo B, Song J, Tan B, Liu G, Li M, Zhang X, Liu B, Shi X, Han S, Hua S, Zhou F, Yu L, Li Y, Wang S, Wang J, Chang R, Qiu L. Development and utilization of a new chemically-induced soybean library with a high mutation density . JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:60-74. [PMID: 27774740 PMCID: PMC5248594 DOI: 10.1111/jipb.12505] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/20/2016] [Indexed: 05/20/2023]
Abstract
Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate (EMS)-induced soybean (Glycine max) population, consisting of 21,600 independent M2 lines, was developed. Over 1,000 M4 (5) families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, gyl, that displayed significantly decreased chlorophyll (Chl) content and abnormal chloroplast development. Sequence analysis showed that gyl is allelic to MinnGold, where a different single nucleotide polymorphism variation in the Mg-chelatase subunit gene (ChlI1a) results in golden yellow leaves. A cleaved amplified polymorphic sequence marker was developed and may be applied to marker-assisted selection for the golden yellow phenotype in soybean breeding. We show that the newly developed soybean EMS mutant population has potential for functional genomics research and genetic improvement in soybean.
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Doitsidou M, Jarriault S, Poole RJ. Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification in Caenorhabditis elegans. Genetics 2016; 204:451-474. [PMID: 27729495 PMCID: PMC5068839 DOI: 10.1534/genetics.115.186197] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023] Open
Abstract
The use of next-generation sequencing (NGS) has revolutionized the way phenotypic traits are assigned to genes. In this review, we describe NGS-based methods for mapping a mutation and identifying its molecular identity, with an emphasis on applications in Caenorhabditis elegans In addition to an overview of the general principles and concepts, we discuss the main methods, provide practical and conceptual pointers, and guide the reader in the types of bioinformatics analyses that are required. Owing to the speed and the plummeting costs of NGS-based methods, mapping and cloning a mutation of interest has become straightforward, quick, and relatively easy. Removing this bottleneck previously associated with forward genetic screens has significantly advanced the use of genetics to probe fundamental biological processes in an unbiased manner.
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Affiliation(s)
- Maria Doitsidou
- Centre for Integrative Physiology, University of Edinburgh, EH8 9XD, Scotland
| | - Sophie Jarriault
- L'Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR 7104/Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, 67404, France
| | - Richard J Poole
- Department of Cell and Developmental Biology, University College London, WC1E 6BT, United Kingdom
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Pulido-Tamayo S, Duitama J, Marchal K. EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis. Nucleic Acids Res 2016; 44:W142-6. [PMID: 27105844 PMCID: PMC4987886 DOI: 10.1093/nar/gkw298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic regions associated with a trait of interest. However, distinguishing true from spuriously linked genomic regions and accurately delineating the genomic positions of these truly linked regions requires the use of complex statistical models currently implemented in software tools that are generally difficult to operate for non-expert users. To facilitate the exploration and analysis of data generated by bulked segregant analysis, we present EXPLoRA-web, a web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium to increase the power and accuracy of quantitative trait loci identification in BSA analysis. EXPLoRA-web provides a user friendly interface that enables easy data upload and parallel processing of different parameter configurations. Results are provided graphically and as BED file and/or text file and the input is expected in widely used formats, enabling straightforward BSA data analysis. The web server is available at http://bioinformatics.intec.ugent.be/explora-web/.
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Affiliation(s)
- Sergio Pulido-Tamayo
- Department of Information Technology, iGent Toren, Technologiepark 15, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, UGent, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Gent, Belgium Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jorge Duitama
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), 763537 Cali, Colombia
| | - Kathleen Marchal
- Department of Information Technology, iGent Toren, Technologiepark 15, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, UGent, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Gent, Belgium Department of Genetics, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
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Baiting for Cancer: Using the Zebrafish as a Model in Liver and Pancreatic Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:391-410. [DOI: 10.1007/978-3-319-30654-4_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Gallego-Llamas J, Timms AE, Geister KA, Lindsay A, Beier DR. Variant mapping and mutation discovery in inbred mice using next-generation sequencing. BMC Genomics 2015; 16:913. [PMID: 26552429 PMCID: PMC4640199 DOI: 10.1186/s12864-015-2173-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/31/2015] [Indexed: 12/04/2022] Open
Abstract
Background The development of powerful new methods for DNA sequencing enable the discovery of sequence variants, their utilization for the mapping of mutant loci, and the identification of causal variants in a single step. We have applied this approach for the analysis of ENU-mutagenized mice maintained on an inbred background. Results We ascertained ENU-induced variants in four different phenotypically mutant lines. These were then used as informative markers for positional cloning of the mutated genes. We tested both whole genome (WGS) and whole exome (WES) datasets. Conclusion Both approaches were successful as a means to localize a region of homozygosity, as well as identifying mutations of candidate genes, which could be individually assessed. As expected, the WGS strategy was more reliable, since many more ENU-induced variants were ascertained. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2173-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jabier Gallego-Llamas
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA. .,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - Krista A Geister
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - Anna Lindsay
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - David R Beier
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA. .,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
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Koltowska K, Paterson S, Bower NI, Baillie GJ, Lagendijk AK, Astin JW, Chen H, Francois M, Crosier PS, Taft RJ, Simons C, Smith KA, Hogan BM. mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. Genes Dev 2015; 29:1618-30. [PMID: 26253536 PMCID: PMC4536310 DOI: 10.1101/gad.263210.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Koltowska et al. used a forward genetic screen in zebrafish to identify the transcription factor mafba as essential for lymphatic vessel development. Vegfc signaling increases mafba expression to control downstream transcription, and this relationship is SoxF transcription factor-dependent. The lymphatic vasculature plays roles in tissue fluid balance, immune cell trafficking, fatty acid absorption, cancer metastasis, and cardiovascular disease. Lymphatic vessels form by lymphangiogenesis, the sprouting of new lymphatics from pre-existing vessels, in both development and disease contexts. The apical signaling pathway in lymphangiogenesis is the VEGFC/VEGFR3 pathway, yet how signaling controls cellular transcriptional output remains unknown. We used a forward genetic screen in zebrafish to identify the transcription factor mafba as essential for lymphatic vessel development. We found that mafba is required for the migration of lymphatic precursors after their initial sprouting from the posterior cardinal vein. mafba expression is enriched in sprouts emerging from veins, and we show that mafba functions cell-autonomously during lymphatic vessel development. Mechanistically, Vegfc signaling increases mafba expression to control downstream transcription, and this regulatory relationship is dependent on the activity of SoxF transcription factors, which are essential for mafba expression in venous endothelium. Here we identify an indispensable Vegfc–SoxF–Mafba pathway in lymphatic development.
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Affiliation(s)
- Katarzyna Koltowska
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Scott Paterson
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Neil I Bower
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Gregory J Baillie
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Anne K Lagendijk
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Jonathan W Astin
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland 1023, New Zealand
| | - Huijun Chen
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Mathias Francois
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Philip S Crosier
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland 1023, New Zealand
| | - Ryan J Taft
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Cas Simons
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Kelly A Smith
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Benjamin M Hogan
- Division of Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
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Simon MM, Moresco EMY, Bull KR, Kumar S, Mallon AM, Beutler B, Potter PK. Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. Mamm Genome 2015; 26:486-500. [PMID: 26449678 PMCID: PMC4602060 DOI: 10.1007/s00335-015-9603-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/01/2015] [Indexed: 02/07/2023]
Abstract
Mutagenesis-based screens in mice are a powerful discovery platform to identify novel genes or gene functions associated with disease phenotypes. An N-ethyl-N-nitrosourea (ENU) mutagenesis screen induces single nucleotide variants randomly in the mouse genome. Subsequent phenotyping of mutant and wildtype mice enables the identification of mutated pathways resulting in phenotypes associated with a particular ENU lesion. This unbiased approach to gene discovery conducts the phenotyping with no prior knowledge of the functional mutations. Before the advent of affordable next generation sequencing (NGS), ENU variant identification was a limiting step in gene characterization, akin to ‘finding a needle in a haystack’. The emergence of a reliable reference genome alongside advances in NGS has propelled ENU mutation discovery from an arduous, time-consuming exercise to an effective and rapid form of mutation discovery. This has permitted large mouse facilities worldwide to use ENU for novel mutation discovery in a high-throughput manner, helping to accelerate basic science at the mechanistic level. Here, we describe three different strategies used to identify ENU variants from NGS data and some of the subsequent steps for mutation characterisation.
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Affiliation(s)
- Michelle M Simon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Katherine R Bull
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Saumya Kumar
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Paul K Potter
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
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Čejková D, Strouhal M, Norris SJ, Weinstock GM, Šmajs D. A Retrospective Study on Genetic Heterogeneity within Treponema Strains: Subpopulations Are Genetically Distinct in a Limited Number of Positions. PLoS Negl Trop Dis 2015; 9:e0004110. [PMID: 26436423 PMCID: PMC4593590 DOI: 10.1371/journal.pntd.0004110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 09/02/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Pathogenic uncultivable treponemes comprise human and animal pathogens including agents of syphilis, yaws, bejel, pinta, and venereal spirochetosis in rabbits and hares. A set of 10 treponemal genome sequences including those of 4 Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14), 4 T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), 1 T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPLC) were examined with respect to the presence of nucleotide intrastrain heterogeneous sites. METHODOLOGY/PRINCIPAL FINDINGS The number of identified intrastrain heterogeneous sites in individual genomes ranged between 0 and 7. Altogether, 23 intrastrain heterogeneous sites (in 17 genes) were found in 5 out of 10 investigated treponemal genomes including TPA strains Nichols (n = 5), DAL-1 (n = 4), and SS14 (n = 7), TPE strain Samoa D (n = 1), and TEN strain Bosnia A (n = 5). Although only one heterogeneous site was identified among 4 tested TPE strains, 16 such sites were identified among 4 TPA strains. Heterogeneous sites were mostly strain-specific and were identified in four tpr genes (tprC, GI, I, K), in genes involved in bacterial motility and chemotaxis (fliI, cheC-fliY), in genes involved in cell structure (murC), translation (prfA), general and DNA metabolism (putative SAM dependent methyltransferase, topA), and in seven hypothetical genes. CONCLUSIONS/SIGNIFICANCE Heterogeneous sites likely represent both the selection of adaptive changes during infection of the host as well as an ongoing diversifying evolutionary process.
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Affiliation(s)
- Darina Čejková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Steven J. Norris
- Pathology & Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - George M. Weinstock
- The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Hematopoietic stem cells develop in the absence of endothelial cadherin 5 expression. Blood 2015; 126:2811-20. [PMID: 26385351 DOI: 10.1182/blood-2015-07-659276] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 09/11/2015] [Indexed: 11/20/2022] Open
Abstract
Rare endothelial cells in the aorta-gonad-mesonephros (AGM) transition into hematopoietic stem cells (HSCs) during embryonic development. Lineage tracing experiments indicate that HSCs emerge from cadherin 5 (Cdh5; vascular endothelial-cadherin)(+) endothelial precursors, and isolated populations of Cdh5(+) cells from mouse embryos and embryonic stem cells can be differentiated into hematopoietic cells. Cdh5 has also been widely implicated as a marker of AGM-derived hemogenic endothelial cells. Because Cdh5(-/-) mice embryos die before the first HSCs emerge, it is unknown whether Cdh5 has a direct role in HSC emergence. Our previous genetic screen yielded malbec (mlb(bw306)), a zebrafish mutant for cdh5, with normal embryonic and definitive blood. Using time-lapse confocal imaging, parabiotic surgical pairing of zebrafish embryos, and blastula transplantation assays, we show that HSCs emerge, migrate, engraft, and differentiate in the absence of cdh5 expression. By tracing Cdh5(-/-)green fluorescent protein (GFP)(+/+) cells in chimeric mice, we demonstrated that Cdh5(-/-)GFP(+/+) HSCs emerging from embryonic day 10.5 and 11.5 (E10.5 and E11.5) AGM or derived from E13.5 fetal liver not only differentiate into hematopoietic colonies but also engraft and reconstitute multilineage adult blood. We also developed a conditional mouse Cdh5 knockout (Cdh5(flox/flox):Scl-Cre-ER(T)) and demonstrated that multipotent hematopoietic colonies form despite the absence of Cdh5. These data establish that Cdh5, a marker of hemogenic endothelium in the AGM, is dispensable for the transition of hemogenic endothelium to HSCs.
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MYB36 regulates the transition from proliferation to differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A 2015; 112:12099-104. [PMID: 26371322 DOI: 10.1073/pnas.1515576112] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Stem cells are defined by their ability to self-renew and produce daughter cells that proliferate and mature. These maturing cells transition from a proliferative state to a terminal state through the process of differentiation. In the Arabidopsis thaliana root the transcription factors SCARECROW and SHORTROOT regulate specification of the bipotent stem cell that gives rise to cortical and endodermal progenitors. Subsequent progenitor proliferation and differentiation generate mature endodermis, marked by the Casparian strip, a cell-wall modification that prevents ion diffusion into and out of the vasculature. We identified a transcription factor, MYB DOMAIN PROTEIN 36 (MYB36), that regulates the transition from proliferation to differentiation in the endodermis. We show that SCARECROW directly activates MYB36 expression, and that MYB36 likely acts in a feed-forward loop to regulate essential Casparian strip formation genes. We show that myb36 mutants have delayed and defective barrier formation as well as extra divisions in the meristem. Our results demonstrate that MYB36 is a critical positive regulator of differentiation and negative regulator of cell proliferation.
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Chen CH, Merriman AF, Savage J, Willer J, Wahlig T, Katsanis N, Yin VP, Poss KD. Transient laminin beta 1a Induction Defines the Wound Epidermis during Zebrafish Fin Regeneration. PLoS Genet 2015; 11:e1005437. [PMID: 26305099 PMCID: PMC4549328 DOI: 10.1371/journal.pgen.1005437] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/10/2015] [Indexed: 12/12/2022] Open
Abstract
The first critical stage in salamander or teleost appendage regeneration is creation of a specialized epidermis that instructs growth from underlying stump tissue. Here, we performed a forward genetic screen for mutations that impair this process in amputated zebrafish fins. Positional cloning and complementation assays identified a temperature-sensitive allele of the ECM component laminin beta 1a (lamb1a) that blocks fin regeneration. lamb1a, but not its paralog lamb1b, is sharply induced in a subset of epithelial cells after fin amputation, where it is required to establish and maintain a polarized basal epithelial cell layer. These events facilitate expression of the morphogenetic factors shha and lef1, basolateral positioning of phosphorylated Igf1r, patterning of new osteoblasts, and regeneration of bone. By contrast, lamb1a function is dispensable for juvenile body growth, homeostatic adult tissue maintenance, repair of split fins, or renewal of genetically ablated osteoblasts. fgf20a mutations or transgenic Fgf receptor inhibition disrupt lamb1a expression, linking a central growth factor to epithelial maturation during regeneration. Our findings reveal transient induction of lamb1a in epithelial cells as a key, growth factor-guided step in formation of a signaling-competent regeneration epidermis. Unlike mammals, adult teleost fish and urodele amphibians can fully regenerate lost appendages. Understanding what initiates regeneration in these vertebrates is of great interest to the scientific community. It has long been known that the epidermis that forms quickly over an amputated limb stump is critical for initiating regenerative programs. Yet, little of understood of the molecular and cellular mechanisms by which a simple adult epithelium transforms into this key signaling source. Here, we performed a large-scale, unbiased genetic screen for epithelial signaling deficiencies during the regeneration of amputated adult zebrafish fins, from which we identified several new mutants. One gene identified from this screen disrupts a specific component of the extracellular matrix material Laminin, Laminin beta 1a, a factor that we find to be dispensable in uninjured adult animals but required for all stages fin regeneration. Transient induction of this component by amputation polarizes the basal layer of the nascent epithelium, and, in turn, facilitates the synthesis of signaling factors, the positioning of ligand receptors, and the patterning of new bone cells. We also find that normal induction of Laminin beta 1a by injury relies on the function of Fibroblast growth factors, secreted polypeptide signals that are released early upon injury. Our results identify key early steps in the endogenous program for vertebrate appendage regeneration.
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Affiliation(s)
- Chen-Hui Chen
- Department of Cell Biology and Howard Hughes Medical Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Alexander F. Merriman
- Department of Cell Biology and Howard Hughes Medical Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Jeremiah Savage
- Department of Cell Biology and Howard Hughes Medical Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Center for Human Disease Modeling, Department of Cell Biology, Duke University, Durham, North Carolina, United States of America
| | - Jason Willer
- Center for Human Disease Modeling, Department of Cell Biology, Duke University, Durham, North Carolina, United States of America
| | - Taylor Wahlig
- Department of Cell Biology and Howard Hughes Medical Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Department of Cell Biology, Duke University, Durham, North Carolina, United States of America
| | - Viravuth P. Yin
- Department of Cell Biology and Howard Hughes Medical Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine, United States of America
| | - Kenneth D. Poss
- Department of Cell Biology and Howard Hughes Medical Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail:
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Rider SA, Mullins LJ, Verdon RF, MacRae CA, Mullins JJ. Renin expression in developing zebrafish is associated with angiogenesis and requires the Notch pathway and endothelium. Am J Physiol Renal Physiol 2015. [PMID: 26202224 DOI: 10.1152/ajprenal.00247.2015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Although renin is a critical regulatory enzyme of the cardiovascular system, its roles in organogenesis and the establishment of cardiovascular homeostasis remain unclear. Mammalian renin-expressing cells are widespread in embryonic kidneys but are highly restricted, specialized endocrine cells in adults. With a functional pronephros, embryonic zebrafish are ideal for delineating the developmental functions of renin-expressing cells and the mechanisms governing renin transcription. Larval zebrafish renin expression originates in the mural cells of the juxtaglomerular anterior mesenteric artery and subsequently at extrarenal sites. The role of renin was determined by assessing responses to renin-angiotensin system blockade, salinity variation, and renal perfusion ablation. Renin expression did not respond to renal flow ablation but was modulated by inhibition of angiotensin-converting enzyme and altered salinity. Our data in larval fish are consistent with conservation of renin's physiological functions. Using transgenic renin reporter fish, with mindbomb and cloche mutants, we show that Notch signaling and the endothelium are essential for developmental renin expression. After inhibition of angiogenesis, renin-expressing cells precede angiogenic sprouts. Arising from separate lineages, but relying on mutual interplay with endothelial cells, renin-expressing cells are among the earliest mural cells observed in larval fish, performing both endocrine and paracrine functions.
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Affiliation(s)
- Sebastien A Rider
- University/BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, Little France, The University of Edinburgh, Edinburgh, United Kingdom; and
| | - Linda J Mullins
- University/BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, Little France, The University of Edinburgh, Edinburgh, United Kingdom; and
| | - Rachel F Verdon
- University/BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, Little France, The University of Edinburgh, Edinburgh, United Kingdom; and
| | - Calum A MacRae
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - John J Mullins
- University/BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, Little France, The University of Edinburgh, Edinburgh, United Kingdom; and
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Candela H, Casanova-Sáez R, Micol JL. Getting started in mapping-by-sequencing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:606-12. [PMID: 25359627 DOI: 10.1111/jipb.12305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/28/2014] [Indexed: 05/06/2023]
Abstract
Next-generation sequencing (NGS) technologies allow the cost-effective sequencing of whole genomes and have expanded the scope of genomics to novel applications, such as the genome-wide characterization of intraspecific polymorphisms and the rapid mapping and identification of point mutations. Next-generation sequencing platforms, such as the Illumina HiSeq2000 platform, are now commercially available at affordable prices and routinely produce an enormous amount of sequence data, but their wide use is often hindered by a lack of knowledge on how to manipulate and process the information produced. In this review, we focus on the strategies that are available to geneticists who wish to incorporate these novel approaches into their research but who are not familiar with the necessary bioinformatic concepts and computational tools. In particular, we comprehensively summarize case studies where the use of NGS technologies has led to the identification of point mutations, a strategy that has been dubbed "mapping-by-sequencing", and review examples from plants and other model species such as Caenorhabditis elegans, Saccharomyces cerevisiae, and Drosophila melanogaster. As these technologies are becoming cheaper and more powerful, their use is also expanding to allow mutation identification in species with larger genomes, such as many crop plants.
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Affiliation(s)
- Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Rubén Casanova-Sáez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
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65
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Haelterman NA, Jiang L, Li Y, Bayat V, Sandoval H, Ugur B, Tan KL, Zhang K, Bei D, Xiong B, Charng WL, Busby T, Jawaid A, David G, Jaiswal M, Venken KJT, Yamamoto S, Chen R, Bellen HJ. Large-scale identification of chemically induced mutations in Drosophila melanogaster. Genome Res 2015; 24:1707-18. [PMID: 25258387 PMCID: PMC4199363 DOI: 10.1101/gr.174615.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Forward genetic screens using chemical mutagens have been successful in defining the function of thousands of genes in eukaryotic model organisms. The main drawback of this strategy is the time-consuming identification of the molecular lesions causative of the phenotypes of interest. With whole-genome sequencing (WGS), it is now possible to sequence hundreds of strains, but determining which mutations are causative among thousands of polymorphisms remains challenging. We have sequenced 394 mutant strains, generated in a chemical mutagenesis screen, for essential genes on the Drosophila X chromosome and describe strategies to reduce the number of candidate mutations from an average of ∼3500 to 35 single-nucleotide variants per chromosome. By combining WGS with a rough mapping method based on large duplications, we were able to map 274 (∼70%) mutations. We show that these mutations are causative, using small 80-kb duplications that rescue lethality. Hence, our findings demonstrate that combining rough mapping with WGS dramatically expands the toolkit necessary for assigning function to genes.
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Affiliation(s)
- Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lichun Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vafa Bayat
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Berrak Ugur
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kai Li Tan
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Theodore Busby
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Adeel Jawaid
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gabriela David
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Koen J T Venken
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Verna and Mars Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
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66
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Wyatt C, Bartoszek EM, Yaksi E. Methods for studying the zebrafish brain: past, present and future. Eur J Neurosci 2015; 42:1746-63. [PMID: 25900095 DOI: 10.1111/ejn.12932] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 04/16/2015] [Accepted: 04/20/2015] [Indexed: 01/16/2023]
Abstract
The zebrafish (Danio rerio) is one of the most promising new model organisms. The increasing popularity of this amazing small vertebrate is evident from the exponentially growing numbers of research articles, funded projects and new discoveries associated with the use of zebrafish for studying development, brain function, human diseases and screening for new drugs. Thanks to the development of novel technologies, the range of zebrafish research is constantly expanding with new tools synergistically enhancing traditional techniques. In this review we will highlight the past and present techniques which have made, and continue to make, zebrafish an attractive model organism for various fields of biology, with a specific focus on neuroscience.
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Affiliation(s)
- Cameron Wyatt
- Neuro-Electronics Research Flanders, Imec Campus, Kapeldreef, Leuven, Belgium.,VIB, Leuven, Belgium
| | - Ewelina M Bartoszek
- Neuro-Electronics Research Flanders, Imec Campus, Kapeldreef, Leuven, Belgium.,VIB, Leuven, Belgium.,Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway
| | - Emre Yaksi
- Neuro-Electronics Research Flanders, Imec Campus, Kapeldreef, Leuven, Belgium.,VIB, Leuven, Belgium.,KU Leuven, Leuven, Belgium.,Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway
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67
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Richards S. It's more than stamp collecting: how genome sequencing can unify biological research. Trends Genet 2015; 31:411-21. [PMID: 26003218 DOI: 10.1016/j.tig.2015.04.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
Abstract
The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, while the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to 'big science' survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need.
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Affiliation(s)
- Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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68
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Kim SH, Wu SY, Baek JI, Choi SY, Su Y, Flynn CR, Gamse JT, Ess KC, Hardiman G, Lipschutz JH, Abumrad NN, Rockey DC. A post-developmental genetic screen for zebrafish models of inherited liver disease. PLoS One 2015; 10:e0125980. [PMID: 25950913 PMCID: PMC4423964 DOI: 10.1371/journal.pone.0125980] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/27/2015] [Indexed: 02/07/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver disease such as simple steatosis, nonalcoholic steatohepatitis (NASH), cirrhosis and fibrosis. However, the molecular pathogenesis and genetic variations causing NAFLD are poorly understood. The high prevalence and incidence of NAFLD suggests that genetic variations on a large number of genes might be involved in NAFLD. To identify genetic variants causing inherited liver disease, we used zebrafish as a model system for a large-scale mutant screen, and adopted a whole genome sequencing approach for rapid identification of mutated genes found in our screen. Here, we report on a forward genetic screen of ENU mutagenized zebrafish. From 250 F2 lines of ENU mutagenized zebrafish during post-developmental stages (5 to 8 days post fertilization), we identified 19 unique mutant zebrafish lines displaying visual evidence of hepatomegaly and/or steatosis with no developmental defects. Histological analysis of mutants revealed several specific phenotypes, including common steatosis, micro/macrovesicular steatosis, hepatomegaly, ballooning, and acute hepatocellular necrosis. This work has identified multiple post-developmental mutants and establishes zebrafish as a novel animal model for post-developmental inherited liver disease.
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Affiliation(s)
- Seok-Hyung Kim
- Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, the United States of America
- * E-mail:
| | - Shu-Yu Wu
- Department of Biology, Vanderbilt University, Nashville, TN, 37232, the United States of America
| | - Jeong-In Baek
- Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, the United States of America
| | - Soo Young Choi
- Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, the United States of America
| | - Yanhui Su
- Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, the United States of America
| | - Charles R. Flynn
- Department of Surgery, Vanderbilt University, Nashville, TN, 37232, the United States of America
| | - Joshua T. Gamse
- Department of Biology, Vanderbilt University, Nashville, TN, 37232, the United States of America
| | - Kevin C. Ess
- Department of Pediatrics, Vanderbilt University, Nashville, TN, 37232, the United States of America
| | - Gary Hardiman
- Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, the United States of America
| | - Joshua H. Lipschutz
- Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, the United States of America
- Department of Medicine, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC, 29401, the United States of America
| | - Naji N. Abumrad
- Department of Surgery, Vanderbilt University, Nashville, TN, 37232, the United States of America
| | - Don C. Rockey
- Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, the United States of America
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69
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Wilkinson GS, Breden F, Mank JE, Ritchie MG, Higginson AD, Radwan J, Jaquiery J, Salzburger W, Arriero E, Barribeau SM, Phillips PC, Renn SCP, Rowe L. The locus of sexual selection: moving sexual selection studies into the post-genomics era. J Evol Biol 2015; 28:739-55. [PMID: 25789690 DOI: 10.1111/jeb.12621] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 02/07/2023]
Abstract
Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology.
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Affiliation(s)
- G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
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70
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Xu L, Tang H, Chen DW, El-Naggar AK, Wei P, Sturgis EM. Genome-wide association study identifies common genetic variants associated with salivary gland carcinoma and its subtypes. Cancer 2015; 121:2367-74. [PMID: 25823930 DOI: 10.1002/cncr.29381] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/20/2015] [Accepted: 02/09/2015] [Indexed: 01/20/2023]
Abstract
BACKGROUND Salivary gland carcinomas (SGCs) are a rare malignancy with unknown etiology. The objective of the current study was to identify genetic variants modifying the risk of SGC and its major subtypes: adenoid cystic carcinoma and mucoepidermoid carcinoma. METHODS The authors conducted a genome-wide association study in 309 well-defined SGC cases and 535 cancer-free controls. A single-nucleotide polymorphism (SNP)-level discovery study was performed in non-Hispanic white individuals followed by a replication study in Hispanic individuals. A logistic regression analysis was applied to calculate odds ratios (ORs) and 95% confidence intervals (95% CIs). A meta-analysis of the results was conducted. RESULTS A genome-wide significant association with SGC in non-Hispanic white individuals was detected at coding SNPs in CHRNA2 (cholinergic receptor, nicotinic, alpha 2 [neuronal]) (OR, 8.55; 95% CI, 4.53-16.13 [P = 3.6 × 10(-11)]), OR4F15 (olfactory receptor, family 4, subfamily F, member 15) (OR, 5.26; 95% CI, 3.13-8.83 [P = 3.5 × 10(-10)]), ZNF343 (zinc finger protein 343) (OR, 3.28; 95% CI, 2.12-5.07 [P = 9.1 × 10(-8)]), and PARP4 (poly(ADP-ribose) polymerase family, member 4) (OR, 2.00; 95% CI, 1.54-2.59 [P = 1.7 × 10(-7)]). Meta-analysis of the non-Hispanic white and Hispanic cohorts identified another genome-wide significant SNP in ELL2 (meta-OR, 1.86; 95% CI, 1.48-2.34 [P = 1.3 × 10(-7)]). Risk alleles were largely enriched in mucoepidermoid carcinoma, in which the SNPs in CHRNA2, OR4F15, and ZNF343 had ORs of 15.71 (95% CI, 6.59-37.47 [P = 5.2 × 10(-10)]), 15.60 (95% CI, 6.50-37.41 [P = 7.5 × 10(-10)]), and 6.49 (95% CI, 3.36-12.52 [P = 2.5 × 10(-8)]), respectively. None of these SNPs retained a significant association with adenoid cystic carcinoma. CONCLUSIONS To the best of the authors' knowledge, the current study is the first to identify a panel of SNPs associated with the risk of SGC. Confirmation of these findings along with functional analysis of identified SNPs are needed.
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Affiliation(s)
- Li Xu
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hongwei Tang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Diane W Chen
- Clincal Research, Quality Improvement, Baylor College of Medicine, Houston, Texas
| | - Adel K El-Naggar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peng Wei
- Division of Biostatistics and Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas
| | - Erich M Sturgis
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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71
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Butler MG, Iben JR, Marsden KC, Epstein JA, Granato M, Weinstein BM. SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish. Development 2015; 142:1542-52. [PMID: 25813542 DOI: 10.1242/dev.118786] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/25/2015] [Indexed: 12/11/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are the benchmark molecular markers for modern genomics. Until recently, relatively few SNPs were known in the zebrafish genome. The use of next-generation sequencing for the positional cloning of zebrafish mutations has increased the number of known SNP positions dramatically. Still, the identified SNP variants remain under-utilized, owing to scant annotation of strain specificity and allele frequency. To address these limitations, we surveyed SNP variation in three common laboratory zebrafish strains using whole-genome sequencing. This survey identified an average of 5.04 million SNPs per strain compared with the Zv9 reference genome sequence. By comparing the three strains, 2.7 million variants were found to be strain specific, whereas the remaining variants were shared among all (2.3 million) or some of the strains. We also demonstrate the broad usefulness of our identified variants by validating most in independent populations of the same laboratory strains. We have made all of the identified SNPs accessible through 'SNPfisher', a searchable online database (snpfisher.nichd.nih.gov). The SNPfisher website includes the SNPfisher Variant Reporter tool, which provides the genomic position, alternate allele read frequency, strain specificity, restriction enzyme recognition site changes and flanking primers for all SNPs and Indels in a user-defined gene or region of the zebrafish genome. The SNPfisher site also contains links to display our SNP data in the UCSC genome browser. The SNPfisher tools will facilitate the use of SNP variation in zebrafish research as well as vertebrate genome evolution.
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Affiliation(s)
- Matthew G Butler
- Section on Vertebrate Development, Program in the Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - James R Iben
- Section on Molecular Dysmorphology, Program in Developmental Endocrinology and Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kurt C Marsden
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Jonathan A Epstein
- Section on Molecular Dysmorphology, Program in Developmental Endocrinology and Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Granato
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Brant M Weinstein
- Section on Vertebrate Development, Program in the Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Epigenetic control of intestinal barrier function and inflammation in zebrafish. Proc Natl Acad Sci U S A 2015; 112:2770-5. [PMID: 25730872 DOI: 10.1073/pnas.1424089112] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The intestinal epithelium forms a barrier protecting the organism from microbes and other proinflammatory stimuli. The integrity of this barrier and the proper response to infection requires precise regulation of powerful immune homing signals such as tumor necrosis factor (TNF). Dysregulation of TNF leads to inflammatory bowel diseases (IBD), but the mechanism controlling the expression of this potent cytokine and the events that trigger the onset of chronic inflammation are unknown. Here, we show that loss of function of the epigenetic regulator ubiquitin-like protein containing PHD and RING finger domains 1 (uhrf1) in zebrafish leads to a reduction in tnfa promoter methylation and the induction of tnfa expression in intestinal epithelial cells (IECs). The increase in IEC tnfa levels is microbe-dependent and results in IEC shedding and apoptosis, immune cell recruitment, and barrier dysfunction, consistent with chronic inflammation. Importantly, tnfa knockdown in uhrf1 mutants restores IEC morphology, reduces cell shedding, and improves barrier function. We propose that loss of epigenetic repression and TNF induction in the intestinal epithelium can lead to IBD onset.
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73
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Schierenbeck L, Ries D, Rogge K, Grewe S, Weisshaar B, Kruse O. Fast forward genetics to identify mutations causing a high light tolerant phenotype in Chlamydomonas reinhardtii by whole-genome-sequencing. BMC Genomics 2015; 16:57. [PMID: 25730202 PMCID: PMC4336690 DOI: 10.1186/s12864-015-1232-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High light tolerance of microalgae is a desired phenotype for efficient cultivation in large scale production systems under fluctuating outdoor conditions. Outdoor cultivation requires the use of either wild-type or non-GMO derived mutant strains due to safety concerns. The identification and molecular characterization of such mutants derived from untagged forward genetics approaches was limited previously by the tedious and time-consuming methods involving techniques such as classical meiotic mapping. The combination of mapping with next generation sequencing technologies offers alternative strategies to identify genes involved in high light adaptation in untagged mutants. RESULTS We used the model alga Chlamydomonas reinhardtii in a non-GMO mutation strategy without any preceding crossing step or pooled progeny to identify genes involved in the regulatory processes of high light adaptation. To generate high light tolerant mutants, wildtype cells were mutagenized only to a low extent, followed by a stringent selection. We performed whole-genome sequencing of two independent mutants hit1 and hit2 and the parental wildtype. The availability of a reference genome sequence and the removal of shared bakground variants between the wildtype strain and each mutant, enabled us to identify two single nucleotide polymorphisms within the same gene Cre02.g085050, hereafter called LRS1 (putative Light Response Signaling protein 1). These two independent single amino acid exchanges are both located in the putative WD40 propeller domain of the corresponding protein LRS1. Both mutants exhibited an increased rate of non-photochemical-quenching (NPQ) and an improved resistance against chemically induced reactive oxygen species. In silico analyses revealed homology of LRS1 to the photoregulatory protein COP1 in plants. CONCLUSIONS In this work we identified the nuclear encoded gene LRS1 as an essential factor for high light adaptation in C. reinhardtii. The causative random mutation within this gene was identified by a rapid and efficient method, avoiding any preceding crossing step, meiotic mapping, or pooled progeny. Our results open up new insights into mechanisms of high light adaptation in microalgae and at the same time provide a simplified strategy for non-GMO forward genetics, a crucial precondition that could result in the identification of key factors for economically relevant biological processes within algae.
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Affiliation(s)
- Lisa Schierenbeck
- />Department of Biology/Center for Biotechnology, Algae Biotechnology and Bioenergy, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - David Ries
- />Department of Biology/Center for Biotechnology, Genome Research, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Kristin Rogge
- />Department of Biology/Center for Biotechnology, Algae Biotechnology and Bioenergy, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Sabrina Grewe
- />Department of Biology/Center for Biotechnology, Algae Biotechnology and Bioenergy, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Bernd Weisshaar
- />Department of Biology/Center for Biotechnology, Genome Research, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Olaf Kruse
- />Department of Biology/Center for Biotechnology, Algae Biotechnology and Bioenergy, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
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Sun H, Schneeberger K. SHOREmap v3.0: fast and accurate identification of causal mutations from forward genetic screens. Methods Mol Biol 2015; 1284:381-95. [PMID: 25757783 DOI: 10.1007/978-1-4939-2444-8_19] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Whole-genome resequencing of pools of recombinant mutant genomes allows direct linking of phenotypic traits to causal mutations. Such analysis, called mapping-by-sequencing, combines classical genetic mapping and next-generation sequencing by relying on selection-induced patterns within genome-wide allele frequency (AF) in pooled genomes. Mapping-by-sequencing can be performed with computational tools such as SHOREmap. Previous versions of SHOREmap, however, did not implement standardized analyses, but were specifically designed for particular experimental settings. Here, we introduce the usage of a novel and advanced implementation of SHOREmap (version 3.0), including several new features like file readers for commonly used file formats, SNP marker selection, and a stable calculation of mapping intervals. SHOREmap can be downloaded at shoremap.org.
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Affiliation(s)
- Hequan Sun
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
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Buchan JG, Gray RS, Gansner JM, Alvarado DM, Burgert L, Gitlin JD, Gurnett CA, Goldsmith MI. Kinesin family member 6 (kif6) is necessary for spine development in zebrafish. Dev Dyn 2014; 243:1646-57. [PMID: 25283277 DOI: 10.1002/dvdy.24208] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 09/16/2014] [Accepted: 09/25/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Idiopathic scoliosis is a form of spinal deformity that affects 2-3% of children and results in curvature of the spine without structural defects of the vertebral units. The pathogenesis of idiopathic scoliosis remains poorly understood, in part due to the lack of a relevant animal model. RESULTS We performed a forward mutagenesis screen in zebrafish to identify new models for idiopathic scoliosis. We isolated a recessive zebrafish mutant, called skolios, which develops isolated spinal curvature that arises independent of vertebral malformations. Using meiotic mapping and whole genome sequencing, we identified a nonsense mutation in kinesin family member 6 (kif6(gw326) ) unique to skolios mutants. Three additional kif6 frameshift alleles (gw327, gw328, gw329) were generated with transcription activator-like effector nucleases (TALENs). Zebrafish homozygous or compound heterozygous for kif6 frameshift mutations developed a scoliosis phenotype indistinguishable from skolios mutants, confirming that skolios is caused by the loss of kif6. Although kif6 may play a role in cilia, no evidence for cilia dysfunction was seen in kif6(gw326) mutants. CONCLUSIONS Overall, these findings demonstrate a novel role for kif6 in spinal development and identify a new candidate gene for human idiopathic scoliosis.
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Affiliation(s)
- Jillian G Buchan
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
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76
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Berger J, Tarakci H, Berger S, Li M, Hall TE, Arner A, Currie PD. Loss of Tropomodulin4 in the zebrafish mutant träge causes cytoplasmic rod formation and muscle weakness reminiscent of nemaline myopathy. Dis Model Mech 2014; 7:1407-15. [PMID: 25288681 PMCID: PMC4257009 DOI: 10.1242/dmm.017376] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Nemaline myopathy is an inherited muscle disease that is mainly diagnosed by the presence of nemaline rods in muscle biopsies. Of the nine genes associated with the disease, five encode components of striated muscle sarcomeres. In a genetic zebrafish screen, the mutant träge (trg) was isolated based on its reduction in muscle birefringence, indicating muscle damage. Myofibres in trg appeared disorganised and showed inhomogeneous cytoplasmic eosin staining alongside malformed nuclei. Linkage analysis of trg combined with sequencing identified a nonsense mutation in tropomodulin4 (tmod4), a regulator of thin filament length and stability. Accordingly, although actin monomers polymerize to form thin filaments in the skeletal muscle of tmod4trg mutants, thin filaments often appeared to be dispersed throughout myofibres. Organised myofibrils with the typical striation rarely assemble, leading to severe muscle weakness, impaired locomotion and early death. Myofibrils of tmod4trg mutants often featured thin filaments of various lengths, widened Z-disks, undefined H-zones and electron-dense aggregations of various shapes and sizes. Importantly, Gomori trichrome staining and the lattice pattern of the detected cytoplasmic rods, together with the reactivity of rods with phalloidin and an antibody against actinin, is reminiscent of nemaline rods found in nemaline myopathy, suggesting that misregulation of thin filament length causes cytoplasmic rod formation in tmod4trg mutants. Although Tropomodulin4 has not been associated with myopathy, the results presented here implicateTMOD4 as a novel candidate for unresolved nemaline myopathies and suggest that the tmod4trg mutant will be a valuable tool to study human muscle disorders.
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Affiliation(s)
- Joachim Berger
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Hakan Tarakci
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Silke Berger
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Mei Li
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, SE 17177, Sweden
| | - Thomas E Hall
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
| | - Anders Arner
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, SE 17177, Sweden
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
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77
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Sequencing pools of individuals — mining genome-wide polymorphism data without big funding. Nat Rev Genet 2014; 15:749-63. [DOI: 10.1038/nrg3803] [Citation(s) in RCA: 512] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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78
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McMenamin SK, Bain EJ, McCann AE, Patterson LB, Eom DS, Waller ZP, Hamill JC, Kuhlman JA, Eisen JS, Parichy DM. Thyroid hormone-dependent adult pigment cell lineage and pattern in zebrafish. Science 2014; 345:1358-61. [PMID: 25170046 PMCID: PMC4211621 DOI: 10.1126/science.1256251] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Pigment patterns are useful for elucidating fundamental mechanisms of pattern formation and how these mechanisms evolve. In zebrafish, several pigment cell classes interact to generate stripes, yet the developmental requirements and origins of these cells remain poorly understood. Using zebrafish and a related species, we identified roles for thyroid hormone (TH) in pigment cell development and patterning, and in postembryonic development more generally. We show that adult pigment cells arise from distinct lineages having distinct requirements for TH and that differential TH dependence can evolve within lineages. Our findings demonstrate critical functions for TH in determining pigment pattern phenotype and highlight the potential for evolutionary diversification at the intersection of developmental and endocrine mechanisms.
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Affiliation(s)
- Sarah K McMenamin
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Emily J Bain
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Anna E McCann
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | | | - Dae Seok Eom
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Zachary P Waller
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - James C Hamill
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Julie A Kuhlman
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Judith S Eisen
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - David M Parichy
- Department of Biology, University of Washington, Seattle, WA 98195, USA. Institute for Stem Cell and Regenerative Medicine, UW Medicine Research, Seattle, WA 98109, USA.
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79
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Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 2014; 15:662-76. [PMID: 25139187 DOI: 10.1038/nrg3745] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The long-lasting success of forward genetic screens relies on the simple molecular basis of the characterized phenotypes, which are typically caused by mutations in single genes. Mapping the location of causal mutations using genetic crosses has traditionally been a complex, multistep procedure, but next-generation sequencing now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds. Recent advances of this mapping-by-sequencing approach include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information, which make forward genetics amenable for species that have not been considered for forward genetic screens so far.
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Affiliation(s)
- Korbinian Schneeberger
- Genome Plasticity and Computational Genetics, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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80
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Krutá M, Šeneklová M, Raška J, Salykin A, Zerzánková L, Pešl M, Bártová E, Franek M, Baumeisterová A, Košková S, Neelsen KJ, Hampl A, Dvořák P, Rotrekl V. Mutation frequency dynamics in HPRT locus in culture-adapted human embryonic stem cells and induced pluripotent stem cells correspond to their differentiated counterparts. Stem Cells Dev 2014; 23:2443-54. [PMID: 24836366 DOI: 10.1089/scd.2013.0611] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The genomic destabilization associated with the adaptation of human embryonic stem cells (hESCs) to culture conditions or the reprogramming of induced pluripotent stem cells (iPSCs) increases the risk of tumorigenesis upon the clinical use of these cells and decreases their value as a model for cell biology studies. Base excision repair (BER), a major genomic integrity maintenance mechanism, has been shown to fail during hESC adaptation. Here, we show that the increase in the mutation frequency (MF) caused by the inhibition of BER was similar to that caused by the hESC adaptation process. The increase in MF reflected the failure of DNA maintenance mechanisms and the subsequent increase in MF rather than being due solely to the accumulation of mutants over a prolonged period, as was previously suggested. The increase in the ionizing-radiation-induced MF in adapted hESCs exceeded the induced MF in nonadapted hESCs and differentiated cells. Unlike hESCs, the overall DNA maintenance in iPSCs, which was reflected by the MF, was similar to that in differentiated cells regardless of the time spent in culture and despite the upregulation of several genes responsible for genome maintenance during the reprogramming process. Taken together, our results suggest that the changes in BER activity during the long-term cultivation of hESCs increase the mutagenic burden, whereas neither reprogramming nor long-term propagation in culture changes the MF in iPSCs.
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Affiliation(s)
- Miriama Krutá
- 1 Department of Biology, Faculty of Medicine, Masaryk University , Brno, Czech Republic
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81
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Kroeger PT, Poureetezadi SJ, McKee R, Jou J, Miceli R, Wingert RA. Production of haploid zebrafish embryos by in vitro fertilization. J Vis Exp 2014. [PMID: 25046024 PMCID: PMC4214630 DOI: 10.3791/51708] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The zebrafish has become a mainstream vertebrate model that is relevant for many disciplines of scientific study. Zebrafish are especially well suited for forward genetic analysis of developmental processes due to their external fertilization, embryonic size, rapid ontogeny, and optical clarity – a constellation of traits that enable the direct observation of events ranging from gastrulation to organogenesis with a basic stereomicroscope. Further, zebrafish embryos can survive for several days in the haploid state. The production of haploid embryos in vitro is a powerful tool for mutational analysis, as it enables the identification of recessive mutant alleles present in first generation (F1) female carriers following mutagenesis in the parental (P) generation. This approach eliminates the necessity to raise multiple generations (F2, F3, etc.) which involves breeding of mutant families, thus saving the researcher time along with reducing the needs for zebrafish colony space, labor, and the husbandry costs. Although zebrafish have been used to conduct forward screens for the past several decades, there has been a steady expansion of transgenic and genome editing tools. These tools now offer a plethora of ways to create nuanced assays for next generation screens that can be used to further dissect the gene regulatory networks that drive vertebrate ontogeny. Here, we describe how to prepare haploid zebrafish embryos. This protocol can be implemented for novel future haploid screens, such as in enhancer and suppressor screens, to address the mechanisms of development for a broad number of processes and tissues that form during early embryonic stages.
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Affiliation(s)
- Paul T Kroeger
- Department of Biological Sciences, University of Notre Dame
| | | | - Robert McKee
- Department of Biological Sciences, University of Notre Dame
| | - Jonathan Jou
- Department of Biological Sciences, University of Notre Dame
| | - Rachel Miceli
- Department of Biological Sciences, University of Notre Dame
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82
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Stottmann R, Beier DR. ENU Mutagenesis in the Mouse. CURRENT PROTOCOLS IN HUMAN GENETICS 2014; 82:15.4.1-15.4.10. [PMID: 25042716 PMCID: PMC4113905 DOI: 10.1002/0471142905.hg1504s82] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This unit describes the treatment of laboratory mice with the mutagen N-ethyl-N-nitrosourea (ENU) to induce very highly increased rates of mutation throughout the genome. Further, it describes several popular mating schemes designed to produce animals displaying phenotypes associated with the induced mutations.
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Affiliation(s)
- Rolf Stottmann
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - David R. Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute
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83
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Mascher M, Stein N. Genetic anchoring of whole-genome shotgun assemblies. Front Genet 2014; 5:208. [PMID: 25071835 PMCID: PMC4083584 DOI: 10.3389/fgene.2014.00208] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
The recent advances in sequencing throughput and genome assembly algorithms have established whole-genome shotgun (WGS) assemblies as the cornerstone of the genomic infrastructure for many species. WGS assemblies can be constructed with comparative ease and give a comprehensive representation of the gene space even of large and complex genomes. One major obstacle in utilizing WGS assemblies for important research applications such as gene isolation or comparative genomics has been the lack of chromosomal positioning and contextualization of short sequence contigs. Assigning chromosomal locations to sequence contigs required the construction and integration of genome-wide physical maps and dense genetic linkage maps as well as synteny to model species. Recently, methods to rapidly construct ultra-dense linkage maps encompassing millions of genetic markers from WGS sequencing data of segregating populations have made possible the direct assignment of genetic positions to short sequence contigs. Here, we review recent developments in the integration of WGS assemblies and sequence-based linkage maps, discuss challenges for further improvement of the methodology and outline possible applications building on genetically anchored WGS assemblies.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Stadt Seeland Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Stadt Seeland Germany
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84
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Kroeger PT, Wingert RA. Using zebrafish to study podocyte genesis during kidney development and regeneration. Genesis 2014; 52:771-92. [PMID: 24920186 DOI: 10.1002/dvg.22798] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 06/08/2014] [Accepted: 06/09/2014] [Indexed: 12/21/2022]
Abstract
During development, vertebrates form a progression of up to three different kidneys that are comprised of functional units termed nephrons. Nephron composition is highly conserved across species, and an increasing appreciation of the similarities between zebrafish and mammalian nephron cell types has positioned the zebrafish as a relevant genetic system for nephrogenesis studies. A key component of the nephron blood filter is a specialized epithelial cell known as the podocyte. Podocyte research is of the utmost importance as a vast majority of renal diseases initiate with the dysfunction or loss of podocytes, resulting in a condition known as proteinuria that causes nephron degeneration and eventually leads to kidney failure. Understanding how podocytes develop during organogenesis may elucidate new ways to promote nephron health by stimulating podocyte replacement in kidney disease patients. In this review, we discuss how the zebrafish model can be used to study kidney development, and how zebrafish research has provided new insights into podocyte lineage specification and differentiation. Further, we discuss the recent discovery of podocyte regeneration in adult zebrafish, and explore how continued basic research using zebrafish can provide important knowledge about podocyte genesis in embryonic and adult environments. genesis 52:771-792, 2014. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Paul T Kroeger
- Department of Biological Sciences and Center for Zebrafish Research, University of Notre Dame, Notre Dame, Indiana, 46556
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85
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Abstract
This article describes the treatment of laboratory mice with the mutagen N-ethyl-N-nitrosourea (ENU) to induce very highly increased rates of mutation throughout the genome. Further, it describes several popular mating schemes designed to produce animals displaying phenotypes associated with the induced mutations.
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Affiliation(s)
- Rolf Stottmann
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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86
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Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014; 15:R78. [PMID: 24917130 PMCID: PMC4073093 DOI: 10.1186/gb-2014-15-6-r78] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/10/2014] [Indexed: 01/02/2023] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
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87
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Mascher M, Jost M, Kuon JE, Himmelbach A, Aßfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol 2014. [PMID: 24917130 DOI: 10.1186/gb‐2014‐15‐6‐r78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
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88
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Davis EE, Frangakis S, Katsanis N. Interpreting human genetic variation with in vivo zebrafish assays. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1960-1970. [PMID: 24887202 DOI: 10.1016/j.bbadis.2014.05.024] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/14/2014] [Accepted: 05/24/2014] [Indexed: 12/15/2022]
Abstract
Rapid advances and cost erosion in exome and genome analysis of patients with both rare and common genetic disorders have accelerated gene discovery and illuminated fundamental biological mechanisms. The thrill of discovery has been accompanied, however, with the sobering appreciation that human genomes are burdened with a large number of rare and ultra rare variants, thereby posing a significant challenge in dissecting both the effect of such alleles on protein function and also the biological relevance of these events to patient pathology. In an effort to develop model systems that are able to generate surrogates of human pathologies, a powerful suite of tools have been developed in zebrafish, taking advantage of the relatively small (compared to invertebrate models) evolutionary distance of that genome to humans, the orthology of several organs and signaling processes, and the suitability of this organism for medium and high throughput phenotypic screening. Here we will review the use of this model organism in dissecting human genetic disorders; we will highlight how diverse strategies have informed disease causality and genetic architecture; and we will discuss relative strengths and limitations of these approaches in the context of medical genome sequencing. This article is part of a Special Issue entitled: From Genome to Function.
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Affiliation(s)
- Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27710, USA.
| | - Stephan Frangakis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27710, USA.
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89
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O'Rourke JA, Bolon YT, Bucciarelli B, Vance CP. Legume genomics: understanding biology through DNA and RNA sequencing. ANNALS OF BOTANY 2014; 113:1107-20. [PMID: 24769535 PMCID: PMC4030821 DOI: 10.1093/aob/mcu072] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 03/13/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The legume family (Leguminosae) consists of approx. 17 000 species. A few of these species, including, but not limited to, Phaseolus vulgaris, Cicer arietinum and Cajanus cajan, are important dietary components, providing protein for approx. 300 million people worldwide. Additional species, including soybean (Glycine max) and alfalfa (Medicago sativa), are important crops utilized mainly in animal feed. In addition, legumes are important contributors to biological nitrogen, forming symbiotic relationships with rhizobia to fix atmospheric N2 and providing up to 30 % of available nitrogen for the next season of crops. The application of high-throughput genomic technologies including genome sequencing projects, genome re-sequencing (DNA-seq) and transcriptome sequencing (RNA-seq) by the legume research community has provided major insights into genome evolution, genomic architecture and domestication. SCOPE AND CONCLUSIONS This review presents an overview of the current state of legume genomics and explores the role that next-generation sequencing technologies play in advancing legume genomics. The adoption of next-generation sequencing and implementation of associated bioinformatic tools has allowed researchers to turn each species of interest into their own model organism. To illustrate the power of next-generation sequencing, an in-depth overview of the transcriptomes of both soybean and white lupin (Lupinus albus) is provided. The soybean transcriptome focuses on analysing seed development in two near-isogenic lines, examining the role of transporters, oil biosynthesis and nitrogen utilization. The white lupin transcriptome analysis examines how phosphate deficiency alters gene expression patterns, inducing the formation of cluster roots. Such studies illustrate the power of next-generation sequencing and bioinformatic analyses in elucidating the gene networks underlying biological processes.
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Affiliation(s)
- Jamie A O'Rourke
- United States Department of Agriculture, Agricultural Research Service, University of Minnesota, St. Paul, MN 55108, USA Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Yung-Tsi Bolon
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Bruna Bucciarelli
- United States Department of Agriculture, Agricultural Research Service, University of Minnesota, St. Paul, MN 55108, USA Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Carroll P Vance
- United States Department of Agriculture, Agricultural Research Service, University of Minnesota, St. Paul, MN 55108, USA Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
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90
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Pathak N, Austin-Tse CA, Liu Y, Vasilyev A, Drummond IA. Cytoplasmic carboxypeptidase 5 regulates tubulin glutamylation and zebrafish cilia formation and function. Mol Biol Cell 2014; 25:1836-44. [PMID: 24743595 PMCID: PMC4055263 DOI: 10.1091/mbc.e13-01-0033] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Glutamylation is a functionally important tubulin posttranslational modification enriched on stable microtubules of neuronal axons, mitotic spindles, centrioles, and cilia. In vertebrates, balanced activities of tubulin glutamyl ligase and cytoplasmic carboxypeptidase deglutamylase enzymes maintain organelle- and cell type-specific tubulin glutamylation patterns. Tubulin glutamylation in cilia is regulated via restricted subcellular localization or expression of tubulin glutamyl ligases (ttlls) and nonenzymatic proteins, including the zebrafish TPR repeat protein Fleer/Ift70. Here we analyze the expression patterns of ccp deglutamylase genes during zebrafish development and the effects of ccp gene knockdown on cilia formation, morphology, and tubulin glutamylation. The deglutamylases ccp2, ccp5, and ccp6 are expressed in ciliated cells, whereas ccp1 expression is restricted to the nervous system. Only ccp5 knockdown increases cilia tubulin glutamylation, induces ciliopathy phenotypes, including axis curvature, hydrocephalus, and pronephric cysts, and disrupts multicilia motility, suggesting that Ccp5 is the principal tubulin deglutamylase that maintains functional levels of cilia tubulin glutamylation. The ability of ccp5 knockdown to restore cilia tubulin glutamylation in fleer/ift70 mutants and rescue pronephric multicilia formation in both fleer- and ift88-deficient zebrafish indicates that tubulin glutamylation is a key driver of ciliogenesis.
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Affiliation(s)
- Narendra Pathak
- Nephrology Division, Massachusetts General Hospital, Charlestown, MA 02129
| | | | - Yan Liu
- Nephrology Division, Massachusetts General Hospital, Charlestown, MA 02129
| | - Aleksandr Vasilyev
- Department of Pathology, Massachusetts General Hospital, Charlestown, MA 02129
| | - Iain A Drummond
- Nephrology Division, Massachusetts General Hospital, Charlestown, MA 02129Department of Genetics, Harvard Medical School, Boston, MA 02115
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91
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Duitama J, Sánchez-Rodríguez A, Goovaerts A, Pulido-Tamayo S, Hubmann G, Foulquié-Moreno MR, Thevelein JM, Verstrepen KJ, Marchal K. Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast. BMC Genomics 2014; 15:207. [PMID: 24640961 PMCID: PMC4003806 DOI: 10.1186/1471-2164-15-207] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 03/10/2014] [Indexed: 12/21/2022] Open
Abstract
Background Bulk segregant analysis (BSA) coupled to high throughput sequencing is a powerful method to map genomic regions related with phenotypes of interest. It relies on crossing two parents, one inferior and one superior for a trait of interest. Segregants displaying the trait of the superior parent are pooled, the DNA extracted and sequenced. Genomic regions linked to the trait of interest are identified by searching the pool for overrepresented alleles that normally originate from the superior parent. BSA data analysis is non-trivial due to sequencing, alignment and screening errors. Results To increase the power of the BSA technology and obtain a better distinction between spuriously and truly linked regions, we developed EXPLoRA (EXtraction of over-rePresented aLleles in BSA), an algorithm for BSA data analysis that explicitly models the dependency between neighboring marker sites by exploiting the properties of linkage disequilibrium through a Hidden Markov Model (HMM). Reanalyzing a BSA dataset for high ethanol tolerance in yeast allowed reliably identifying QTLs linked to this phenotype that could not be identified with statistical significance in the original study. Experimental validation of one of the least pronounced linked regions, by identifying its causative gene VPS70, confirmed the potential of our method. Conclusions EXPLoRA has a performance at least as good as the state-of-the-art and it is robust even at low signal to noise ratio’s i.e. when the true linkage signal is diluted by sampling, screening errors or when few segregants are available.
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Affiliation(s)
| | | | | | | | | | | | - Johan M Thevelein
- VIB Laboratory of Systems Biology & Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics, KU Leuven, Gaston Geenslaan 1, Leuven B-3001, Belgium.
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92
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Exploiting the extraordinary genetic polymorphism of ciona for developmental genetics with whole genome sequencing. Genetics 2014; 197:49-59. [PMID: 24532781 DOI: 10.1534/genetics.114.161778] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Studies in tunicates such as Ciona have revealed new insights into the evolutionary origins of chordate development. Ciona populations are characterized by high levels of natural genetic variation, between 1 and 5%. This variation has provided abundant material for forward genetic studies. In the current study, we make use of deep sequencing and homozygosity mapping to map spontaneous mutations in outbred populations. With this method we have mapped two spontaneous developmental mutants. In Ciona intestinalis we mapped a short-tail mutation with strong phenotypic similarity to a previously identified mutant in the related species Ciona savignyi. Our bioinformatic approach mapped the mutation to a narrow interval containing a single mutated gene, α-laminin3,4,5, which is the gene previously implicated in C. savignyi. In addition, we mapped a novel genetic mutation disrupting neural tube closure in C. savignyi to a T-type Ca(2+) channel gene. The high efficiency and unprecedented mapping resolution of our study is a powerful advantage for developmental genetics in Ciona, and may find application in other outbred species.
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93
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Li L, Chen D, Li J, Wang X, Wang N, Xu C, Wang QK. Aggf1 acts at the top of the genetic regulatory hierarchy in specification of hemangioblasts in zebrafish. Blood 2014; 123:501-8. [PMID: 24277077 PMCID: PMC3901065 DOI: 10.1182/blood-2013-07-514612] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 11/17/2013] [Indexed: 11/20/2022] Open
Abstract
The hemangioblast is a multipotential progenitor, which is derived from the mesoderm and can further differentiate into hematopoietic and endothelial lineages. The molecular mechanism governing the specification of hemangioblasts is fundamental to regenerative medicine based on embryonic stem cells for the treatment of various hematologic and vascular diseases. Here we show that aggf1 acts at the top of the genetic regulatory hierarchy in the specification of hemangioblasts in zebrafish. Knockdown of aggf1 expression decreases expression of endothelial cell-specific markers (cdh5, admr) and disrupts primitive hematopoiesis as shown by a decreased number of erythroid cells and reduced expression of gata1 (marker for erythroid progenitors) and pu.1 (myeloid progenitors). Aggf1 knockdown also decreases expression of runx1 and c-myb, indicating that it is required for specification of hematopoietic stem cells (definitive hematopoiesis). Aggf1 knockdown led to dramatically reduced expression of hemangioblast markers fli1, etsrp, lmo2, and scl, and hematopoietic/endothelial defects in aggf1 morphants were rescued by messenger RNA for scl, fli-vp16, or etsrp. Taken together, these data indicate that aggf1 is involved in differentiation of both hematopoietic and endothelial lineages and that aggf1 acts upstream of scl, fli1, and etsrp in specification of hemangioblasts.
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Affiliation(s)
- Lei Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Center for Human Genome Research, Cardio-X Institute, Huazhong University of Science and Technology, Wuhan, People's Republic of China; and
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94
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Ryan S, Willer J, Marjoram L, Bagwell J, Mankiewicz J, Leshchiner I, Goessling W, Bagnat M, Katsanis N. Rapid identification of kidney cyst mutations by whole exome sequencing in zebrafish. Development 2013; 140:4445-51. [PMID: 24130329 DOI: 10.1242/dev.101170] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Forward genetic approaches in zebrafish have provided invaluable information about developmental processes. However, the relative difficulty of mapping and isolating mutations has limited the number of new genetic screens. Recent improvements in the annotation of the zebrafish genome coupled to a reduction in sequencing costs prompted the development of whole genome and RNA sequencing approaches for gene discovery. Here we describe a whole exome sequencing (WES) approach that allows rapid and cost-effective identification of mutations. We used our WES methodology to isolate four mutations that cause kidney cysts; we identified novel alleles in two ciliary genes as well as two novel mutants. The WES approach described here does not require specialized infrastructure or training and is therefore widely accessible. This methodology should thus help facilitate genetic screens and expedite the identification of mutants that can inform basic biological processes and the causality of genetic disorders in humans.
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Affiliation(s)
- Sean Ryan
- Department of Cell Biology, Duke University, 333 B, Nanaline Duke Building, Durham, NC 27710, USA
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95
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Spitsbergen JM, Buhler DR, Peterson TS. Neoplasia and neoplasm-associated lesions in laboratory colonies of zebrafish emphasizing key influences of diet and aquaculture system design. ILAR J 2013; 53:114-25. [PMID: 23382343 DOI: 10.1093/ilar.53.2.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During the past decade, the zebrafish has emerged as a leading model for mechanistic cancer research because of its sophisticated genetic and genomic resources, its tractability for tissue targeting of transgene expression, its efficiency for forward genetic approaches to cancer model development, and its cost effectiveness for enhancer and suppressor screens once a cancer model is established. However, in contrast with other laboratory animal species widely used as cancer models, much basic cancer biology information is lacking in zebrafish. As yet, data are not published regarding dietary influences on neoplasm incidences in zebrafish. Little information is available regarding spontaneous tumor incidences or histologic types in wild-type lines of zebrafish. So far, a comprehensive database documenting the full spectrum of neoplasia in various organ systems and tissues is not available for zebrafish as it is for other intensely studied laboratory animal species. This article confirms that, as in other species, diet and husbandry can profoundly influence tumor incidences and histologic spectra in zebrafish. We show that in many laboratory colonies wild-type lines of zebrafish exhibit elevated neoplasm incidences and neoplasm-associated lesions such as heptocyte megalocytosis. We present experimental evidence showing that certain diet and water management regimens can result in high incidences of neoplasia and neoplasm-associated lesions. We document the wide array of benign and malignant neoplasms affecting nearly every organ, tissue, and cell type in zebrafish, in some cases as a spontaneous aging change, and in other cases due to carcinogen treatment or genetic manipulation.
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Affiliation(s)
- Jan M Spitsbergen
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA.
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96
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Ha S, Stottmann RW, Furley AJ, Beier DR. A forward genetic screen in mice identifies mutants with abnormal cortical patterning. ACTA ACUST UNITED AC 2013; 25:167-79. [PMID: 23968836 DOI: 10.1093/cercor/bht209] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Formation of a 6-layered cortical plate and axon tract patterning are key features of cerebral cortex development. Abnormalities of these processes may be the underlying cause for a range of functional disabilities seen in human neurodevelopmental disorders. To identify mouse mutants with defects in cortical lamination or corticofugal axon guidance, N-ethyl-N-nitrosourea (ENU) mutagenesis was performed using mice expressing LacZ reporter genes in layers II/III and V of the cortex (Rgs4-lacZ) or in corticofugal axons (TAG1-tau-lacZ). Four lines with abnormal cortical lamination have been identified. One of these was a splice site mutation in reelin (Reln) that results in a premature stop codon and the truncation of the C-terminal region (CTR) domain of reelin. Interestingly, this novel allele of Reln did not display cerebellar malformation or ataxia, and this is the first report of a Reln mutant without a cerebellar defect. Four lines with abnormal cortical axon development were also identified, one of which was found by whole-genome resequencing to carry a mutation in Lrp2. These findings demonstrated that the application of ENU mutagenesis to mice carrying transgenic reporters marking cortical anatomy is a sensitive and specific method to identify mutations that disrupt patterning of the developing brain.
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Affiliation(s)
- Seungshin Ha
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Rolf W Stottmann
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Divisions of Human Genetics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA and
| | - Andrew J Furley
- Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - David R Beier
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA 98101, USA
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97
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Gemberling M, Bailey TJ, Hyde DR, Poss KD. The zebrafish as a model for complex tissue regeneration. Trends Genet 2013; 29:611-20. [PMID: 23927865 DOI: 10.1016/j.tig.2013.07.003] [Citation(s) in RCA: 366] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/21/2013] [Accepted: 07/08/2013] [Indexed: 12/22/2022]
Abstract
For centuries, philosophers and scientists have been fascinated by the principles and implications of regeneration in lower vertebrate species. Two features have made zebrafish an informative model system for determining mechanisms of regenerative events. First, they are highly regenerative, able to regrow amputated fins, as well as a lesioned brain, retina, spinal cord, heart, and other tissues. Second, they are amenable to both forward and reverse genetic approaches, with a research toolset regularly updated by an expanding community of zebrafish researchers. Zebrafish studies have helped identify new mechanistic underpinnings of regeneration in multiple tissues and, in some cases, have served as a guide for contemplating regenerative strategies in mammals. Here, we review the recent history of zebrafish as a genetic model system for understanding how and why tissue regeneration occurs.
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Affiliation(s)
- Matthew Gemberling
- Department of Cell Biology and Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
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98
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Henke K, Bowen ME, Harris MP. Perspectives for identification of mutations in the zebrafish: Making use of next-generation sequencing technologies for forward genetic approaches. Methods 2013; 62:185-96. [DOI: 10.1016/j.ymeth.2013.05.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 05/21/2013] [Accepted: 05/22/2013] [Indexed: 01/13/2023] Open
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99
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James GV, Patel V, Nordström KJV, Klasen JR, Salomé PA, Weigel D, Schneeberger K. User guide for mapping-by-sequencing in Arabidopsis. Genome Biol 2013; 14:R61. [PMID: 23773572 PMCID: PMC3706810 DOI: 10.1186/gb-2013-14-6-r61] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/17/2013] [Indexed: 12/27/2022] Open
Abstract
Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.
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100
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Miller AC, Obholzer ND, Shah AN, Megason SG, Moens CB. RNA-seq-based mapping and candidate identification of mutations from forward genetic screens. Genome Res 2013; 23:679-86. [PMID: 23299976 PMCID: PMC3613584 DOI: 10.1101/gr.147322.112] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 12/18/2012] [Indexed: 11/24/2022]
Abstract
Forward genetic screens have elucidated molecular pathways required for innumerable aspects of life; however, identifying the causal mutations from such screens has long been the bottleneck in the process, particularly in vertebrates. We have developed an RNA-seq-based approach that identifies both the region of the genome linked to a mutation and candidate lesions that may be causal for the phenotype of interest. We show that our method successfully identifies zebrafish mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Furthermore, we develop an easily accessible bioinformatics pipeline allowing for implementation of all steps of the method. Overall, we show that RNA-seq is a fast, reliable, and cost-effective method to map and identify mutations that will greatly facilitate the power of forward genetics in vertebrate models.
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Affiliation(s)
- Adam C. Miller
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Nikolaus D. Obholzer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Arish N. Shah
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Sean G. Megason
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Cecilia B. Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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