1001
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Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown C, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res 2018; 46:D718-D725. [PMID: 29149270 PMCID: PMC5753386 DOI: 10.1093/nar/gkx1108] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/22/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
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Affiliation(s)
| | | | | | - Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Emmanuel Faure
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
- Team VORTEX, Institut de Recherche en Informatique de Toulouse, Universities Toulouse I and III, CNRS, INPT, ENSEEIHT; 2 rue Camichel, BP 7122, F-31071 Toulouse Cedex 7, France
| | | | - Alexandra Louis
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Kazuhiro R Nitta
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Jacques Piette
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, Kansas
| | | | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Renaud Vincentelli
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Sameh Ben Aicha
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | | | | | - Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Edwin Jacox
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
| | - Mickael Mendez
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rui Yokomori
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - C Titus Brown
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Christian Cambillau
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Lionel Christiaen
- New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, NY10003, USA
| | - Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Emmanuel Douzery
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Takehiro Kusakabe
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Kenta Nakai
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Billie Swalla
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, Montpellier, France
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
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1002
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Ifuku M, Iwabuchi KA, Tanaka M, Lung MSY, Hotta A. Restoration of Dystrophin Protein Expression by Exon Skipping Utilizing CRISPR-Cas9 in Myoblasts Derived from DMD Patient iPS Cells. Methods Mol Biol 2018; 1828:191-217. [PMID: 30171543 DOI: 10.1007/978-1-4939-8651-4_12] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a congenital X-linked disease caused by mutations in the gene encoding the dystrophin protein, which is required for myofiber integrity. Exon skipping therapy is an emerging strategy for restoring the open reading frame of the dystrophin gene to produce functional protein in DMD patients by skipping single or multiple exons. Although antisense oligonucleotides are able to target pre-mRNA for exon skipping, their half-lives are short and any therapeutic benefit is transient. In contrast, genome editing by DNA nucleases, such as the CRISPR-Cas9 system, could offer permanent correction by targeting genomic DNA. Our laboratory previously reported that disrupting the splicing acceptor site in exon 45 by plasmid delivery of the CRISPR-Cas9 system in iPS cells, derived from a DMD patient lacking exon 44, successfully restored dystrophin protein expression in differentiated myoblasts. Herein, we describe an optimized methodology to prepare myoblasts differentiated from iPS cells by mRNA transfection of the CRISPR-Cas9 system to skip exon 45 in myoblasts, and evaluate the restored dystrophin by RT-PCR and Western blotting.
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Affiliation(s)
- Masataka Ifuku
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kumiko A Iwabuchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Masami Tanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Mandy Siu Yu Lung
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
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1003
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Gandhi S, Razy-Krajka F, Christiaen L, Stolfi A. CRISPR Knockouts in Ciona Embryos. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1029:141-152. [PMID: 29542087 PMCID: PMC6061950 DOI: 10.1007/978-981-10-7545-2_13] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 has emerged as a revolutionary tool for fast and efficient targeted gene knockouts and genome editing in almost any organism. The laboratory model tunicate Ciona is no exception. Here, we describe our latest protocol for the design, implementation, and evaluation of successful CRISPR/Cas9-mediated gene knockouts in somatic cells of electroporated Ciona embryos. Using commercially available reagents, publicly accessible plasmids, and free web-based software applications, any Ciona researcher can easily knock out any gene of interest in their favorite embryonic cell lineage.
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Affiliation(s)
- Shashank Gandhi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Florian Razy-Krajka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lionel Christiaen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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1004
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Bier E, Harrison MM, O'Connor-Giles KM, Wildonger J. Advances in Engineering the Fly Genome with the CRISPR-Cas System. Genetics 2018; 208:1-18. [PMID: 29301946 PMCID: PMC5753851 DOI: 10.1534/genetics.117.1113] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/08/2017] [Indexed: 12/26/2022] Open
Abstract
Drosophila has long been a premier model for the development and application of cutting-edge genetic approaches. The CRISPR-Cas system now adds the ability to manipulate the genome with ease and precision, providing a rich toolbox to interrogate relationships between genotype and phenotype, to delineate and visualize how the genome is organized, to illuminate and manipulate RNA, and to pioneer new gene drive technologies. Myriad transformative approaches have already originated from the CRISPR-Cas system, which will likely continue to spark the creation of tools with diverse applications. Here, we provide an overview of how CRISPR-Cas gene editing has revolutionized genetic analysis in Drosophila and highlight key areas for future advances.
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Affiliation(s)
- Ethan Bier
- Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093-0349
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Kate M O'Connor-Giles
- Laboratory of Genetics and Laboratory of Cell and Molecular Biology, Wisconsin 53706
| | - Jill Wildonger
- Biochemistry Department, University of Wisconsin-Madison, Wisconsin 53706
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1005
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Markossian S, Guyot R, Richard S, Teixeira M, Aguilera N, Bouchet M, Plateroti M, Guan W, Gauthier K, Aubert D, Flamant F. CRISPR/Cas9 Editing of the Mouse Thra Gene Produces Models with Variable Resistance to Thyroid Hormone. Thyroid 2018; 28:139-150. [PMID: 29205102 DOI: 10.1089/thy.2017.0389] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Resistance to thyroid hormone due to THRA mutations (RTHα) is a recently discovered genetic disease, displaying important variability in its clinical presentation. The mutations alter the function of TRα1, one of the two nuclear receptors for thyroid hormone. METHODS The aim of this study was to understand the relationship between specific THRA mutations and phenotype. CRISPR/Cas9 genome editing was used to generate five new mouse models of RTHα, with frameshift or missense mutations. RESULTS Like human patients, mutant mice displayed a hypothyroid-like phenotype, with altered development. Phenotype severity varied between the different mouse models, mainly depending on the ability of the mutant receptor to interact with transcription corepressor in the presence of thyroid hormone. CONCLUSION The present mutant mice represent highly relevant models for the human genetic disease which will be useful for future investigations.
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Affiliation(s)
- Suzy Markossian
- 1 Institut de Génomique Fonctionnelle de Lyon, Université de Lyon CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon , Lyon, France
| | - Romain Guyot
- 1 Institut de Génomique Fonctionnelle de Lyon, Université de Lyon CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon , Lyon, France
| | - Sabine Richard
- 1 Institut de Génomique Fonctionnelle de Lyon, Université de Lyon CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon , Lyon, France
| | - Marie Teixeira
- 2 Plateau de Biologie Expérimentale de la Souris SFR Biosciences, Ecole Normale Supérieure de Lyon , Lyon, France
| | - Nadine Aguilera
- 2 Plateau de Biologie Expérimentale de la Souris SFR Biosciences, Ecole Normale Supérieure de Lyon , Lyon, France
| | - Mathilde Bouchet
- 1 Institut de Génomique Fonctionnelle de Lyon, Université de Lyon CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon , Lyon, France
| | | | - Wenyue Guan
- 1 Institut de Génomique Fonctionnelle de Lyon, Université de Lyon CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon , Lyon, France
| | - Karine Gauthier
- 1 Institut de Génomique Fonctionnelle de Lyon, Université de Lyon CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon , Lyon, France
| | - Denise Aubert
- 1 Institut de Génomique Fonctionnelle de Lyon, Université de Lyon CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon , Lyon, France
| | - Frédéric Flamant
- 1 Institut de Génomique Fonctionnelle de Lyon, Université de Lyon CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon , Lyon, France
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1006
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Naert T, Vleminckx K. Methods for CRISPR/Cas9 Xenopus tropicalis Tissue-Specific Multiplex Genome Engineering. Methods Mol Biol 2018; 1865:33-54. [PMID: 30151757 DOI: 10.1007/978-1-4939-8784-9_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this chapter, we convey a state-of-the art update to the 2014 Nakayama protocol for CRISPR/Cas9 genome engineering in Xenopus tropicalis (X. tropicalis). We discuss in depth, gRNA design software and rules, gRNA synthesis, and procedures for tissue- and tissue-specific CRISPR/Cas9 genome editing by targeted microinjection in X. tropicalis embryos. We demonstrate the methodology by which any standard equipped Xenopus researcher with microinjection experience can generate F0 CRISPR/Cas9 mediated mosaic mutants (crispants) within one to two work-week(s). The described methodology allows CRISPR/Cas9 efficiencies to be high enough to read out phenotypic consequences, and thus perform gene function analysis, in the F0 crispant. Additionally, we provide the framework for performing multiplex tissue-specific CRISPR/Cas9 experiments generating crispants mosaic mutant in up to four genes simultaneously, which can be of importance for Laevis researchers aiming to target by CRISPR/Cas9 both the S and L homeolog of a gene simultaneously. Finally, we discuss off-target concerns, how to minimize these and ways to rapidly bypass reviewer off-target critique by exploiting the advantages of X. tropicalis.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
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1007
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Lessard S, Francioli L, Alfoldi J, Tardif JC, Ellinor PT, MacArthur DG, Lettre G, Orkin SH, Canver MC. Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci. Proc Natl Acad Sci U S A 2017; 114:E11257-E11266. [PMID: 29229813 PMCID: PMC5748207 DOI: 10.1073/pnas.1714640114] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The CRISPR-Cas9 nuclease system holds enormous potential for therapeutic genome editing of a wide spectrum of diseases. Large efforts have been made to further understanding of on- and off-target activity to assist the design of CRISPR-based therapies with optimized efficacy and safety. However, current efforts have largely focused on the reference genome or the genome of cell lines to evaluate guide RNA (gRNA) efficiency, safety, and toxicity. Here, we examine the effect of human genetic variation on both on- and off-target specificity. Specifically, we utilize 7,444 whole-genome sequences to examine the effect of variants on the targeting specificity of ∼3,000 gRNAs across 30 therapeutically implicated loci. We demonstrate that human genetic variation can alter the off-target landscape genome-wide including creating and destroying protospacer adjacent motifs (PAMs). Furthermore, single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) can result in altered on-target sites and novel potent off-target sites, which can predispose patients to treatment failure and adverse effects, respectively; however, these events are rare. Taken together, these data highlight the importance of considering individual genomes for therapeutic genome-editing applications for the design and evaluation of CRISPR-based therapies to minimize risk of treatment failure and/or adverse outcomes.
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Affiliation(s)
- Samuel Lessard
- Research Center, Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Laurent Francioli
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Jessica Alfoldi
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Jean-Claude Tardif
- Research Center, Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Guillaume Lettre
- Research Center, Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115;
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Boston, MA 02115
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115;
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
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1008
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Moreb EA, Hoover B, Yaseen A, Valyasevi N, Roecker Z, Menacho-Melgar R, Lynch MD. Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity. ACS Synth Biol 2017; 6:2209-2218. [PMID: 28915012 DOI: 10.1021/acssynbio.7b00174] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes, and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well as mutation rates through induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants. We report an approach to inhibiting the SOS response and RecA activity through the expression of a mutant dominant negative form of RecA, which incorporates into wild type RecA filaments and inhibits activity. Using a plasmid-based system in which Cas9 and recA mutants are coexpressed, we can achieve increased efficiency and consistency of CRISPR-Cas9-mediated selection and recombineering in E. coli, while reducing the induction of the SOS response. To date, this approach has been shown to be independent of recA genotype and host strain lineage. Using this system, we demonstrate increased CRISPR-Cas selection efficacy with over 10 000 guides covering the E. coli chromosome. The use of dominant negative RecA or homologues may be of broad use in bacterial CRISPR-Cas-based genome editing where the SOS pathways are present.
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Affiliation(s)
- Eirik Adim Moreb
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Benjamin Hoover
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Adam Yaseen
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Nisakorn Valyasevi
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Zoe Roecker
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Romel Menacho-Melgar
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Michael D. Lynch
- Department of Biomedical
Engineering, Duke University, Durham, North Carolina 27708, United States
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1009
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Yu R, Longo J, van Leeuwen JE, Mullen PJ, Ba-Alawi W, Haibe-Kains B, Penn LZ. Statin-Induced Cancer Cell Death Can Be Mechanistically Uncoupled from Prenylation of RAS Family Proteins. Cancer Res 2017; 78:1347-1357. [PMID: 29229608 DOI: 10.1158/0008-5472.can-17-1231] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 10/04/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022]
Abstract
The statin family of drugs preferentially triggers tumor cell apoptosis by depleting mevalonate pathway metabolites farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP), which are used for protein prenylation, including the oncoproteins of the RAS superfamily. However, accumulating data indicate that activation of the RAS superfamily are poor biomarkers of statin sensitivity, and the mechanism of statin-induced tumor-specific apoptosis remains unclear. Here we demonstrate that cancer cell death triggered by statins can be uncoupled from prenylation of the RAS superfamily of oncoproteins. Ectopic expression of different members of the RAS superfamily did not uniformly sensitize cells to fluvastatin, indicating that increased cellular demand for protein prenylation cannot explain increased statin sensitivity. Although ectopic expression of HRAS increased statin sensitivity, expression of myristoylated HRAS did not rescue this effect. HRAS-induced epithelial-to-mesenchymal transition (EMT) through activation of zinc finger E-box binding homeobox 1 (ZEB1) sensitized tumor cells to the antiproliferative activity of statins, and induction of EMT by ZEB1 was sufficient to phenocopy the increase in fluvastatin sensitivity; knocking out ZEB1 reversed this effect. Publicly available gene expression and statin sensitivity data indicated that enrichment of EMT features was associated with increased sensitivity to statins in a large panel of cancer cell lines across multiple cancer types. These results indicate that the anticancer effect of statins is independent from prenylation of RAS family proteins and is associated with a cancer cell EMT phenotype.Significance: The use of statins to target cancer cell EMT may be useful as a therapy to block cancer progression. Cancer Res; 78(5); 1347-57. ©2017 AACR.
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Affiliation(s)
- Rosemary Yu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Joseph Longo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jenna E van Leeuwen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Peter J Mullen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wail Ba-Alawi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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1010
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Abstract
Exciting new technologies are often self-limiting in their rollout, as access to state-of-the-art instrumentation or the need for years of hands-on experience, for better or worse, ensures slow adoption by the community. CRISPR technology, however, presents the opposite dilemma, where the simplicity of the system enabled the parallel development of many applications, improvements and derivatives, and new users are now presented with an almost paralyzing abundance of choices. This Review intends to guide users through the process of applying CRISPR technology to their biological problems of interest, especially in the context of discovering gene function at scale.
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Affiliation(s)
- John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA
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1011
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Engelholm LH, Riaz A, Serra D, Dagnæs-Hansen F, Johansen JV, Santoni-Rugiu E, Hansen SH, Niola F, Frödin M. CRISPR/Cas9 Engineering of Adult Mouse Liver Demonstrates That the Dnajb1-Prkaca Gene Fusion Is Sufficient to Induce Tumors Resembling Fibrolamellar Hepatocellular Carcinoma. Gastroenterology 2017; 153:1662-1673.e10. [PMID: 28923495 PMCID: PMC5801691 DOI: 10.1053/j.gastro.2017.09.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/05/2017] [Accepted: 09/09/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS Fibrolamellar hepatocellular carcinoma (FL-HCC) is a primary liver cancer that predominantly affects children and young adults with no underlying liver disease. A somatic, 400 Kb deletion on chromosome 19 that fuses part of the DnaJ heat shock protein family (Hsp40) member B1 gene (DNAJB1) to the protein kinase cAMP-activated catalytic subunit alpha gene (PRKACA) has been repeatedly identified in patients with FL-HCC. However, the DNAJB1-PRKACA gene fusion has not been shown to induce liver tumorigenesis. We used the CRISPR/Cas9 technique to delete in mice the syntenic region on chromosome 8 to create a Dnajb1-Prkaca fusion and monitored the mice for liver tumor development. METHODS We delivered CRISPR/Cas9 vectors designed to juxtapose exon 1 of Dnajb1 with exon 2 of Prkaca to create the Dnajb1-Prkaca gene fusion associated with FL-HCC, or control Cas9 vector, via hydrodynamic tail vein injection to livers of 8-week-old female FVB/N mice. These mice did not have any other engineered genetic alterations and were not exposed to liver toxins or carcinogens. Liver tissues were collected 14 months after delivery; genomic DNA was analyzed by PCR to detect the Dnajb1-Prkaca fusion, and tissues were characterized by histology, immunohistochemistry, RNA sequencing, and whole-exome sequencing. RESULTS Livers from 12 of the 15 mice given the vectors to induce the Dnajb1-Prkaca gene fusion, but none of the 11 mice given the control vector, developed neoplasms. The tumors contained the Dnajb1-Prkaca gene fusion and had histologic and cytologic features of human FL-HCCs: large polygonal cells with granular, eosinophilic, and mitochondria-rich cytoplasm, prominent nucleoli, and markers of hepatocytes and cholangiocytes. In comparing expression levels of genes between the mouse tumor and non-tumor liver cells, we identified changes similar to those detected in human FL-HCC, which included genes that affect cell cycle and mitosis regulation. Genomic analysis of mouse neoplasms induced by the Dnajb1-Prkaca fusion revealed a lack of mutations in genes commonly associated with liver cancers, as observed in human FL-HCC. CONCLUSIONS Using CRISPR/Cas9 technology, we found generation of the Dnajb1-Prkaca fusion gene in wild-type mice to be sufficient to initiate formation of tumors that have many features of human FL-HCC. Strategies to block DNAJB1-PRKACA might be developed as therapeutics for this form of liver cancer.
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Affiliation(s)
- Lars H Engelholm
- Finsen Laboratory, Rigshospitalet, Copenhagen Biocenter, Copenhagen, Denmark,Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anjum Riaz
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Denise Serra
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Jens V Johansen
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Steen H Hansen
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark,GI Cell Biology Research Laboratory, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Francesco Niola
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Morten Frödin
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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1012
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The Conspicuity of CRISPR-Cpf1 System as a Significant Breakthrough in Genome Editing. Curr Microbiol 2017; 75:107-115. [DOI: 10.1007/s00284-017-1406-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/23/2017] [Indexed: 12/20/2022]
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1013
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Zhou H, Zhou M, Li D, Manthey J, Lioutikova E, Wang H, Zeng X. Whole genome analysis of CRISPR Cas9 sgRNA off-target homologies via an efficient computational algorithm. BMC Genomics 2017; 18:826. [PMID: 29219081 PMCID: PMC5773898 DOI: 10.1186/s12864-017-4225-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA, single guide RNA (sgRNA), to cleave double stranded DNA, allowing the introduction of wanted mutations. Unfortunately, it has been reported repeatedly that the sgRNA can also guide Cas9 to off-target sites where the DNA sequence is homologous to sgRNA. RESULTS Using human genome and Streptococcus pyogenes Cas9 (SpCas9) as an example, this article mathematically analyzed the probabilities of off-target homologies of sgRNAs and discovered that for large genome size such as human genome, potential off-target homologies are inevitable for sgRNA selection. A highly efficient computationl algorithm was developed for whole genome sgRNA design and off-target homology searches. By means of a dynamically constructed sequence-indexed database and a simplified sequence alignment method, this algorithm achieves very high efficiency while guaranteeing the identification of all existing potential off-target homologies. Via this algorithm, 1,876,775 sgRNAs were designed for the 19,153 human mRNA genes and only two sgRNAs were found to be free of off-target homology. CONCLUSIONS By means of the novel and efficient sgRNA homology search algorithm introduced in this article, genome wide sgRNA design and off-target analysis were conducted and the results confirmed the mathematical analysis that for a sgRNA sequence, it is almost impossible to escape potential off-target homologies. Future innovations on the CRISPR Cas9 gene editing technology need to focus on how to eliminate the Cas9 off-target activity.
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Affiliation(s)
- Hong Zhou
- Department of Mathematical Science, University of Saint Joseph, 1678 Asylum Avenue, West Hartford, CT 06117 USA
| | - Michael Zhou
- Hall High School, 975 N Main Street, West Hartford, CT 06117 USA
| | - Daisy Li
- Hall High School, 975 N Main Street, West Hartford, CT 06117 USA
| | - Joseph Manthey
- Department of Mathematical Science, University of Saint Joseph, 1678 Asylum Avenue, West Hartford, CT 06117 USA
| | - Ekaterina Lioutikova
- Department of Mathematical Science, University of Saint Joseph, 1678 Asylum Avenue, West Hartford, CT 06117 USA
| | - Hong Wang
- Susan L. Cullman Laboratory for Cancer Research, Department of Chemical Biology and Centre for Cancer Prevention Research, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 164 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Xiao Zeng
- PBSG, LLC, P. O. Box 771, Braddock Heights, MD 21714 USA
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1014
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Killian T, Dickopf S, Haas AK, Kirstenpfad C, Mayer K, Brinkmann U. Disruption of diphthamide synthesis genes and resulting toxin resistance as a robust technology for quantifying and optimizing CRISPR/Cas9-mediated gene editing. Sci Rep 2017; 7:15480. [PMID: 29133816 PMCID: PMC5684134 DOI: 10.1038/s41598-017-15206-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 10/24/2017] [Indexed: 12/26/2022] Open
Abstract
We have devised an effective and robust method for the characterization of gene-editing events. The efficacy of editing-mediated mono- and bi-allelic gene inactivation and integration events is quantified based on colony counts. The combination of diphtheria toxin (DT) and puromycin (PM) selection enables analyses of 10,000-100,000 individual cells, assessing hundreds of clones with inactivated genes per experiment. Mono- and bi-allelic gene inactivation is differentiated by DT resistance, which occurs only upon bi-allelic inactivation. PM resistance indicates integration. The robustness and generalizability of the method were demonstrated by quantifying the frequency of gene inactivation and cassette integration under different editing approaches: CRISPR/Cas9-mediated complete inactivation was ~30-50-fold more frequent than cassette integration. Mono-allelic inactivation without integration occurred >100-fold more frequently than integration. Assessment of gRNA length confirmed 20mers to be most effective length for inactivation, while 16-18mers provided the highest overall integration efficacy. The overall efficacy was ~2-fold higher for CRISPR/Cas9 than for zinc-finger nuclease and was significantly increased upon modulation of non-homologous end joining or homology-directed repair. The frequencies and ratios of editing events were similar for two different DPH genes (independent of the target sequence or chromosomal location), which indicates that the optimization parameters identified with this method can be generalized.
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Affiliation(s)
- Tobias Killian
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Steffen Dickopf
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Alexander K Haas
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Claudia Kirstenpfad
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Therapeutic Modalities - Large Molecule Research, Roche Innovation Center Munich, Nonnenwald 2, D-82372, Penzberg, Germany.
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1015
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Yang J, Meng X, Pan J, Jiang N, Zhou C, Wu Z, Gong Z. CRISPR/Cas9-mediated noncoding RNA editing in human cancers. RNA Biol 2017; 15:35-43. [PMID: 29028415 DOI: 10.1080/15476286.2017.1391443] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cancer is characterized by multiple genetic and epigenetic alterations, including a higher prevalence of mutations of oncogenes and/or tumor suppressors. Mounting evidences have shown that noncoding RNAs (ncRNAs) are involved in the epigenetic regulation of cancer genes and their associated pathways. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system, a revolutionary genome-editing technology, has shed light on ncRNA-based cancer therapy. Here, we briefly introduce the classifications and mechanisms of CRISPR/Cas9 system. Importantly, we mainly focused on the applications of CRISPR/Cas9 system as a molecular tool for ncRNA (microRNA, long noncoding RNA and circular RNA, etc.) editing in human cancers, and the novel techniques that are based on CRISPR/Cas9 system. Additionally, the off-target effects and the corresponding solutions as well as the challenges toward CRISPR/Cas9 were also evaluated and discussed. Long- and short-ncRNAs have been employed as targets in precision oncology, and CRISPR/Cas9-mediated ncRNA editing may provide an excellent way to cure cancer.
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Affiliation(s)
- Jie Yang
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Xiaodan Meng
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Jinchang Pan
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Nan Jiang
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Chengwei Zhou
- c Department of Thoracic Surgery , The Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Zhenhua Wu
- d Department of Otolaryngology Head and Neck Surgery , The Affiliated Ningbo Medical Center Lihuili Eastern Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Zhaohui Gong
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
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1016
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Highly Efficient, Rapid and Co-CRISPR-Independent Genome Editing in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2017; 7:3693-3698. [PMID: 28893845 PMCID: PMC5677160 DOI: 10.1534/g3.117.300216] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We describe a rapid and highly efficient method to generate point mutations in Caenorhabditis elegans using direct injection of CRISPR-Cas9 ribonucleoproteins. This versatile method does not require sensitized genetic backgrounds or co-CRISPR selection-based methods, and represents a single strategy that can be used for creating genomic point mutations, regardless of location. As proof of principle, we show that knock-in mutants more faithfully report variant-associated phenotypes as compared to transgenic overexpression. Data for nine knock-in mutants across five genes are presented that demonstrate high editing efficiencies (60%), a reduced screening workload (24 F1 progeny), and a rapid timescale (4–5 d). This optimized method simplifies genome engineering and is readily adaptable to other model systems.
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1017
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PAXX and Xlf interplay revealed by impaired CNS development and immunodeficiency of double KO mice. Cell Death Differ 2017; 25:444-452. [PMID: 29077092 DOI: 10.1038/cdd.2017.184] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 12/26/2022] Open
Abstract
The repair of DNA double-stranded breaks (DNAdsb) through non-homologous end joining (NHEJ) is a prerequisite for the proper development of the central nervous system and the adaptive immune system. Yet, mice with Xlf or PAXX loss of function are viable and present with very mild immune phenotypes, although their lymphoid cells are sensitive to ionizing radiation attesting for the role of these factors in NHEJ. In contrast, we show here that mice defective for both Xlf and PAXX are embryonically lethal owing to a massive apoptosis of post-mitotic neurons, a situation reminiscent to XRCC4 or DNA Ligase IV KO conditions. The development of the adaptive immune system in Xlf-/-PAXX-/- E18.5 embryos is severely affected with the block of B- and T-cell maturation at the stage of IgH and TCRβ gene rearrangements, respectively. This damaging phenotype highlights the functional nexus between Xlf and PAXX, which is critical for the completion of NHEJ-dependent mechanisms during mouse development.
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1018
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Abadi S, Yan WX, Amar D, Mayrose I. A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. PLoS Comput Biol 2017; 13:e1005807. [PMID: 29036168 PMCID: PMC5658169 DOI: 10.1371/journal.pcbi.1005807] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/26/2017] [Accepted: 10/02/2017] [Indexed: 12/21/2022] Open
Abstract
The adaptation of the CRISPR-Cas9 system as a genome editing technique has generated much excitement in recent years owing to its ability to manipulate targeted genes and genomic regions that are complementary to a programmed single guide RNA (sgRNA). However, the efficacy of a specific sgRNA is not uniquely defined by exact sequence homology to the target site, thus unintended off-targets might additionally be cleaved. Current methods for sgRNA design are mainly concerned with predicting off-targets for a given sgRNA using basic sequence features and employ elementary rules for ranking possible sgRNAs. Here, we introduce CRISTA (CRISPR Target Assessment), a novel algorithm within the machine learning framework that determines the propensity of a genomic site to be cleaved by a given sgRNA. We show that the predictions made with CRISTA are more accurate than other available methodologies. We further demonstrate that the occurrence of bulges is not a rare phenomenon and should be accounted for in the prediction process. Beyond predicting cleavage efficiencies, the learning process provides inferences regarding patterns that underlie the mechanism of action of the CRISPR-Cas9 system. We discover that attributes that describe the spatial structure and rigidity of the entire genomic site as well as those surrounding the PAM region are a major component of the prediction capabilities.
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Affiliation(s)
- Shiran Abadi
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Winston X. Yan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Graduate Program in Biophysics, Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Amar
- Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, United States of America
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
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1019
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Gundry MC, Dever DP, Yudovich D, Bauer DE, Haas S, Wilkinson AC, Singbrant S. Technical considerations for the use of CRISPR/Cas9 in hematology research. Exp Hematol 2017; 54:4-11. [PMID: 28757433 PMCID: PMC5603407 DOI: 10.1016/j.exphem.2017.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 07/19/2017] [Indexed: 11/23/2022]
Abstract
The hematopoietic system is responsible for transporting oxygen and nutrients, fighting infections, and repairing tissue damage. Hematopoietic system dysfunction therefore causes a range of serious health consequences. Lifelong hematopoiesis is maintained by repopulating multipotent hematopoietic stem cells (HSCs) that replenish shorter-lived, mature blood cell types. A prokaryotic mechanism of immunity, the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 nuclease system, has been recently "repurposed" to mutate mammalian genomes efficiently and in a sequence-specific manner. The application of this genome-editing technology to hematology has afforded new approaches for functional genomics and even the prospect of "correcting" dysfunctional HSCs in the treatment of serious genetic hematological diseases. In this Perspective, we provide an overview of three recent CRISPR/Cas9 methods in hematology: gene disruption, gene targeting, and saturating mutagenesis. We also summarize the technical considerations and advice provided during the May 2017 International Society of Experimental Hematology New Investigator Committee webinar on the same topic.
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Affiliation(s)
- Michael C Gundry
- Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA
| | - David Yudovich
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Simon Haas
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine and Division of Stem Cells and Cancer, DKFZ German Cancer Research Centre, Heidelberg, Germany
| | - Adam C Wilkinson
- Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA.
| | - Sofie Singbrant
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden
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1020
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Macias VM, Ohm JR, Rasgon JL. Gene Drive for Mosquito Control: Where Did It Come from and Where Are We Headed? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14091006. [PMID: 28869513 PMCID: PMC5615543 DOI: 10.3390/ijerph14091006] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 02/08/2023]
Abstract
Mosquito-borne pathogens place an enormous burden on human health. The existing toolkit is insufficient to support ongoing vector-control efforts towards meeting disease elimination and eradication goals. The perspective that genetic approaches can potentially add a significant set of tools toward mosquito control is not new, but the recent improvements in site-specific gene editing with CRISPR/Cas9 systems have enhanced our ability to both study mosquito biology using reverse genetics and produce genetics-based tools. Cas9-mediated gene-editing is an efficient and adaptable platform for gene drive strategies, which have advantages over innundative release strategies for introgressing desirable suppression and pathogen-blocking genotypes into wild mosquito populations; until recently, an effective gene drive has been largely out of reach. Many considerations will inform the effective use of new genetic tools, including gene drives. Here we review the lengthy history of genetic advances in mosquito biology and discuss both the impact of efficient site-specific gene editing on vector biology and the resulting potential to deploy new genetic tools for the abatement of mosquito-borne disease.
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Affiliation(s)
- Vanessa M Macias
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Johanna R Ohm
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.
| | - Jason L Rasgon
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA.
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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1021
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Farboud B. Targeted genome editing in Caenorhabditis elegans using CRISPR/Cas9. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28810059 DOI: 10.1002/wdev.287] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/04/2017] [Accepted: 07/05/2017] [Indexed: 12/26/2022]
Abstract
Utilization of programmable nucleases to generate DNA lesions at precise endogenous sequences has transformed the ability to edit genomes from microbes to plants and animals. This is especially true in organisms that previously lacked the means to engineer precise genomic changes, like Caenorhabditis elegans. C. elegans is a 1 mm long free-living, nonparasitic, nematode worm, which is easily cultivated in a laboratory. Its detailed genetic map and relatively compact genome (~100 megabases) helped make it the first metazoan to have its entire genome sequenced. With detailed sequence information came development of numerous molecular tools to dissect gene function. Initially absent from this toolbox, however, were methods to make precise edits at chosen endogenous loci. Adapting site-specific nucleases for use in C. elegans, revolutionized studies of C. elegans biology. Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and then CRISPR-associated protein 9 (Cas9) were used to target specific endogenous DNA sequences to make double-strand DNA breaks (DSBs). Precise changes could be engineered by providing repair templates targeting the DSB in trans. The ease of programming Cas9 to bind and cleave DNA sequences with few limitations has led to its widespread use in C. elegans research and sped the development of strategies to facilitate mutant recovery. Numerous innovative CRISPR/Cas9 methodologies are now primed for use in C. elegans. WIREs Dev Biol 2017, 6:e287. doi: 10.1002/wdev.287 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Behnom Farboud
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
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1022
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Hart T, Tong AHY, Chan K, Van Leeuwen J, Seetharaman A, Aregger M, Chandrashekhar M, Hustedt N, Seth S, Noonan A, Habsid A, Sizova O, Nedyalkova L, Climie R, Tworzyanski L, Lawson K, Sartori MA, Alibeh S, Tieu D, Masud S, Mero P, Weiss A, Brown KR, Usaj M, Billmann M, Rahman M, Constanzo M, Myers CL, Andrews BJ, Boone C, Durocher D, Moffat J. Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens. G3 (BETHESDA, MD.) 2017; 7:2719-2727. [PMID: 28655737 PMCID: PMC5555476 DOI: 10.1534/g3.117.041277] [Citation(s) in RCA: 294] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/12/2017] [Indexed: 12/26/2022]
Abstract
The adaptation of CRISPR/SpCas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs) targeting human protein-coding genes and encoded in viral vectors have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled-library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we reanalyze 17 genome-scale knockout screens in human cell lines from three research groups, using three different genome-scale gRNA libraries. Using the Bayesian Analysis of Gene Essentiality algorithm to identify essential genes, we refine and expand our previously defined set of human core essential genes from 360 to 684 genes. We use this expanded set of reference core essential genes, CEG2, plus empirical data from six CRISPR knockout screens to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We then demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes, as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines.
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Affiliation(s)
- Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | | | - Katie Chan
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | | | - Michael Aregger
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Nicole Hustedt
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - Sahil Seth
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Avery Noonan
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Andrea Habsid
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Olga Sizova
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Ryan Climie
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Keith Lawson
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | | | - Sabriyeh Alibeh
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - David Tieu
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
| | - Sanna Masud
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
| | - Patricia Mero
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mahfuzur Rahman
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | | | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Brenda J Andrews
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Ontario M5S3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G1Z8, Canada
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1023
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Jacobs TB, Zhang N, Patel D, Martin GB. Generation of a Collection of Mutant Tomato Lines Using Pooled CRISPR Libraries. PLANT PHYSIOLOGY 2017; 174. [PMID: 28646085 PMCID: PMC5543939 DOI: 10.1104/pp.17.00489] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The high efficiency of clustered regularly interspaced short palindromic repeats (CRISPR)-mediated mutagenesis in plants enables the development of high-throughput mutagenesis strategies. By transforming pooled CRISPR libraries into tomato (Solanum lycopersicum), collections of mutant lines were generated with minimal transformation attempts and in a relatively short period of time. Identification of the targeted gene(s) was easily determined by sequencing the incorporated guide RNA(s) in the primary transgenic events. From a single transformation with a CRISPR library targeting the immunity-associated leucine-rich repeat subfamily XII genes, heritable mutations were recovered in 15 of the 54 genes targeted. To increase throughput, a second CRISPR library was made containing three guide RNAs per construct to target 18 putative transporter genes. This resulted in stable mutations in 15 of the 18 targeted genes, with some primary transgenic plants having as many as five mutated genes. Furthermore, the redundancy in this collection of plants allowed for the association of aberrant T0 phenotypes with the underlying targeted genes. Plants with mutations in a homolog of an Arabidopsis (Arabidopsis thaliana) boron efflux transporter displayed boron deficiency phenotypes. The strategy described here provides a technically simple yet high-throughput approach for generating a collection of lines with targeted mutations and should be applicable to any plant transformation system.
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Affiliation(s)
- Thomas B Jacobs
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Ning Zhang
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Dhruv Patel
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Gregory B Martin
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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1024
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Jia G, Wang X, Xiao G. A permutation-based non-parametric analysis of CRISPR screen data. BMC Genomics 2017; 18:545. [PMID: 28724352 PMCID: PMC5518132 DOI: 10.1186/s12864-017-3938-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/12/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Clustered regularly-interspaced short palindromic repeats (CRISPR) screens are usually implemented in cultured cells to identify genes with critical functions. Although several methods have been developed or adapted to analyze CRISPR screening data, no single specific algorithm has gained popularity. Thus, rigorous procedures are needed to overcome the shortcomings of existing algorithms. METHODS We developed a Permutation-Based Non-Parametric Analysis (PBNPA) algorithm, which computes p-values at the gene level by permuting sgRNA labels, and thus it avoids restrictive distributional assumptions. Although PBNPA is designed to analyze CRISPR data, it can also be applied to analyze genetic screens implemented with siRNAs or shRNAs and drug screens. RESULTS We compared the performance of PBNPA with competing methods on simulated data as well as on real data. PBNPA outperformed recent methods designed for CRISPR screen analysis, as well as methods used for analyzing other functional genomics screens, in terms of Receiver Operating Characteristics (ROC) curves and False Discovery Rate (FDR) control for simulated data under various settings. Remarkably, the PBNPA algorithm showed better consistency and FDR control on published real data as well. CONCLUSIONS PBNPA yields more consistent and reliable results than its competitors, especially when the data quality is low. R package of PBNPA is available at: https://cran.r-project.org/web/packages/PBNPA/ .
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Affiliation(s)
- Gaoxiang Jia
- Department of Statistical Science, Southern Methodist University, Dallas, TX 75205 USA
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, Dallas, TX 75205 USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
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1025
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Clements TP, Tandon B, Lintel HA, McCarty JH, Wagner DS. RICE CRISPR: Rapidly increased cut ends by an exonuclease Cas9 fusion in zebrafish. Genesis 2017; 55. [PMID: 28653435 DOI: 10.1002/dvg.23044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 11/10/2022]
Abstract
Application of CRISPR-Cas9 technology in diverse organisms has resulted in an explosion of genome modification efforts. To expand the toolbox of applications, we have created an E. coli Exonuclease I (sbcB)-Cas9 fusion that has altered enzymatic activity in zebrafish embryos. This Cas9 variant has increased mutation efficiency and favors longer deletions relative to wild-type Cas9. We anticipate that this variant will allow for more efficient screening for F0 phenotypes and mutation of a larger spectrum of genomic targets including deletion of regulatory regions and creating loss of function mutations in transcription units with poor sequence conservation such as lncRNAs where larger deletions may be required for loss of function.
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Affiliation(s)
| | - Bhavna Tandon
- Department of BioSciences, Rice University, Houston, Texas
| | | | - Joseph H McCarty
- Department of Neurosurgery, University of Texas M. D. Anderson Cancer Center, Houston, Texas
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1026
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Gut P, Reischauer S, Stainier DYR, Arnaout R. LITTLE FISH, BIG DATA: ZEBRAFISH AS A MODEL FOR CARDIOVASCULAR AND METABOLIC DISEASE. Physiol Rev 2017; 97:889-938. [PMID: 28468832 PMCID: PMC5817164 DOI: 10.1152/physrev.00038.2016] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/17/2022] Open
Abstract
The burden of cardiovascular and metabolic diseases worldwide is staggering. The emergence of systems approaches in biology promises new therapies, faster and cheaper diagnostics, and personalized medicine. However, a profound understanding of pathogenic mechanisms at the cellular and molecular levels remains a fundamental requirement for discovery and therapeutics. Animal models of human disease are cornerstones of drug discovery as they allow identification of novel pharmacological targets by linking gene function with pathogenesis. The zebrafish model has been used for decades to study development and pathophysiology. More than ever, the specific strengths of the zebrafish model make it a prime partner in an age of discovery transformed by big-data approaches to genomics and disease. Zebrafish share a largely conserved physiology and anatomy with mammals. They allow a wide range of genetic manipulations, including the latest genome engineering approaches. They can be bred and studied with remarkable speed, enabling a range of large-scale phenotypic screens. Finally, zebrafish demonstrate an impressive regenerative capacity scientists hope to unlock in humans. Here, we provide a comprehensive guide on applications of zebrafish to investigate cardiovascular and metabolic diseases. We delineate advantages and limitations of zebrafish models of human disease and summarize their most significant contributions to understanding disease progression to date.
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Affiliation(s)
- Philipp Gut
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sven Reischauer
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Didier Y R Stainier
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Rima Arnaout
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
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1027
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Wang HX, Li M, Lee CM, Chakraborty S, Kim HW, Bao G, Leong KW. CRISPR/Cas9-Based Genome Editing for Disease Modeling and Therapy: Challenges and Opportunities for Nonviral Delivery. Chem Rev 2017. [PMID: 28640612 DOI: 10.1021/acs.chemrev.6b00799] [Citation(s) in RCA: 361] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Genome editing offers promising solutions to genetic disorders by editing DNA sequences or modulating gene expression. The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) technology can be used to edit single or multiple genes in a wide variety of cell types and organisms in vitro and in vivo. Herein, we review the rapidly developing CRISPR/Cas9-based technologies for disease modeling and gene correction and recent progress toward Cas9/guide RNA (gRNA) delivery based on viral and nonviral vectors. We discuss the relative merits of delivering the genome editing elements in the form of DNA, mRNA, or protein, and the opportunities of combining viral delivery of a transgene encoding Cas9 with nonviral delivery of gRNA. We highlight the lessons learned from nonviral gene delivery in the past three decades and consider their applicability for CRISPR/Cas9 delivery. We also include a discussion of bioinformatics tools for gRNA design and chemical modifications of gRNA. Finally, we consider the extracellular and intracellular barriers to nonviral CRISPR/Cas9 delivery and propose strategies that may overcome these barriers to realize the clinical potential of CRISPR/Cas9-based genome editing.
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Affiliation(s)
- Hong-Xia Wang
- Department of Biomedical Engineering, Columbia University , New York, New York 10027, United States
| | - Mingqiang Li
- Department of Biomedical Engineering, Columbia University , New York, New York 10027, United States
| | - Ciaran M Lee
- Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - Syandan Chakraborty
- Department of Biomedical Engineering, Columbia University , New York, New York 10027, United States
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering (ITREN) and Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University , Cheonan 31116, Korea
| | - Gang Bao
- Department of Bioengineering, Rice University , Houston, Texas 77005, United States
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University , New York, New York 10027, United States
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1028
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Skvarova Kramarzova K, Osborn MJ, Webber BR, DeFeo AP, McElroy AN, Kim CJ, Tolar J. CRISPR/Cas9-Mediated Correction of the FANCD1 Gene in Primary Patient Cells. Int J Mol Sci 2017; 18:ijms18061269. [PMID: 28613254 PMCID: PMC5486091 DOI: 10.3390/ijms18061269] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/02/2017] [Accepted: 06/09/2017] [Indexed: 11/16/2022] Open
Abstract
Fanconi anemia (FA) is an inherited condition characterized by impaired DNA repair, physical anomalies, bone marrow failure, and increased incidence of malignancy. Gene editing holds great potential to precisely correct the underlying genetic cause such that gene expression remains under the endogenous control mechanisms. This has been accomplished to date only in transformed cells or their reprogrammed induced pluripotent stem cell counterparts; however, it has not yet been reported in primary patient cells. Here we show the ability to correct a mutation in Fanconi anemia D1 (FANCD1) primary patient fibroblasts. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system was employed to target and correct a FANCD1 gene deletion. Homologous recombination using an oligonucleotide donor was achieved and a pure population of modified cells was obtained by using inhibitors of poly adenosine diphosphate-ribose polymerase (poly ADP-ribose polymerase). FANCD1 function was restored and we did not observe any promiscuous cutting of the CRISPR/Cas9 at off target sites. This consideration is crucial in the context of the pre-malignant FA phenotype. Altogether we show the ability to correct a patient mutation in primary FANCD1 cells in a precise manner. These proof of principle studies support expanded application of gene editing for FA.
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Affiliation(s)
- Karolina Skvarova Kramarzova
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
- Childhood Leukemia Investigation Prague (CLIP), Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University, Prague 15006, Czech Republic.
| | - Mark J Osborn
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
- Asan-Minnesota Institute for Innovating Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Beau R Webber
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Anthony P DeFeo
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Amber N McElroy
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Chong Jai Kim
- Asan Institute for Life Sciences, Asan Medical Center, Asan-Minnesota Institute for Innovating Transplantation, Seoul 138-736, Korea.
| | - Jakub Tolar
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA.
- Asan-Minnesota Institute for Innovating Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
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1029
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Kuan PF, Powers S, He S, Li K, Zhao X, Huang B. A systematic evaluation of nucleotide properties for CRISPR sgRNA design. BMC Bioinformatics 2017; 18:297. [PMID: 28587596 PMCID: PMC5461693 DOI: 10.1186/s12859-017-1697-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/18/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND CRISPR is a versatile gene editing tool which has revolutionized genetic research in the past few years. Optimizing sgRNA design to improve the efficiency of target/DNA cleavage is critical to ensure the success of CRISPR screens. RESULTS By borrowing knowledge from oligonucleotide design and nucleosome occupancy models, we systematically evaluated candidate features computed from a number of nucleic acid, thermodynamic and secondary structure models on real CRISPR datasets. Our results showed that taking into account position-dependent dinucleotide features improved the design of effective sgRNAs with area under the receiver operating characteristic curve (AUC) >0.8, and the inclusion of additional features offered marginal improvement (∼2% increase in AUC). CONCLUSION Using a machine-learning approach, we proposed an accurate prediction model for sgRNA design efficiency. An R package predictSGRNA implementing the predictive model is available at http://www.ams.sunysb.edu/~pfkuan/softwares.html#predictsgrna .
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Affiliation(s)
- Pei Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, 11794, USA.
| | - Scott Powers
- Department of Pathology, Stony Brook University, 100 Nicolls Road, Stony Brook, 11794, USA
| | - Shuyao He
- Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, 11794, USA
| | - Kaiqiao Li
- Department of Applied Mathematics and Statistics, Stony Brook University, 100 Nicolls Road, Stony Brook, 11794, USA
| | - Xiaoyu Zhao
- Department of Pathology, Stony Brook University, 100 Nicolls Road, Stony Brook, 11794, USA
| | - Bo Huang
- Oncology Business Unit, Pfizer Inc., 558 Eastern Point Rd, Groton, 06340, USA
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1030
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Harayama T, Riezman H. Detection of genome-edited mutant clones by a simple competition-based PCR method. PLoS One 2017; 12:e0179165. [PMID: 28586390 PMCID: PMC5460891 DOI: 10.1371/journal.pone.0179165] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/24/2017] [Indexed: 12/26/2022] Open
Abstract
Genome editing by the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats / CRISPR-associated protein 9) system is a revolutionary strategy to study gene functions. Since the efficiency of gene disruption in cell culture does not reach 100% typically, cloning of mutant cells is often performed to obtain fully mutated cells. Therefore, a method to discriminate accurately mutated clones easily and quickly is crucial to accelerate the research using CRISPR/Cas9. Here, we show that knockout cells can be discriminated by a competition-based PCR, using a mixture of three primers, among which one primer overlaps with the Cas9 cleavage site. Together, we show how to optimize primer design in order to improve the effectiveness of the discrimination. Finally, we applied this method to show that mutations conferring drug resistance can be detected with high accuracy. The provided method is easy to perform and requires only basic laboratory equipment, making it suitable for almost all laboratories.
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Affiliation(s)
- Takeshi Harayama
- Department of Biochemistry and NCCR Chemical Biology, Sciences II, University of Geneva, Geneva, Switzerland
- * E-mail: (TH); (HR)
| | - Howard Riezman
- Department of Biochemistry and NCCR Chemical Biology, Sciences II, University of Geneva, Geneva, Switzerland
- * E-mail: (TH); (HR)
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1031
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Morineau C, Bellec Y, Tellier F, Gissot L, Kelemen Z, Nogué F, Faure J. Selective gene dosage by CRISPR-Cas9 genome editing in hexaploid Camelina sativa. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:729-739. [PMID: 27885771 PMCID: PMC5425392 DOI: 10.1111/pbi.12671] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 05/03/2023]
Abstract
In many plant species, gene dosage is an important cause of phenotype variation. Engineering gene dosage, particularly in polyploid genomes, would provide an efficient tool for plant breeding. The hexaploid oilseed crop Camelina sativa, which has three closely related expressed subgenomes, is an ideal species for investigation of the possibility of creating a large collection of combinatorial mutants. Selective, targeted mutagenesis of the three delta-12-desaturase (FAD2) genes was achieved by CRISPR-Cas9 gene editing, leading to reduced levels of polyunsaturated fatty acids and increased accumulation of oleic acid in the oil. Analysis of mutations over four generations demonstrated the presence of a large variety of heritable mutations in the three isologous CsFAD2 genes. The different combinations of single, double and triple mutants in the T3 generation were isolated, and the complete loss-of-function mutants revealed the importance of delta-12-desaturation for Camelina development. Combinatorial association of different alleles for the three FAD2 loci provided a large diversity of Camelina lines with various lipid profiles, ranging from 10% to 62% oleic acid accumulation in the oil. The different allelic combinations allowed an unbiased analysis of gene dosage and function in this hexaploid species, but also provided a unique source of genetic variability for plant breeding.
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Affiliation(s)
- Céline Morineau
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Yannick Bellec
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Frédérique Tellier
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Lionel Gissot
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Zsolt Kelemen
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Fabien Nogué
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
| | - Jean‐Denis Faure
- Institut Jean‐Pierre Bourgin (IJPB)INRAAgroParisTechCNRSSaclay Plant Sciences (SPS)Université Paris‐SaclayVersaillesFrance
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1032
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Quinn ME, Goh Q, Kurosaka M, Gamage DG, Petrany MJ, Prasad V, Millay DP. Myomerger induces fusion of non-fusogenic cells and is required for skeletal muscle development. Nat Commun 2017; 8:15665. [PMID: 28569755 PMCID: PMC5461499 DOI: 10.1038/ncomms15665] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/19/2017] [Indexed: 12/22/2022] Open
Abstract
Despite the importance of cell fusion for mammalian development and physiology, the factors critical for this process remain to be fully defined, which has severely limited our ability to reconstitute cell fusion. Myomaker (Tmem8c) is a muscle-specific protein required for myoblast fusion. Expression of myomaker in fibroblasts drives their fusion with myoblasts, but not with other myomaker-expressing fibroblasts, highlighting the requirement of additional myoblast-derived factors for fusion. Here we show that Gm7325, which we name myomerger, induces the fusion of myomaker-expressing fibroblasts. Thus, myomaker and myomerger together confer fusogenic activity to otherwise non-fusogenic cells. Myomerger is skeletal muscle-specific and genetic deletion in mice results in a paucity of muscle fibres demonstrating its requirement for normal muscle formation. Myomerger deficient myocytes differentiate and harbour organized sarcomeres but are fusion-incompetent. Our findings identify myomerger as a fundamental myoblast fusion protein and establish a system that begins to reconstitute mammalian cell fusion. Cellular fusion is fundamental for skeletal muscle development. Here the authors show that myomerger is expressed in myoblasts, is essential for myoblast fusion in mice, and in co-operation with myomaker confers fusogenic ability to non-fusogenic cells.
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Affiliation(s)
- Malgorzata E Quinn
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, Ohio 45229, USA
| | - Qingnian Goh
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, Ohio 45229, USA
| | - Mitsutoshi Kurosaka
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, Ohio 45229, USA
| | - Dilani G Gamage
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, Ohio 45229, USA
| | - Michael J Petrany
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, Ohio 45229, USA
| | - Vikram Prasad
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, Ohio 45229, USA
| | - Douglas P Millay
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, Ohio 45229, USA
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1033
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Jaiswal A, Peddinti G, Akimov Y, Wennerberg K, Kuznetsov S, Tang J, Aittokallio T. Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells. Genome Med 2017; 9:51. [PMID: 28569207 PMCID: PMC5452371 DOI: 10.1186/s13073-017-0440-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/15/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Genome-wide loss-of-function profiling is widely used for systematic identification of genetic dependencies in cancer cells; however, the poor reproducibility of RNA interference (RNAi) screens has been a major concern due to frequent off-target effects. Currently, a detailed understanding of the key factors contributing to the sub-optimal consistency is still a lacking, especially on how to improve the reliability of future RNAi screens by controlling for factors that determine their off-target propensity. METHODS We performed a systematic, quantitative analysis of the consistency between two genome-wide shRNA screens conducted on a compendium of cancer cell lines, and also compared several gene summarization methods for inferring gene essentiality from shRNA level data. We then devised novel concepts of seed essentiality and shRNA family, based on seed region sequences of shRNAs, to study in-depth the contribution of seed-mediated off-target effects to the consistency of the two screens. We further investigated two seed-sequence properties, seed pairing stability, and target abundance in terms of their capability to minimize the off-target effects in post-screening data analysis. Finally, we applied this novel methodology to identify genetic interactions and synthetic lethal partners of cancer drivers, and confirmed differential essentiality phenotypes by detailed CRISPR/Cas9 experiments. RESULTS Using the novel concepts of seed essentiality and shRNA family, we demonstrate how genome-wide loss-of-function profiling of a common set of cancer cell lines can be actually made fairly reproducible when considering seed-mediated off-target effects. Importantly, by excluding shRNAs having higher propensity for off-target effects, based on their seed-sequence properties, one can remove noise from the genome-wide shRNA datasets. As a translational application case, we demonstrate enhanced reproducibility of genetic interaction partners of common cancer drivers, as well as identify novel synthetic lethal partners of a major oncogenic driver, PIK3CA, supported by a complementary CRISPR/Cas9 experiment. CONCLUSIONS We provide practical guidelines for improved design and analysis of genome-wide loss-of-function profiling and demonstrate how this novel strategy can be applied towards improved mapping of genetic dependencies of cancer cells to aid development of targeted anticancer treatments.
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Affiliation(s)
- Alok Jaiswal
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Gopal Peddinti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Yevhen Akimov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sergey Kuznetsov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
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1034
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Chari R, Yeo NC, Chavez A, Church GM. sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity. ACS Synth Biol 2017; 6:902-904. [PMID: 28146356 PMCID: PMC5793212 DOI: 10.1021/acssynbio.6b00343] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It has been possible to create tools to predict single guide RNA (sgRNA) activity in the CRISPR/Cas9 system derived from Streptococcus pyogenes due to the large amount of data that has been generated in sgRNA library screens. However, with the discovery of additional CRISPR systems from different bacteria, which show potent activity in eukaryotic cells, the approach of generating large data sets for each of these systems to predict their activity is not tractable. Here, we present a new guide RNA tool that can predict sgRNA activity across multiple CRISPR systems. In addition to predicting activity for Cas9 from S. pyogenes and Streptococcus thermophilus CRISPR1, we experimentally demonstrate that our algorithm can predict activity for Cas9 from Staphylococcus aureus and S. thermophilus CRISPR3. We also have made available a new version of our software, sgRNA Scorer 2.0, which will allow users to identify sgRNA sites for any PAM sequence of interest.
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Affiliation(s)
- Raj Chari
- Department of Genetics, Harvard Medical School
| | - Nan Cher Yeo
- Department of Genetics, Harvard Medical School
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - Alejandro Chavez
- Department of Genetics, Harvard Medical School
- Wyss Institute for Biologically Inspired Engineering, Harvard University
| | - George M. Church
- Department of Genetics, Harvard Medical School
- Wyss Institute for Biologically Inspired Engineering, Harvard University
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1035
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Wefers B, Bashir S, Rossius J, Wurst W, Kühn R. Gene editing in mouse zygotes using the CRISPR/Cas9 system. Methods 2017; 121-122:55-67. [PMID: 28263886 DOI: 10.1016/j.ymeth.2017.02.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/09/2017] [Accepted: 02/27/2017] [Indexed: 12/26/2022] Open
Abstract
The generation of targeted mouse mutants is a key technology for biomedical research. Using the CRISPR/Cas9 system for induction of targeted double-strand breaks, gene editing can be performed in a single step directly in mouse zygotes. This article covers the design of knockout and knockin alleles, preparation of reagents, microinjection or electroporation of zygotes and the genotyping of pups derived from gene editing projects. In addition we include a section for the control of experimental settings by targeting the Rosa26 locus and PCR based genotyping of blastocysts.
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Affiliation(s)
- Benedikt Wefers
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen Str. 17, 81377 Munich, Germany; Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Developmental Genetics, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
| | - Sanum Bashir
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle Str. 10, 13125 Berlin, Germany; Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin, Germany.
| | - Jana Rossius
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle Str. 10, 13125 Berlin, Germany.
| | - Wolfgang Wurst
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen Str. 17, 81377 Munich, Germany; Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Developmental Genetics, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Technische Universität München-Weihenstephan, Chair of Developmental Genetics, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377 Munich, Germany.
| | - Ralf Kühn
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle Str. 10, 13125 Berlin, Germany; Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin, Germany.
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1036
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Yumlu S, Stumm J, Bashir S, Dreyer AK, Lisowski P, Danner E, Kühn R. Gene editing and clonal isolation of human induced pluripotent stem cells using CRISPR/Cas9. Methods 2017; 121-122:29-44. [PMID: 28522326 DOI: 10.1016/j.ymeth.2017.05.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/04/2017] [Accepted: 05/10/2017] [Indexed: 12/28/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) represent an ideal in vitro platform to study human genetics and biology. The recent advent of programmable nucleases makes also the human genome amenable to experimental genetics through either the correction of mutations in patient-derived iPSC lines or the de novo introduction of mutations into otherwise healthy iPSCs. The production of specific and sometimes complex genotypes in multiple cell lines requires efficient and streamlined gene editing technologies. In this article we provide protocols for gene editing in hiPSCs. We presently achieve high rates of gene editing at up to three loci using a modified iCRISPR system. This system includes a doxycycline inducible Cas9 and sgRNA/reporter plasmids for the enrichment of transfected cells by fluorescence-activated cell sorting (FACS). Here we cover the selection of target sites, vector construction, transfection, and isolation and genotyping of modified hiPSC clones.
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Affiliation(s)
- Saniye Yumlu
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin, Germany.
| | - Jürgen Stumm
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Helmholtz Center Munich, 85764 Neuherberg, Germany.
| | - Sanum Bashir
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin, Germany.
| | - Anne-Kathrin Dreyer
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin, Germany.
| | - Pawel Lisowski
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Institute of Genetics and Animal Breeding, Polish Academy of Sciences, 05-552 Magdalenka, Poland.
| | - Eric Danner
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany.
| | - Ralf Kühn
- Max-Delbrück-Centrum für Molekulare Medizin, 13125 Berlin, Germany; Berlin Institute of Health, Kapelle-Ufer 2, 10117 Berlin, Germany.
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1037
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Albadri S, Del Bene F, Revenu C. Genome editing using CRISPR/Cas9-based knock-in approaches in zebrafish. Methods 2017; 121-122:77-85. [PMID: 28300641 DOI: 10.1016/j.ymeth.2017.03.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/13/2017] [Accepted: 03/03/2017] [Indexed: 12/19/2022] Open
Abstract
With its variety of applications, the CRISPR/Cas9 genome editing technology has been rapidly evolving in the last few years. In the zebrafish community, knock-out reports are constantly increasing but insertion studies have been so far more challenging. With this review, we aim at giving an overview of the homologous directed repair (HDR)-based knock-in generation in zebrafish. We address the critical points and limitations of the procedure such as cutting efficiency of the chosen single guide RNA, use of cas9 mRNA or Cas9 protein, homology arm size etc. but also ways to circumvent encountered issues with HDR insertions by the development of non-homologous dependent strategies. While imprecise, these homology-independent mechanisms based on non-homologous-end-joining (NHEJ) repair have been employed in zebrafish to generate reporter lines or to accurately edit an open reading frame by the use of intron-targeting modifications. Therefore, with higher efficiency and insertion rate, NHEJ-based knock-in seems to be a promising approach to target endogenous loci and to circumvent the limitations of HDR whenever it is possible and appropriate. In this perspective, we propose new strategies to generate cDNA edited or tagged insertions, which once established will constitute a new and versatile toolbox for CRISPR/Cas9-based knock-ins in zebrafish.
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Affiliation(s)
- Shahad Albadri
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France.
| | - Céline Revenu
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France
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1038
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Mianné J, Codner GF, Caulder A, Fell R, Hutchison M, King R, Stewart ME, Wells S, Teboul L. Analysing the outcome of CRISPR-aided genome editing in embryos: Screening, genotyping and quality control. Methods 2017; 121-122:68-76. [PMID: 28363792 DOI: 10.1016/j.ymeth.2017.03.016] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/02/2017] [Accepted: 03/13/2017] [Indexed: 01/25/2023] Open
Abstract
The application of CRISPR/Cas9 technology has revolutionised genetics by greatly enhancing the efficacy of genome editing in the early embryo. Furthermore, the system has enabled the generation of allele types previously incompatible with in vivo mutagenesis. Despite its versatility and ease of implementation, CRISPR/Cas9 editing outcome is unpredictable and can generate mosaic founders. Therefore, careful genotyping and characterisation of new mutants is proving essential. The literature presents a wide range of protocols for molecular characterisation, each representing different levels of investment. We present strategies and protocols for designing, producing and screening CRISPR/Cas9 edited founders and genotyping their offspring according to desired allele type (indel, point mutation and deletion).
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Affiliation(s)
- Joffrey Mianné
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Gemma F Codner
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Rachel Fell
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Marie Hutchison
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Ruairidh King
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | | | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxon OX11 0RD, UK.
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1039
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Canver MC, Bauer DE, Orkin SH. Functional interrogation of non-coding DNA through CRISPR genome editing. Methods 2017; 121-122:118-129. [PMID: 28288828 PMCID: PMC5483188 DOI: 10.1016/j.ymeth.2017.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/18/2017] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA.
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Affiliation(s)
| | - Daniel E Bauer
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
| | - Stuart H Orkin
- Harvard Medical School, Boston, MA 02115, United States; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, United States; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States; Howard Hughes Medical Institute, Boston, MA 02115, United States.
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1040
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Wassef M, Luscan A, Battistella A, Le Corre S, Li H, Wallace MR, Vidaud M, Margueron R. Versatile and precise gene-targeting strategies for functional studies in mammalian cell lines. Methods 2017; 121-122:45-54. [PMID: 28499832 DOI: 10.1016/j.ymeth.2017.05.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/03/2017] [Accepted: 05/05/2017] [Indexed: 11/28/2022] Open
Abstract
The advent of programmable nucleases such as ZFNs, TALENs and CRISPR/Cas9 has brought the power of genetic manipulation to widely used model systems. In mammalian cells, nuclease-mediated DNA double strand break is mainly repaired through the error-prone non-homologous end-joining (NHEJ) repair pathway, eventually leading to accumulation of small deletions or insertions (indels) that can inactivate gene function. However, due to the variable size of the indels and the polyploid status of many cell lines (e.g., cancer-derived cells), obtaining a knockout usually requires lengthy screening and characterization procedures. Given the more precise type of modifications that can be introduced upon homology-directed repair (HDR), we have developed HDR-based gene-targeting strategies that greatly facilitate the process of knockout generation in cell lines. To generate reversible knockouts (R-KO), a selectable promoter-less STOP cassette is inserted in an intron, interrupting transcription. Loss-of-function can be validated by RT-qPCR and is removable, enabling subsequent restoration of gene function. A variant of the R-KO procedure can be used to introduce point mutations. To generate constitutive knockouts (C-KO), an exon is targeted, which makes use of HDR-based gene disruption together with NHEJ-induced indels on non-HDR targeted allele(s). Hence the C-KO procedure greatly facilitates simultaneous inactivation of multiple alleles. Overall these genome-editing tools offer superior precision and efficiency for functional genetic approaches. We provide detailed protocols guiding in the design of targeting vectors and in the analysis and validation of gene targeting experiments.
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Affiliation(s)
- M Wassef
- Institut Curie, PSL Research University, 75005 Paris, France; INSERM U934, Paris, France; CNRS UMR3215, Paris, France.
| | - A Luscan
- INSERM UMR_S745 et EA7331, Université Paris Descartes, Sorbonne Paris Cité, Facultée des Sciences Pharmaceutiques et Biologiques, 75006 Paris, France; Service de Biochimie et Génétique Moléculaire, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
| | - A Battistella
- Institut Curie, PSL Research University, 75005 Paris, France; INSERM U934, Paris, France; CNRS UMR3215, Paris, France
| | - S Le Corre
- Institut Curie, PSL Research University, 75005 Paris, France; INSERM U934, Paris, France; CNRS UMR3215, Paris, France
| | - H Li
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
| | - M R Wallace
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA; University of Florida Health Cancer Center, University of Florida, Gainesville, FL, USA; University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - M Vidaud
- INSERM UMR_S745 et EA7331, Université Paris Descartes, Sorbonne Paris Cité, Facultée des Sciences Pharmaceutiques et Biologiques, 75006 Paris, France; Service de Biochimie et Génétique Moléculaire, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
| | - R Margueron
- Institut Curie, PSL Research University, 75005 Paris, France; INSERM U934, Paris, France; CNRS UMR3215, Paris, France
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1041
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Ritter A, Iñigo S, Fernández-Calvo P, Heyndrickx KS, Dhondt S, Shi H, De Milde L, Vanden Bossche R, De Clercq R, Eeckhout D, Ron M, Somers DE, Inzé D, Gevaert K, De Jaeger G, Vandepoele K, Pauwels L, Goossens A. The transcriptional repressor complex FRS7-FRS12 regulates flowering time and growth in Arabidopsis. Nat Commun 2017; 8:15235. [PMID: 28492275 PMCID: PMC5437275 DOI: 10.1038/ncomms15235] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 03/06/2017] [Indexed: 12/15/2022] Open
Abstract
Most living organisms developed systems to efficiently time environmental changes. The plant-clock acts in coordination with external signals to generate output responses determining seasonal growth and flowering time. Here, we show that two Arabidopsis thaliana transcription factors, FAR1 RELATED SEQUENCE 7 (FRS7) and FRS12, act as negative regulators of these processes. These proteins accumulate particularly in short-day conditions and interact to form a complex. Loss-of-function of FRS7 and FRS12 results in early flowering plants with overly elongated hypocotyls mainly in short days. We demonstrate by molecular analysis that FRS7 and FRS12 affect these developmental processes in part by binding to the promoters and repressing the expression of GIGANTEA and PHYTOCHROME INTERACTING FACTOR 4 as well as several of their downstream signalling targets. Our data reveal a molecular machinery that controls the photoperiodic regulation of flowering and growth and offer insight into how plants adapt to seasonal changes.
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Affiliation(s)
- Andrés Ritter
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Sabrina Iñigo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Patricia Fernández-Calvo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Ken S. Heyndrickx
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Stijn Dhondt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Hua Shi
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA
| | - Liesbeth De Milde
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Robin Vanden Bossche
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Rebecca De Clercq
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Dominique Eeckhout
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Mily Ron
- Department of Plant Biology, UC Davis, Davis, California 95616, USA
| | - David E. Somers
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Geert De Jaeger
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Laurens Pauwels
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Gent, Belgium
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1042
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Gandhi S, Haeussler M, Razy-Krajka F, Christiaen L, Stolfi A. Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona. Dev Biol 2017; 425:8-20. [PMID: 28341547 PMCID: PMC5502750 DOI: 10.1016/j.ydbio.2017.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 02/06/2017] [Accepted: 03/05/2017] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas9 system has emerged as an important tool for various genome engineering applications. A current obstacle to high throughput applications of CRISPR/Cas9 is the imprecise prediction of highly active single guide RNAs (sgRNAs). We previously implemented the CRISPR/Cas9 system to induce tissue-specific mutations in the tunicate Ciona. In the present study, we designed and tested 83 single guide RNA (sgRNA) vectors targeting 23 genes expressed in the cardiopharyngeal progenitors and surrounding tissues of Ciona embryo. Using high-throughput sequencing of mutagenized alleles, we identified guide sequences that correlate with sgRNA mutagenesis activity and used this information for the rational design of all possible sgRNAs targeting the Ciona transcriptome. We also describe a one-step cloning-free protocol for the assembly of sgRNA expression cassettes. These cassettes can be directly electroporated as unpurified PCR products into Ciona embryos for sgRNA expression in vivo, resulting in high frequency of CRISPR/Cas9-mediated mutagenesis in somatic cells of electroporated embryos. We found a strong correlation between the frequency of an Ebf loss-of-function phenotype and the mutagenesis efficacies of individual Ebf-targeting sgRNAs tested using this method. We anticipate that our approach can be scaled up to systematically design and deliver highly efficient sgRNAs for the tissue-specific investigation of gene functions in Ciona.
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Affiliation(s)
| | - Maximilian Haeussler
- Santa Cruz Genomics Institute, University of California, MS CBSE, Santa Cruz, USA
| | | | | | - Alberto Stolfi
- Department of Biology, New York University, New York, USA.
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1043
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Zhou M, Li D, Huan X, Manthey J, Lioutikova E, Zhou H. Mathematical and computational analysis of CRISPR Cas9 sgRNA off-target homologies. INT J BIOMATH 2017. [DOI: 10.1142/s1793524517500851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Revolutionary in scope and application, the CRISPR Cas9 endonuclease system can be guided by 20-nt single guide RNA (sgRNA) to any complementary loci on the double-stranded DNA. Once the target site is located, Cas9 can then cleave the DNA and introduce mutations. Despite the power of this system, sgRNA is highly susceptible to off-target homologous attachment and can consequently cause Cas9 to cleave DNA at off-target sites. In order to better understand this flaw in the system, the human genome and Streptococcus pyogenes Cas9 (SpCas9) were used in a mathematical and computational study to analyze the probabilities of potential sgRNA off-target homologies. It has been concluded that off-target sites are nearly unavoidable for large-size genomes, such as the human genome. Backed by mathematical analysis, a viable solution is the double-nicking method which has the promise for genome editing specificity. Also applied in this study was a computational algorithm for off-target homology search that was implemented in Java to confirm the mathematical analysis.
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Affiliation(s)
- Michael Zhou
- Hall High School, 975N Main Street, West Hartford, CT 06117, USA
| | - Daisy Li
- Hall High School, 975N Main Street, West Hartford, CT 06117, USA
| | - Xiaoli Huan
- Department of Computer Science, Troy University, Troy AL 36082, USA
| | - Joseph Manthey
- Department of Mathematical Science, University of Saint Joseph, 1678 Asylum Avenue, West Hartford CT 06117, USA
| | - Ekaterina Lioutikova
- Department of Mathematical Science, University of Saint Joseph, 1678 Asylum Avenue, West Hartford CT 06117, USA
| | - Hong Zhou
- Department of Mathematical Science, University of Saint Joseph, 1678 Asylum Avenue, West Hartford CT 06117, USA
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1044
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Control of gene editing by manipulation of DNA repair mechanisms. Mamm Genome 2017; 28:262-274. [DOI: 10.1007/s00335-017-9688-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/25/2017] [Indexed: 12/22/2022]
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1045
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Hough SH, Kancleris K, Brody L, Humphryes-Kirilov N, Wolanski J, Dunaway K, Ajetunmobi A, Dillard V. Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments. BMC Bioinformatics 2017; 18:167. [PMID: 28288556 PMCID: PMC5348774 DOI: 10.1186/s12859-017-1581-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Guide Picker ( https://www.deskgen.com/guide-picker/ ) serves as a meta tool for designing CRISPR experiments by presenting ten different guide RNA scoring functions in one simple graphical interface. It allows investigators to simultaneously visualize and sort through every guide targeting the protein-coding regions of any mouse or human gene. RESULTS Utilizing a multidimensional graphical display featuring two plots and four axes, Guide Picker can analyze all guides while filtering based on four different criteria at a time. Guide Picker further facilitates the CRISPR design process by using pre-computed scores for all guides, thereby offering rapid guide RNA generation and selection. CONCLUSIONS The ease-of-use of Guide Picker complements CRISPR itself, matching a powerful and modular biological system with a flexible online web tool that can be used in a variety of genome editing experimental contexts.
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Affiliation(s)
- Soren H. Hough
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | - Kris Kancleris
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | - Leigh Brody
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | | | - Joseph Wolanski
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | - Keith Dunaway
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
| | | | - Victor Dillard
- Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR UK
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1046
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Xu X, Duan D, Chen SJ. CRISPR-Cas9 cleavage efficiency correlates strongly with target-sgRNA folding stability: from physical mechanism to off-target assessment. Sci Rep 2017; 7:143. [PMID: 28273945 PMCID: PMC5427927 DOI: 10.1038/s41598-017-00180-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/13/2017] [Indexed: 12/22/2022] Open
Abstract
The CRISPR/Cas9 complex, a bacterial immune response system, has been widely adopted for RNA-guided genome editing and transcription regulation in applications such as targeted genome modification and site-directed mutagenesis. However, the physical basis for its target specificity is not fully understood. In this study, based on a statistical mechanical analysis for the whole ensemble of sgRNA-target complex conformations, we identify a strong correlation between Cas9 cleavage efficiency and the stability of the DNA-RNA (R-loop) complex structures, with a Pearson correlation coefficient ranging from 0.775 to 0.886 for the tested systems. The finding leads to quantitative insights into important experimental results, such as the greater Cas9 tolerance to single-base mismatches in PAM-distal region than to PAM-proximal region and the high specificity and efficiency for shorter protospacers. Moreover, the results from the genome-wide off-target assessments, compared with other off-target scoring tools, indicate that the statistical mechanics-based approach provides more reliable off-target analyses and sgRNA design. To facilitate the genome engineering applications, a new web-based tool for genome-wide off-target assessment is established.
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Affiliation(s)
- Xiaojun Xu
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, MO, USA
| | - Dongsheng Duan
- Department of Molecular Microbiology and Immunology, Department of Neurology, School of Medicine; Department of Biomedical Sciences, College of Veterinary Medicine; and Department of Bioengineering, University of Missouri, Columbia, MO, USA
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, MO, USA.
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1047
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Abstract
Inborn errors of metabolism (IEM) include many disorders for which current treatments aim to ameliorate disease manifestations, but are not curative. Advances in the field of genome editing have recently resulted in the in vivo correction of murine models of IEM. Site-specific endonucleases, such as zinc-finger nucleases and the CRISPR/Cas9 system, in combination with delivery vectors engineered to target disease tissue, have enabled correction of mutations in disease models of hemophilia B, hereditary tyrosinemia type I, ornithine transcarbamylase deficiency, and lysosomal storage disorders. These in vivo gene correction studies, as well as an overview of genome editing and future directions for the field, are reviewed and discussed herein.
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1048
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Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Gonzalez JN, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2017 update. Nucleic Acids Res 2017; 45:D626-D634. [PMID: 27899642 PMCID: PMC5210591 DOI: 10.1093/nar/gkw1134] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/17/2016] [Accepted: 10/31/2016] [Indexed: 12/14/2022] Open
Abstract
Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.
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Affiliation(s)
- Cath Tyner
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Galt P Barber
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jonathan Casper
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Hiram Clawson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Clayton M Fischer
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Gibson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Luvina Guruvadoo
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Maximilian Haeussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Steve Heitner
- Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Donna Karolchik
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian T Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christopher M Lee
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Parisa Nejad
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian J Raney
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kate R Rosenbloom
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew L Speir
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Chris Villarreal
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John Vivian
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ann S Zweig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, CA 95064, USA
| | - Robert M Kuhn
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - W James Kent
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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1049
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Bajda S, Dermauw W, Panteleri R, Sugimoto N, Douris V, Tirry L, Osakabe M, Vontas J, Van Leeuwen T. A mutation in the PSST homologue of complex I (NADH:ubiquinone oxidoreductase) from Tetranychus urticae is associated with resistance to METI acaricides. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 80:79-90. [PMID: 27919778 DOI: 10.1016/j.ibmb.2016.11.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/25/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
The acaricidal compounds pyridaben, tebufenpyrad and fenpyroximate are frequently used in the control of phytophagous mites such as Tetranychus urticae, and are referred to as Mitochondrial Electron Transport Inhibitors, acting at the quinone binding pocket of complex I (METI-I acaricides). Because of their very frequent use, resistance evolved fast more than 20 years ago, and is currently wide-spread. Increased activity of P450 monooxygenases has been often associated with resistance, but target-site based resistance mechanisms were never reported. Here, we report the discovery of a mutation (H92R) in the PSST homologue of complex I in METI-I resistant T. urticae strains. The position of the mutation was studied using the high-resolution crystal structure of Thermus thermophilus, and was located in a stretch of amino acids previously photo-affinity labeled by fenpyroximate. Selection experiments with a strain segregating for the mutant allele, together with marker-assisted back-crossing of the mutation in a susceptible background, confirmed the involvement of the mutation in METI-I resistance. Additionally, an independent genetic mapping approach; QTL analysis identified the genomic region of pyridaben resistance, which included the PSST gene. Last, we used CRISPR-Cas9 genome editing tools to introduce the mutation in the Drosophila PSST homologue.
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Affiliation(s)
- Sabina Bajda
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 9424, 1090 GE Amsterdam, The Netherlands
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium
| | - Rafaela Panteleri
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece
| | - Naoya Sugimoto
- Kyoto University, Graduate School of Agriculture, Laboratory of Ecological Information, Kyoto 606-8502, Japan
| | - Vassilis Douris
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece; Department of Biology, University of Crete, 71409 Heraklion, Greece
| | - Luc Tirry
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium
| | - Masahiro Osakabe
- Kyoto University, Graduate School of Agriculture, Laboratory of Ecological Information, Kyoto 606-8502, Japan
| | - John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece; Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece
| | - Thomas Van Leeuwen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 9424, 1090 GE Amsterdam, The Netherlands; Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Coupure Links 653, Ghent University, B-9000 Ghent, Belgium.
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1050
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A Transgenic Core Facility’s Experience in Genome Editing Revolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1016:75-90. [DOI: 10.1007/978-3-319-63904-8_4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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