CRISPR-Based Methods for Caenorhabditis elegans Genome Engineering

The advent of genome editing techniques based on the clustered regularly interspersed short palindromic repeats (CRISPR)–Cas9 system has revolutionized research in the biological sciences. CRISPR is quickly becoming an indispensible experimental tool for researchers using genetic model organisms, including the nematode Caenorhabditis elegans. Here, we provide an overview of CRISPR-based strategies for genome editing in C. elegans. We focus on practical considerations for successful genome editing, including a discussion of which strategies are best suited to producing different kinds of targeted genome modifications.

[1]  E. Jorgensen,et al.  SapTrap, a Toolkit for High-Throughput CRISPR/Cas9 Gene Modification in Caenorhabditis elegans , 2016, Genetics.

[2]  A. Fire,et al.  Cas9 Variants Expand the Target Repertoire in Caenorhabditis elegans , 2015, Genetics.

[3]  D. Dickinson,et al.  Crescerin uses a TOG domain array to regulate microtubules in the primary cilium , 2015, Molecular biology of the cell.

[4]  Xuezhu Feng,et al.  Targeted Chromosomal Translocations and Essential Gene Knockout Using CRISPR/Cas9 Technology in Caenorhabditis elegans , 2015, Genetics.

[5]  F. Conlon,et al.  Identifying Regulators of Morphogenesis Common to Vertebrate Neural Tube Closure and Caenorhabditis elegans Gastrulation , 2015, Genetics.

[6]  A. Regev,et al.  Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System , 2015, Cell.

[7]  Clifford A. Meyer,et al.  Sequence determinants of improved CRISPR sgRNA design , 2015, Genome research.

[8]  John A. Calarco,et al.  Efficient Genome Editing in Caenorhabditis elegans with a Toolkit of Dual-Marker Selection Cassettes , 2015, Genetics.

[9]  Zheng Wei,et al.  CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation , 2015, Bioinform..

[10]  Andrew W. Folkmann,et al.  High Efficiency, Homology-Directed Genome Editing in Caenorhabditis elegans Using CRISPR-Cas9 Ribonucleoprotein Complexes , 2015, Genetics.

[11]  Martin J. Aryee,et al.  Engineered CRISPR-Cas9 nucleases with altered PAM specificities , 2015, Nature.

[12]  S. van den Heuvel,et al.  Polymerase Θ is a key driver of genome evolution and of CRISPR/Cas9-mediated mutagenesis , 2015, Nature Communications.

[13]  D. Dickinson,et al.  Streamlined Genome Engineering with a Self-Excising Drug Selection Cassette , 2015, Genetics.

[14]  I. Katic,et al.  CRISPR/Cas9 Genome Editing in Caenorhabditis elegans: Evaluation of Templates for Homology-Mediated Repair and Knock-Ins by Homology-Independent DNA Repair , 2015, G3: Genes, Genomes, Genetics.

[15]  David A. Scott,et al.  In vivo genome editing using Staphylococcus aureus Cas9 , 2015, Nature.

[16]  B. Meyer,et al.  Dramatic Enhancement of Genome Editing by CRISPR/Cas9 Through Improved Guide RNA Design , 2015, Genetics.

[17]  J. Ward,et al.  Rapid and Precise Engineering of the Caenorhabditis elegans Genome with Lethal Mutation Co-Conversion and Inactivation of NHEJ Repair , 2014, Genetics.

[18]  Yanhui Hu,et al.  Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. , 2014, Cell reports.

[19]  M. Krause,et al.  Scalable and Versatile Genome Editing Using Linear DNAs with Microhomology to Cas9 Sites in Caenorhabditis elegans , 2014, Genetics.

[20]  Zhiwen Zhu,et al.  Conditional knockouts generated by engineered CRISPR-Cas9 endonuclease reveal the roles of coronin in C. elegans neural development. , 2014, Developmental cell.

[21]  Meagan E. Sullender,et al.  Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation , 2014, Nature Biotechnology.

[22]  Joshua A. Arribere,et al.  Efficient Marker-Free Recovery of Custom Genetic Modifications with CRISPR/Cas9 in Caenorhabditis elegans , 2014, Genetics.

[23]  E. Lander,et al.  Development and Applications of CRISPR-Cas9 for Genome Engineering , 2014, Cell.

[24]  Zuoyan Zhu,et al.  Heritable/conditional genome editing in C. elegans using a CRISPR-Cas9 feeding system , 2014, Cell Research.

[25]  C. Mello,et al.  A Co-CRISPR Strategy for Efficient Genome Editing in Caenorhabditis elegans , 2014, Genetics.

[26]  Mazhar Adli,et al.  Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease , 2014, Nature Biotechnology.

[27]  David A. Scott,et al.  Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells , 2014, Nature Biotechnology.

[28]  Jennifer A. Doudna,et al.  DNA interrogation by the CRISPR RNA-guided endonuclease Cas9 , 2014, Nature.

[29]  Wei Zhang,et al.  Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System , 2014, Cell.

[30]  Yiren Yue,et al.  Oligonucleotide-based targeted gene editing in C. elegans via the CRISPR/Cas9 system , 2014, Cell Research.

[31]  Luke A. Gilbert,et al.  Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System , 2013, Cell.

[32]  E. Lander,et al.  Genetic Screens in Human Cells Using the CRISPR-Cas9 System , 2013, Science.

[33]  I. Katic,et al.  Targeted Heritable Mutation and Gene Conversion by Cas9-CRISPR in Caenorhabditis elegans , 2013, Genetics.

[34]  P. Sternberg,et al.  Transgene-Free Genome Editing in Caenorhabditis elegans Using CRISPR-Cas , 2013, Genetics.

[35]  Dana Carroll,et al.  Heritable Gene Knockout in Caenorhabditis elegans by Direct Injection of Cas9–sgRNA Ribonucleoproteins , 2013, Genetics.

[36]  Mike Boxem,et al.  CRISPR/Cas9-Targeted Mutagenesis in Caenorhabditis elegans , 2013, Genetics.

[37]  Steven Lin,et al.  Precise and Heritable Genome Editing in Evolutionarily Diverse Nematodes Using TALENs and CRISPR/Cas9 to Engineer Insertions and Deletions , 2013, Genetics.

[38]  M. de Bono,et al.  Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination , 2013, Nucleic acids research.

[39]  Bob Goldstein,et al.  Engineering the Caenorhabditis elegans Genome Using Cas9-Triggered Homologous Recombination , 2013, Nature Methods.

[40]  David A. Scott,et al.  Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity , 2013, Cell.

[41]  David R. Liu,et al.  High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity , 2013, Nature Biotechnology.

[42]  Eli J. Fine,et al.  DNA targeting specificity of RNA-guided Cas9 nucleases , 2013, Nature Biotechnology.

[43]  George M. Church,et al.  Heritable genome editing in C. elegans via a CRISPR-Cas9 system , 2013, Nature Methods.

[44]  J. Keith Joung,et al.  High frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells , 2013, Nature Biotechnology.

[45]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[46]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[47]  M. Davis,et al.  Improved Mos1-mediated transgenesis in C. elegans , 2012, Nature Methods.

[48]  J. Chin,et al.  Expanding the Genetic Code of an Animal , 2011, Journal of the American Chemical Society.

[49]  Erik M. Jorgensen,et al.  Targeted gene deletions in C. elegans using transposon excision , 2010, Nature Methods.

[50]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[51]  Carola Engler,et al.  A One Pot, One Step, Precision Cloning Method with High Throughput Capability , 2008, PloS one.

[52]  Erik M Jorgensen,et al.  Single-copy insertion of transgenes in Caenorhabditis elegans , 2008, Nature Genetics.

[53]  V. Robert,et al.  Targeted engineering of the Caenorhabditis elegans genome following Mos1‐triggered chromosomal breaks , 2007, The EMBO journal.

[54]  Cori Bargmann,et al.  Homologous gene targeting in Caenorhabditis elegans by biolistic transformation. , 2004, Nucleic acids research.

[55]  Alessandra Carbone,et al.  Codon adaptation index as a measure of dominating codon bias , 2003, Bioinform..

[56]  Elizabeth Casey,et al.  Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. , 2001, Genetics.

[57]  V. Ambros,et al.  Efficient gene transfer in C.elegans: extrachromosomal maintenance and integration of transforming sequences. , 1991, The EMBO journal.

[58]  Feng Zhang,et al.  rNA-guided editing of bacterial genomes using crisPr-cas systems , 2016 .

[59]  R. Pulak,et al.  Techniques for analysis, sorting, and dispensing of C. elegans on the COPAS flow-sorting system. , 2006, Methods in molecular biology.