Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

The type II CRISPR/Cas system from Streptococcus pyogenes and its simplified derivative, the Cas9/single guide RNA (sgRNA) system, have emerged as potent new tools for targeted gene knockout in bacteria, yeast, fruit fly, zebrafish and human cells. Here, we describe adaptations of these systems leading to successful expression of the Cas9/sgRNA system in two dicot plant species, Arabidopsis and tobacco, and two monocot crop species, rice and sorghum. Agrobacterium tumefaciens was used for delivery of genes encoding Cas9, sgRNA and a non-fuctional, mutant green fluorescence protein (GFP) to Arabidopsis and tobacco. The mutant GFP gene contained target sites in its 5′ coding regions that were successfully cleaved by a CAS9/sgRNA complex that, along with error-prone DNA repair, resulted in creation of functional GFP genes. DNA sequencing confirmed Cas9/sgRNA-mediated mutagenesis at the target site. Rice protoplast cells transformed with Cas9/sgRNA constructs targeting the promoter region of the bacterial blight susceptibility genes, OsSWEET14 and OsSWEET11, were confirmed by DNA sequencing to contain mutated DNA sequences at the target sites. Successful demonstration of the Cas9/sgRNA system in model plant and crop species bodes well for its near-term use as a facile and powerful means of plant genetic engineering for scientific and agricultural applications.

[1]  R. Kanaar,et al.  DNA double-strand break repair: all's well that ends well. , 2006, Annual review of genetics.

[2]  Claudio Mussolino,et al.  A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity , 2011, Nucleic acids research.

[3]  D. Voytas,et al.  Rapid and efficient gene modification in rice and Brachypodium using TALENs. , 2013, Molecular plant.

[4]  Rudolf Jaenisch,et al.  One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering , 2013, Cell.

[5]  P. Quail,et al.  Ubiquitin promoter-based vectors for high-level expression of selectable and/or screenable marker genes in monocotyledonous plants , 1996, Transgenic Research.

[6]  Daniel F. Voytas,et al.  Efficient TALEN-mediated gene knockout in livestock , 2012, Proceedings of the National Academy of Sciences.

[7]  Kunling Chen,et al.  TALENs: customizable molecular DNA scissors for genome engineering of plants. , 2013, Journal of genetics and genomics = Yi chuan xue bao.

[8]  George M. Church,et al.  Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers , 2012, Nucleic acids research.

[9]  Xiaojun Zhu,et al.  Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos , 2013, Cell Research.

[10]  J. Doudna,et al.  RNA-guided genetic silencing systems in bacteria and archaea , 2012, Nature.

[11]  R. Beerli,et al.  Engineering polydactyl zinc-finger transcription factors , 2002, Nature Biotechnology.

[12]  George M. Church,et al.  Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9 , 2013, Nature Biotechnology.

[13]  Susan Carpenter,et al.  Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes , 2011, Nucleic acids research.

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

[15]  C. Blanpain Tracing the cellular origin of cancer , 2013, Nature Cell Biology.

[16]  G. Gobbi,et al.  Characterization of serotonin neurotransmission in knockout mice: implications for major depression , 2012, Reviews in the neurosciences.

[17]  Fyodor D Urnov,et al.  Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases , 2007, Proceedings of the National Academy of Sciences.

[18]  C. Meyer,et al.  Animal models of chronic liver diseases. , 2013, American journal of physiology. Gastrointestinal and liver physiology.

[19]  M. Fromm,et al.  Rapid and reproducible Agrobacterium-mediated transformation of sorghum , 2006, Plant Cell Reports.

[20]  George M. Church,et al.  Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems , 2013, Nucleic acids research.

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

[22]  Yuge Li,et al.  A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes , 2011, Plant Methods.

[23]  Luke A. Gilbert,et al.  Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.

[24]  Jeffry D. Sander,et al.  Efficient In Vivo Genome Editing Using RNA-Guided Nucleases , 2013, Nature Biotechnology.

[25]  Shuo Lin,et al.  TALEN-mediated precise genome modification by homologous recombination in zebrafish , 2013, Nature Methods.

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

[27]  R. Wu,et al.  Isolation of an efficient actin promoter for use in rice transformation. , 1990, The Plant cell.

[28]  C. Barbas,et al.  ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. , 2013, Trends in biotechnology.

[29]  G. Church,et al.  Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. , 2011, Nature biotechnology.

[30]  D. Adams,et al.  Cancer of mice and men: old twists and new tails , 2013, The Journal of pathology.

[31]  M. Spalding,et al.  High-efficiency TALEN-based gene editing produces disease-resistant rice , 2012, Nature Biotechnology.

[32]  Jun Li,et al.  Targeted genome modification of crop plants using a CRISPR-Cas system , 2013, Nature Biotechnology.

[33]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[34]  Melissa M. Harrison,et al.  Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease , 2013, Genetics.

[35]  R. Kucherlapati,et al.  Insertion of DNA sequences into the human chromosomal β-globin locus by homologous recombination , 1985, Nature.

[36]  Bo Zhang,et al.  Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish , 2013, Nucleic acids research.

[37]  Tobias Schmidt,et al.  A ligation-independent cloning technique for high-throughput assembly of transcription activator–like effector genes , 2012, Nature Biotechnology.

[38]  Jens Boch,et al.  Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors , 2009, Science.

[39]  J. Glazebrook,et al.  An efficient Agrobacterium-mediated transient transformation of Arabidopsis. , 2012, The Plant journal : for cell and molecular biology.

[40]  Shondra M Pruett-Miller,et al.  High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases , 2011, Nature Methods.

[41]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[42]  Bernard R. Baum,et al.  Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components , 1997, Plant Molecular Biology Reporter.

[43]  Mario R. Capecchi,et al.  High frequency targeting of genes to specific sites in the mammalian genome , 1986, Cell.

[44]  Seung Woo Cho,et al.  Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease , 2013, Nature Biotechnology.

[45]  Detlef Weigel,et al.  Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease , 2013, Nature Biotechnology.

[46]  Matthew J. Moscou,et al.  A Simple Cipher Governs DNA Recognition by TAL Effectors , 2009, Science.

[47]  M. Conrad,et al.  Glutathione and thioredoxin dependent systems in neurodegenerative disease: What can be learned from reverse genetics in mice , 2013, Neurochemistry International.

[48]  Mario R. Capecchi,et al.  Generating mice with targeted mutations , 2001, Nature Medicine.