CRISPR/Cas9 and genome editing in Drosophila.

Recent advances in our ability to design DNA binding factors with specificity for desired sequences have resulted in a revolution in genetic engineering, enabling directed changes to the genome to be made relatively easily. Traditional techniques for generating genetic mutations in most organisms have relied on selection from large pools of randomly induced mutations for those of particular interest, or time-consuming gene targeting by homologous recombination. Drosophila melanogaster has always been at the forefront of genetic analysis, and application of these new genome editing techniques to this organism will revolutionise our approach to performing analysis of gene function in the future. We discuss the recent techniques that apply the CRISPR/Cas9 system to Drosophila, highlight potential uses for this technology and speculate upon the future of genome engineering in this model organism.

[1]  J. Rinn,et al.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.

[2]  R. Barrangou,et al.  Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria , 2012, Proceedings of the National Academy of Sciences.

[3]  G. Rubin,et al.  The BDGP Gene Disruption Project , 2004, Genetics.

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

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

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

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

[8]  Connor T. Skennerton,et al.  Crass: identification and reconstruction of CRISPR from unassembled metagenomic data , 2013, Nucleic acids research.

[9]  Andrew R. Bassett,et al.  Mutagenesis and homologous recombination in Drosophila cell lines using CRISPR/Cas9 , 2013, Biology Open.

[10]  Jeffry D Sander,et al.  FLAsH assembly of TALeNs for high-throughput genome editing , 2022 .

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

[12]  Jacques Nicolas,et al.  CRISPI: a CRISPR interactive database , 2009, Bioinform..

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

[14]  R. Jiao,et al.  TALEN or Cas9 - rapid, efficient and specific choices for genome modifications. , 2013, Journal of genetics and genomics = Yi chuan xue bao.

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

[16]  Jianzhong Xi,et al.  Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9 , 2013, Proceedings of the National Academy of Sciences.

[17]  S. Lindquist,et al.  The FLP recombinase of yeast catalyzes site-specific recombination in the drosophila genome , 1989, Cell.

[18]  Philippe Horvath,et al.  The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA , 2010, Nature.

[19]  Chris P Ponting,et al.  Highly Efficient Targeted Mutagenesis of Drosophila with the CRISPR/Cas9 System , 2014, Cell reports.

[20]  T. Cech,et al.  Promiscuous RNA binding by Polycomb Repressive Complex 2 , 2013, Nature Structural &Molecular Biology.

[21]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[22]  R. Jiao,et al.  Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy. , 2012, Journal of genetics and genomics = Yi chuan xue bao.

[23]  Y. Rong,et al.  Gene targeting by homologous recombination in Drosophila. , 2000, Science.

[24]  처치 죠지엠.,et al.  Orthogonal cas9 proteins for rna-guided gene regulation and editing , 2014 .

[25]  Daniel F. Voytas,et al.  Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool , 2007, Nucleic Acids Res..

[26]  U. Bonas,et al.  Genetic and structural characterization of the avirulence gene avrBs3 from Xanthomonas campestris pv. vesicatoria , 1989, Molecular and General Genetics MGG.

[27]  Michele P Calos,et al.  Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. , 2004, Genetics.

[28]  G. Church,et al.  CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering , 2013, Nature Biotechnology.

[29]  Ibtissem Grissa,et al.  CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats , 2008, Nucleic Acids Res..

[30]  S. Del Río,et al.  The function of individual zinc fingers in sequence-specific DNA recognition by transcription factor IIIA. , 1993, Journal of molecular biology.

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

[32]  N. Brockdorff.  Noncoding RNA and Polycomb recruitment. , 2013, RNA.

[33]  Luke A. Gilbert,et al.  CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes , 2013, Cell.

[34]  J. Keith Joung,et al.  FLASH Assembly of TALENs Enables High-Throughput Genome Editing , 2012, Nature Biotechnology.

[35]  C. Ponting,et al.  Massive turnover of functional sequence in human and other mammalian genomes. , 2010, Genome research.

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

[37]  Daniel F. Voytas,et al.  Simple Methods for Generating and Detecting Locus-Specific Mutations Induced with TALENs in the Zebrafish Genome , 2012, PLoS genetics.

[38]  P. Park.  ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.

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

[40]  Gos Micklem,et al.  Supporting Online Material Materials and Methods Figs. S1 to S50 Tables S1 to S18 References Identification of Functional Elements and Regulatory Circuits by Drosophila Modencode , 2022 .

[41]  K. Vasquez,et al.  Gene Targeting by Homologous Recombination , 2014 .

[42]  M. McCarthy,et al.  Genome-wide association studies for complex traits: consensus, uncertainty and challenges , 2008, Nature Reviews Genetics.

[43]  Bo Zhang,et al.  Highly Efficient Genome Modifications Mediated by CRISPR/Cas9 in Drosophila , 2013, Genetics.

[44]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[45]  S. Wolfe,et al.  Targeted chromosomal deletions and inversions in zebrafish , 2013, Genome research.

[46]  Dana Carroll,et al.  Enhancing Gene Targeting with Designed Zinc Finger Nucleases , 2003, Science.

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

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

[49]  Neville E. Sanjana,et al.  Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells , 2014, Science.

[50]  B. Dujon,et al.  Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae , 1995, Molecular and cellular biology.

[51]  Martin Renqiang Min,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[52]  Stan J. J. Brouns,et al.  Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes , 2008, Science.

[53]  N. Nassif,et al.  Targeted gene replacement in Drosophila via P element-induced gap repair , 1991, Science.

[54]  A Klug,et al.  Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[55]  A. J. Schroeder,et al.  Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. , 2007, Genome research.

[56]  Ibtissem Grissa,et al.  CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats , 2007, Nucleic Acids Res..

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

[58]  A Klug,et al.  Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[59]  Chris M. Brown,et al.  CRISPRTarget , 2013, RNA biology.

[60]  Yarden Katz,et al.  Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system , 2013, Cell Research.

[61]  T. Lu,et al.  Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas , 2013, ACS synthetic biology.

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

[63]  J. Gall,et al.  Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases , 2008, Proceedings of the National Academy of Sciences.

[64]  D. Carroll,et al.  Donor DNA Utilization During Gene Targeting with Zinc-Finger Nucleases , 2013, G3: Genes, Genomes, Genetics.

[65]  M. Bibikova,et al.  Efficient Gene Targeting in Drosophila With Zinc-Finger Nucleases , 2006, Genetics.

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

[67]  G. Church,et al.  Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. , 2002, Nucleic acids research.

[68]  Ying Peng,et al.  A simplified and efficient germline-specific CRISPR/Cas9 system for Drosophila genomic engineering , 2013, Fly.

[69]  L. Schouls,et al.  Identification of genes that are associated with DNA repeats in prokaryotes , 2002, Molecular microbiology.

[70]  Ibtissem Grissa,et al.  The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats , 2007, BMC Bioinformatics.

[71]  J. García-Martínez,et al.  Short motif sequences determine the targets of the prokaryotic CRISPR defence system. , 2009, Microbiology.

[72]  Dana Carroll,et al.  Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. , 2002, Genetics.

[73]  Yanhui Hu,et al.  FlyRNAi.org—the database of the Drosophila RNAi screening center: 2012 update , 2011, Nucleic Acids Res..

[74]  Rolf Backofen,et al.  CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems , 2013, Nucleic acids research.

[75]  Jennifer Doudna,et al.  RNA-programmed genome editing in human cells , 2013, eLife.

[76]  Y. Jan,et al.  Efficient Ends-Out Gene Targeting In Drosophila , 2008, Genetics.

[77]  Shu Kondo,et al.  Highly Improved Gene Targeting by Germline-Specific Cas9 Expression in Drosophila , 2013, Genetics.

[78]  Norbert Perrimon,et al.  FlyRNAi: the Drosophila RNAi screening center database , 2005, Nucleic Acids Res..

[79]  Craig D Wenger,et al.  RNA–protein analysis using a conditional CRISPR nuclease , 2013, Proceedings of the National Academy of Sciences.

[80]  Erin L. Doyle,et al.  Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting , 2011, Nucleic acids research.

[81]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[82]  C. Alexandre,et al.  Accelerated homologous recombination and subsequent genome modification in Drosophila , 2013, Development.

[83]  Toshiro K. Ohsumi,et al.  Genome-wide identification of polycomb-associated RNAs by RIP-seq. , 2010, Molecular cell.

[84]  P. Rouet,et al.  Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells. , 1995, Nucleic acids research.

[85]  A. Spradling,et al.  The Drosophila Gene Disruption Project: Progress Using Transposons With Distinctive Site Specificities , 2011, Genetics.

[86]  Neville E Sanjana,et al.  A transcription activator-like effector toolbox for genome engineering , 2012, Nature Protocols.

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

[88]  Drena Dobbs,et al.  ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool , 2010, Nucleic Acids Res..

[89]  Christopher M. Vockley,et al.  RNA-guided gene activation by CRISPR-Cas9-based transcription factors , 2013, Nature Methods.

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

[91]  K. Makino,et al.  Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product , 1987, Journal of bacteriology.