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Genome Editing

Recent advances in genome editing technologies have substantially improved our ability to make precise changes in the genomes of eukaryotic cells. Programmable nucleases, particularly the CRISPR/Cas system, are already revolutionizing our ability to interrogate the function of the genome and can potentially be used clinically to correct or introduce genetic mutations to treat diseases that are refractory to traditional therapies. This collection of articles from the Nature Research journals provides an overview of current progress in developing targeted genome editing technologies. A selection of protocols for using and adapting these tools in your own lab is also included.

News and comments

  • Nature Methods | Method to Watch

    Engineered genome structure explores function.

    • Nicole Rusk
  • Nature Biotechnology | News & Views

    Cas9 can induce extensive on-target damage, including large deletions, inversions, and insertions.

    • Hyunji Lee
    •  &  Jin-Soo Kim
  • Nature Medicine | News & Views

    Base editors function in mouse fetuses and in the livers of adult mice to treat a genetic disorder.

    • Huiyun Seo
    •  &  Jin-Soo Kim
  • Nature Methods | Technology Feature

    A way to gene edit without double-stranded DNA breaks is now entering labs.

    • Vivien Marx
  • Nature Medicine | News & Views

    Signaling by the tumor-suppressor protein p53 antagonizes CRISPR–Cas9 gene editing of human pluripotent stem cells and immortalized human retinal pigment epithelial cells.

    • Fyodor D. Urnov

Research

  • Nature | Article

    The authors use a machine-learning algorithm to predict the spectrum of CRISPR–Cas9-nuclease-mediated DNA repair outcomes at human genomic target sites.

    • Max W. Shen
    • , Mandana Arbab
    • , Jonathan Y. Hsu
    • , Daniel Worstell
    • , Sannie J. Culbertson
    • , Olga Krabbe
    • , Christopher A. Cassa
    • , David R. Liu
    • , David K. Gifford
    •  &  Richard I. Sherwood
  • Nature Medicine | Letter

    Mitochondrially targeted zinc-finger nucleases reduce mutational burden and correct biochemical defects in a mouse model of mitochondrial disease.

    • Payam A. Gammage
    • , Carlo Viscomi
    • , Marie-Lune Simard
    • , Ana S. H. Costa
    • , Edoardo Gaude
    • , Christopher A. Powell
    • , Lindsey Van Haute
    • , Beverly J. McCann
    • , Pedro Rebelo-Guiomar
    • , Raffaele Cerutti
    • , Lei Zhang
    • , Edward J. Rebar
    • , Massimo Zeviani
    • , Christian Frezza
    • , James B. Stewart
    •  &  Michal Minczuk
  • Nature Biomedical Engineering | Article

    CRISPR–Cas9-mediated genome editing can be activated locally in vivo via an applied magnetic field, after complexation of magnetic nanoparticles with recombinant baculoviral vectors packaging the CRISPR–Cas9 machinery.

    • Haibao Zhu
    • , Linlin Zhang
    • , Sheng Tong
    • , Ciaran M. Lee
    • , Harshavardhan Deshmukh
    •  &  Gang Bao
  • Nature Communications | Article | open

    The absence of effective gene activators in bacteria limits regulated expression programs. Here the authors design synthetic bacterial CRISPR-Cas transcriptional activators that can be used to construct multi-gene programs of activation and repression.

    • Chen Dong
    • , Jason Fontana
    • , Anika Patel
    • , James M. Carothers
    •  &  Jesse G. Zalatan
  • Nature Methods | Brief Communication

    The length of the guide RNA for Cas12a-VPR determines whether a target gene is edited or activated and allows for multiplexed, combinatorial gene modifications.

    • Marco Breinig
    • , Anabel Y. Schweitzer
    • , Anna M. Herianto
    • , Steffie Revia
    • , Lisa Schaefer
    • , Lena Wendler
    • , Ana Cobos Galvez
    •  &  Darjus F. Tschaharganeh
  • Nature Plants | Brief Communication

    A study developed genomic resources and efficient transformation in the orphan crop groundcherry, and managed to improve productivity traits by editing the orthologues of tomato domestication and improvement genes using CRISPR–Cas9.

    • Zachary H. Lemmon
    • , Nathan T. Reem
    • , Justin Dalrymple
    • , Sebastian Soyk
    • , Kerry E. Swartwood
    • , Daniel Rodriguez-Leal
    • , Joyce Van Eck
    •  &  Zachary B. Lippman

Reviews

  • Nature Reviews Microbiology | Review Article

    In this Review, Pedra and colleagues describe the advances and challenges in the genetic engineering of obligate intracellular bacteria, and highlight examples of how the use of genetically manipulated pathogens has improved our understanding of microbial pathogenesis and host–pathogen interactions.

    • Erin E. McClure
    • , Adela S. Oliva Chávez
    • , Dana K. Shaw
    • , Jason A. Carlyon
    • , Roman R. Ganta
    • , Susan M. Noh
    • , David O. Wood
    • , Patrik M. Bavoil
    • , Kelly A. Brayton
    • , Juan J. Martinez
    • , Jere W. McBride
    • , Raphael H. Valdivia
    • , Ulrike G. Munderloh
    •  &  Joao H. F. Pedra
  • Nature Communications | Review Article | open

    CRISPR has rapidly become an indispensable tool for biological research. Here Mazhar Adli reviews the current toolbox for editing and manipulating the genome and looks toward future developments in this fast moving field.

    • Mazhar Adli

Protocols

  • Nature Protocols | Protocol

    In this protocol, the authors describe how to design, synthesize, and deliver CRISPR–Cas9 RNPs to primary CD4+ T cells for targeted gene knockout. They then show how the edited cells can be used for the analysis of host factors in HIV replication.

    • Judd F. Hultquist
    • , Joseph Hiatt
    • , Kathrin Schumann
    • , Michael J. McGregor
    • , Theodore L. Roth
    • , Paige Haas
    • , Jennifer A. Doudna
    • , Alexander Marson
    •  &  Nevan J. Krogan
  • Nature Protocols | Protocol

    This protocol describes CIRCLE-seq (circularization for in vitro reporting of cleavage effects by sequencing), a sensitive and unbiased method for defining the on-target and off-target activity of CRISPR–Cas9 nucleases genome-wide.

    • Cicera R. Lazzarotto
    • , Nhu T. Nguyen
    • , Xing Tang
    • , Jose Malagon-Lopez
    • , Jimmy A. Guo
    • , Martin J. Aryee
    • , J. Keith Joung
    •  &  Shengdar Q. Tsai
  • Nature Protocols | Protocol

    CRISPR-EZ achieves 100% delivery of Cas9/sgRNA RNPs by zygote electroporation, enabling efficient incorporation of indels, exon deletions, point mutations, and small insertions into the mouse genome, and outperforming microinjection-based methods.

    • Andrew J Modzelewski
    • , Sean Chen
    • , Brandon J Willis
    • , K C Kent Lloyd
    • , Joshua A Wood
    •  &  Lin He