Collection |

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 Plants | Editorial

    Gene editing techniques have the potential to substantially accelerate plant breeding. Now, officials in the United States and Europe are arguing that it is not genetic modification — and that is a good thing!

  • Nature Microbiology | Editorial

    Although the spotlight on CRISPR–Cas systems has shone on their immense potential as genome-editing tools, the field’s origins are rooted in the microbiology of phage–bacterium interactions. Furthering our understanding of these processes can uncover more systems and generate new reagents with revolutionary properties.

  • Nature Medicine | News Feature

    Finding poetry in gene editing and ways to improve it

    • Peter Andrey Smith

Research

  • Nature | Article

    Phage-assisted continuous evolution of Cas9 variants with broad PAM compatibility and high DNA specificity that can be used for transcriptional activation, gene disruption and base editing.

    • Johnny H. Hu
    • , Shannon M. Miller
    • , Maarten H. Geurts
    • , Weixin Tang
    • , Liwei Chen
    • , Ning Sun
    • , Christina M. Zeina
    • , Xue Gao
    • , Holly A. Rees
    • , Zhi Lin
    •  &  David R. Liu
  • Nature Plants | Brief Communication

    Plant-compatible adenine base editor systems are now demonstrated to work in protoplasts and individual plants of Arabidopsis thaliana and Brassica napus, yielding plants with predicted nucleotide substitutions and stably inherited phenotypes.

    • Beum-Chang Kang
    • , Jae-Young Yun
    • , Sang-Tae Kim
    • , YouJin Shin
    • , Jahee Ryu
    • , Minkyung Choi
    • , Je Wook Woo
    •  &  Jin-Soo Kim
  • Nature | Letter

    A single-cell sequencing method is developed that uses transcriptomics and CRISPR–Cas9 technology to investigate clonal relationships in cells present in different zebrafish tissues.

    • Anna Alemany
    • , Maria Florescu
    • , Chloé S. Baron
    • , Josi Peterson-Maduro
    •  &  Alexander van Oudenaarden
  • Nature Microbiology | Letter

    Nuclease-mediated genome editing in bacteria has been limited by toxicity problems linked to DNA cleavage. The use of cytidine deaminase fused to a nuclease-deficient Cas9 bypasses some of these problems, enabling modification of multiple loci simultaneously.

    • Satomi Banno
    • , Keiji Nishida
    • , Takayuki Arazoe
    • , Hitoshi Mitsunobu
    •  &  Akihiko Kondo

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

    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
  • Nature Protocols | Protocol

    This protocol describes how to set up arrayed and pooled CRISPR genome-editing experiments. It describes the design of sgRNAs using CRISPOR, the wet-lab implementations, and analysis of the generated results by CRISPResso.

    • Matthew C Canver
    • , Maximilian Haeussler
    • , Daniel E Bauer
    • , Stuart H Orkin
    • , Neville E Sanjana
    • , Ophir Shalem
    • , Guo-Cheng Yuan
    • , Feng Zhang
    • , Jean-Paul Concordet
    •  &  Luca Pinello
  • Nature Protocols | Protocol

    This protocol enables genome editing using the CRISPR–Cpf1 system, an alternative to CRISPR–Cas9. The authors detail the design and assessment of engineered components of the system, both crRNAs and Cpf1 mRNAs, and their use for effective genome editing.

    • Bin Li
    • , Chunxi Zeng
    •  &  Yizhou Dong