Genetic engineering articles within Nature Reviews Genetics

Featured

  • Research Highlight |

    A study in Nature Biotechnology reports a platform that combines lentivirus capabilities with antibody recognition for targeted cell delivery and genome editing.

    • Linda Koch

  • Research Highlight |

    Breda et al. developed a method for gene editing bone marrow cells in vivo, circumventing the need for toxic conditioning regimens such as chemotherapy or radiation.

    • Michael Attwaters

  • Review Article |

    In this Review, Chen and Liu discuss the latest developments in prime editing systems, including improvements to their editing efficiency and capabilities, as well as diverse emerging applications in research and preclinical therapeutic studies.

    • Peter J. Chen
    •  & David R. Liu

  • Review Article |

    The authors review the field of mammalian mitochondrial genome engineering, culminating in the recent development of mitochondrially targeted programmable nucleases and base editors. They describe research that led to the development of animal models of mitochondrial disease, as well as the potential for translating these approaches to the clinic.

    • Pedro Silva-Pinheiro
    •  & Michal Minczuk

  • Review Article |

    Loci that encode long non-coding RNAs (lncRNAs) can be complex and function through multiple modalities. The authors provide a framework for elucidating the physiological roles of lncRNAs using genetically engineered mouse models, including whole-gene deletion, transcription termination, reporters and transgene rescue strategies.

    • Daniel Andergassen
    •  & John L. Rinn

  • Research Highlight |

    Two recent studies demonstrate that putative nucleases encoded by IS200/IS605 family transposons are programmable RNA-guided DNA endonucleases, which could represent a new source of genome-editing enzymes for biotechnological applications.

    • Grant Otto

  • Research Highlight |

    Three recent studies report the generation of miniature CRISPR systems based on compact Cas effector proteins, showing high efficiency of genome editing or transcriptional regulation in mammalian cells.

    • Linda Koch

  • Review Article |

    In this Review, Ethan Bier discusses how several impactful technical advancements, particularly involving CRISPR-based methods, are providing a diverse toolkit of gene-drive systems for the control of populations such as insect vectors of disease.

    • Ethan Bier

  • Review Article |

    This Review discusses strategies for the genetic engineering of adoptive T cell immunotherapies with a focus on approaches harnessing transgenic T cell receptors or chimeric antigen receptors to treat cancer. The authors also discuss the more complex levels of genetic regulation that will be needed to ensure both safety and efficacy.

    • Gavin I. Ellis
    • , Neil C. Sheppard
    •  & James L. Riley

  • Review Article |

    There is a rapidly growing appreciation of the complexities of 3D genome organization, as well as associations with gene expression and wider cellular and organismal phenotypes, including diseases. In this Review, the authors describe diverse experimental methods for manipulating 3D genome organization — from fine-scale control of DNA contacts to large-scale nuclear repositioning — which are facilitating detailed testing of the biological functions of 3D genome organization.

    • Haifeng Wang
    • , Mengting Han
    •  & Lei S. Qi

  • Research Highlight |

    A study in Nature reports that adenine base editors can correct the mutation that causes Hutchinson–Gilford progeria syndrome in a mouse model of this disease, extending lifespan.

    • Katharine H. Wrighton

  • Review Article |

    The ability to reprogramme cellular translation and genomes to produce non-canonical biopolymers has wide-ranging applications, including in therapeutics, but has yet to be fully realized. In this Review, de la Torre and Chin discuss recent advances towards achieving this goal.

    • Daniel de la Torre
    •  & Jason W. Chin

  • Research Highlight |

    Pathogens are wreaking havoc on bee populations. A study in Science describes how bacteria in the guts of bees can be engineered to protect their hosts from two particular pests, deformed wing virus and Varroa mites.

    • Dorothy Clyde

  • Review Article |

    Adeno-associated virus (AAV) vector-mediated gene delivery has had long-term therapeutic effects for several diseases, including haemophilia and Duchenne muscular dystrophy. Genetically modifying AAV vectors to increase their transduction efficiency, vector tropism and ability to avoid the host immune response may further increase the success of AAV gene therapy.

    • Chengwen Li
    •  & R. Jude Samulski

  • Research Highlight |

    A new genome editing strategy called prime editing uses a catalytically impaired Cas9 fused to an engineered reverse transcriptase to write desired genetic sequence information directly into a target locus.

    • Linda Koch

  • Research Highlight |

    Two studies in Science show that cytosine base editors, but not adenine base editors or CRISPR–Cas9, induce notable off-target single-nucleotide variants in rice and in mouse embryos.

    • Katharine H. Wrighton

  • Research Highlight |

    A study published in Nature reports the functional and structural characterization of CasX, an RNA-guided DNA endonuclease with potential for use as a new genome editing platform.

    • Linda Koch

  • Research Highlight |

    A study in Nature shows the feasibility of using the CRISPR–Cas9 system for efficient and precise genotypic correction of pathogenic mutations without a donor template.

    • Ross Cloney

  • Review Article |

    Genome editing through direct editing of bases holds promise for achieving precise genomic changes at single-nucleotide resolution while minimizing the occurrence of potentially mutagenic double-strand DNA breaks. In this Review, Rees and Liu provide a comprehensive account of the state of the art of base editing of DNA and RNA, including the progressive improvements to methodologies, understanding and avoiding unintended edits, cellular and organismal delivery of editing reagents and diverse applications in research and therapeutic settings.

    • Holly A. Rees
    •  & David R. Liu

  • Review Article |

    CRISPR–Cas genome editing and next-generation sequencing are driving advances in cancer modelling and functional cancer genomics. Their application to autochthonous mouse models of human cancer to generate and analyse multiplexed and/or combinatorial alterations in vivo is reviewed here.

    • Ian P. Winters
    • , Christopher W. Murray
    •  & Monte M. Winslow

  • Review Article |

    In this Review, Sheth and Wang describe emerging synthetic biology approaches for using DNA as a memory device for recording cellular events, including the various methodological steps from detecting diverse signals, converting them into DNA alterations and reading out and interpreting the recorded information. Furthermore, they discuss potential applications as biotechnological and environmental biosensors.

    • Ravi U. Sheth
    •  & Harris H. Wang

  • Research Highlight |

    A study in Nature Biomedical Engineering reports improvements in neurological symptoms in a mouse model of fragile X syndrome after non-viral delivery of Cas9 ribonucleoproteins to the brain.

    • Michelle Trenkmann

  • Review Article |

    Although the field of functional genomics is increasingly adopting genome-scale approaches, a comprehensive understanding of gene functions requires the parallel development of deep phenotyping platforms. This Review discusses strategies for broad-based mouse phenomics, applied both to gene knockout collections and to diverse strains harbouring natural genetic variation. The authors discuss technical challenges, analysis pipelines and insights into human disease genetics.

    • Steve D. M. Brown
    • , Chris C. Holmes
    •  & Sara Wells

  • Review Article |

    The rapid development of CRISPR-based gene manipulation has enabled various approaches for high-throughput functional genomics. This Review guides users through the practicalities of CRISPR-based functional genomics screens, including study design options, best-practice approaches, pitfalls to avoid and data analysis strategies.

    • John G. Doench

  • Opinion |

    Advances in genome sequencing, editing and synthetic biology have enhanced the feasibility of large-scale genome engineering, termed genome writing. In this Opinion article, Chari and Church discuss the strengths and limitations of diverse strategies for genome writing, including extensively modifying existing genomes versus synthesizing genomesde novo, and they provide future visions for writing large genomes.

    • Raj Chari
    •  & George M. Church

  • Review Article |

    A wealth of data is emerging from diverse studies of epigenomics, including genome-scale profiles of DNA methylation, histone modifications and higher-order chromatin features. In this Review, the authors discuss how, despite all this information, many challenges remain for inferring and proving the physiological and pathological functions of chromatin states. They describe the degrees of 'functionality' that are revealed by different experimental approaches, the value of integrative strategies and visions for the future.

    • Stefan H. Stricker
    • , Anna Köferle
    •  & Stephan Beck

  • Review Article |

    Loss-of-function (LOF) approaches are powerful experimental tools for characterizing gene functions. However, emerging discrepancies when genes are investigated using different tools or organisms has triggered debate about how such LOF results should be biologically interpreted. In this Review, experts from varied fields discuss how understanding the underlying features of each LOF approach can provide explanations for different experimental outcomes and can guide their optimal and reliable application.

    • Benjamin E. Housden
    • , Matthias Muhar
    •  & Norbert Perrimon

  • Review Article |

    Applying CRISPR–Cas9 genome editing technologies in safe and reliable ways requires a firm appreciation of the specificity of target-site recognition and cleavage. In this Review the authors discuss various approaches for characterizing off-target effects of CRISPR–Cas9 genome editing, how mechanistic knowledge can drive the engineering of more-specific nucleases, and the implications for research and therapeutic applications.

    • Shengdar Q. Tsai
    •  & J. Keith Joung

  • Review Article |

    RNA-guided endonucleases have the potential to revolutionize the engineering of synthetic gene drives, which may be particularly useful for the control of vector-borne diseases. Here, the authors review different types of engineered gene drives and their potential applications, as well as considerations regarding the safety and regulation of gene drives for the manipulation of wild populations.

    • Jackson Champer
    • , Anna Buchman
    •  & Omar S. Akbari

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