Molecular engineering articles within Nature Reviews Genetics

Featured

  • Journal Club |

    Vincent Courdavault and Nicolas Papon highlight two articles in Nature, published in 2006 and 2013, that reported the biosynthesis of a complex natural plant product to treat malaria in engineered yeast.

    • Vincent Courdavault
    •  & Nicolas Papon

  • Review Article |

    In this Review, the authors summarize recent progress in cell–cell interaction (CCI) research. They describe the recent evolution in computational tools that underpin CCI studies, discuss improvements in experimental methods enabling more high-throughput analyses of CCIs, and highlight future directions for the field.

    • Erick Armingol
    • , Hratch M. Baghdassarian
    •  & Nathan E. Lewis

  • Research Highlight |

    Two new studies in Nature Biotechnology describe cellular recording systems that incorporate time-resolved optical signals into self-assembling protein filaments.

    • Darren J. Burgess

  • Research Highlight |

    Two new studies in Science characterize a CRISPR-associated nuclease–protease system that can be leveraged as a programmable protease-based RNA sensor.

    • Darren J. Burgess

  • 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

  • Research Highlight |

    A paper in Science describes a system in synthetic yeast chromosomes in which the properties of genetic sequences change depending on the neighbouring transcriptional activity.

    • Lucia Brunello

  • Research Highlight |

    Three new studies in Nature Biotechnology combine the adenine and cytosine deaminase activities of single base editors to generate dual base editor systems for combinatorial editing in human cells.

    • Darren J. Burgess

  • Research Highlight |

    A study reports on the suitability of the yeast Saccharomyces cerevisiae as a platform for the assembly and maintenance of diverse RNA virus genomes, including SARS-CoV-2.

    • Linda Koch

  • Research Highlight |

    A new study in Science reports a synthetic biology approach to encode an ultrasound-based gene expression reporter that is applicable to mammalian cells in vitro and in vivo.

    • Darren J. Burgess

  • Research Highlight |

    A recent study in Nature Microbiology reports metagenomic signatures of early-life antibiotic treatment and hospitalization associated with preterm birth that persist long-term.

    • Linda Koch

  • Research Highlight |

    Two recent studies report innovative RNA base editing tools: adenine editing without the requirement for exogenous enzymes, and a new ability to edit cytosines.

    • Darren J. Burgess

  • Review Article |

    Next-generation sequencing has improved the identification and characterization of antimicrobial resistance. Focusing on sequence-based discovery of antibiotic resistance genes, this Review discusses computational strategies and resources for resistance gene identification in genomic and metagenomic samples, including recent deep-learning approaches.

    • Manish Boolchandani
    • , Alaric W. D’Souza
    •  & Gautam Dantas

  • Research Highlight |

    A study in Cell reports the development of a synthetic, modular and programmable read–write system that serves as a platform for programming epigenetic functions in mammalian cells and can aid the analysis of epigenetic regulatory mechanisms.

    • Michelle Trenkmann

  • 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 |

    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

  • Review Article |

    Identifying which genes in a genome are essential for survival has been a long-standing goal of geneticists. This Review discusses our evolving understanding of cellular gene essentiality across diverse organisms. It describes how essentiality is often non-absolute but is instead dependent on the environment or genetic background and how this knowledge can be exploited therapeutically.

    • Giulia Rancati
    • , Jason Moffat
    •  & Norman Pavelka

  • 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 |

    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

  • Review Article |

    Genome engineering can be used to introduce targeted genetic changes to design and reprogramme organisms, to introduce new functionalities and to discover causal associations in evolving phenotypes. In this Review, the rationale, techniques and applications in genome engineering are described, outlining key advances, technological goals and challenges, as genome engineering approaches move towards massively parallel platforms.

    • Adrian D. Haimovich
    • , Paul Muir
    •  & Farren J. Isaacs

  • Review Article |

    Directed evolution uses laboratory-based evolution to enhance the properties of biomolecules, primarily to generate proteins with optimized or novel activities. This Review discusses the diverse range of technologies for the directed evolution of proteins, particularly methods for generating diversity in the gene library and approaches for screening and selecting for variants with desired properties. The relative strengths and limitations of these approaches are highlighted to guide readers to appropriate strategies.

    • Michael S. Packer
    •  & David R. Liu

  • Review Article |

    Synthetic biology approaches to characterize gene regulation have largely used transcription factor circuits in bacteria. However, the multilayered regulation of genes by chromatin in eukaryotes provides opportunities for more sophisticated control of gene expression. This Review describes diverse approaches for engineering eukaryotic chromatin states, the insights gained into physiological gene regulation principles, and the broad potential applications throughout biomedical research and industry.

    • Albert J. Keung
    • , J. Keith Joung
    •  & James J. Collins

  • Review Article |

    Synthetic biological devices can be engineered to achieve high levels of precision and specificity, which makes them ideally suited for use in clinical settings. Devices are being developed to meet a range of biomedical needs, including specific cancer therapies and metabolic control.

    • Wilfried Weber
    •  & Martin Fussenegger

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