Biotechnology articles within Nature Reviews Genetics

Featured

  • Journal Club |

    Renée Beekman discusses the possibilities for research into transient enhancers by highlighting a recent paper by Vermunt et al. that identifies how they can modulate gene silencing dynamics.

    • Renée Beekman

  • Tools of the Trade |

    In this Tools of the Trade article, Dongsheng Bai and Chenxu Zhu describe SIMPLE-seq, a scalable single-cell sequencing method that simultaneously decodes the cytosine modifications 5mC and 5hmC.

    • Dongsheng Bai
    •  & Chenxu Zhu

  • Journal Club |

    In this Journal Club, Hajk-Georg Drost highlights a recent study by Pavlopoulos et al. that organizes proteins at tree-of-life scale using massively parallel graph-based clustering.

    • Hajk-Georg Drost

  • 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

  • Research Highlight |

    Four papers in Nature describe how ancient European migration patterns have shaped the modern human genome.

    • Michael Attwaters

  • 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

  • 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

  • Perspective |

    This Perspective reviews large-scale genomics and longitudinal phenomics efforts and the insights they can provide into wellness. The authors describe their vision for the transformation of the current health care from disease-oriented to data-driven, wellness-oriented and personalized population health.

    • James T. Yurkovich
    • , Simon J. Evans
    •  & Leroy E. Hood

  • Research Highlight |

    Three papers in Nature report on the largest open-access plasma proteomics dataset to date, a valuable resource for understanding human disease and the identification of drug targets.

    • Michael Attwaters

  • Research Highlight |

    Guhlin et al. sequenced the genomes of almost the entire extant population of the critically-endangered kākāpō, revealing genetic variants for fitness-related traits that can inform conservation strategies.

    • Michael Attwaters

  • Review Article |

    Antimicrobial resistance (AMR) is an important public health issue that affects human, animal and environmental sectors worldwide. The authors review the role of genomics in AMR surveillance using a One Health approach, and how genomic approaches can help mitigate the spread of AMR to improve global health.

    • Steven P. Djordjevic
    • , Veronica M. Jarocki
    •  & Benjamin P. Howden

  • Comment |

    In April 2023, leading experts met with members of US Congress to discuss strategies to ensure global food security. Following on from this, Pamela Ronald emphasizes the role that plant genetics has in achieving these goals.

    • Pamela C. Ronald

  • Editorial |

    Single-cell omics approaches are providing unprecedented insights into cellular function and dysfunction. This Editorial highlights the remarkable potential of these technologies and their profound impact on our understanding of biology and disease.

  • Research Highlight |

    A study in Science identifies Mavericks, a class of ancient, virus-like transposable elements, as a vector for horizontal gene transfer in nematodes.

    • Linda Koch

  • Research Highlight |

    Hao et al. present a workflow to integrate single-cell datasets of diverse modalities using a multi-omic dataset as a molecular bridge.

    • Michael Attwaters

  • Research Highlight |

    Wagner et al. report an organism-wide map of non-coding RNA expression in ageing and rejuvenated mice, identifying a set of broadly deregulated microRNAs that may act as systemic regulators of ageing.

    • Linda Koch

  • Review Article |

    Variant calling is the process of identifying genetic variants, which is important for characterizing population genetic diversity and for identifying disease-associated variants in clinical sequencing projects. In this Review, the authors discuss the state-of-the-art in variant calling, focusing on challenging types of genetic variants, advances in both sequencing technologies and computational pipelines, and benchmarking strategies to assess the robustness of variant-calling strategies.

    • Nathan D. Olson
    • , Justin Wagner
    •  & Justin M. Zook

  • Research Highlight |

    Xu et al. report the development of genetic scores that predict multi-omic traits, enabling cost-effective and powerful analyses for studies that do not include multi-omics data.

    • Linda Koch

  • Research Highlight |

    Zhang et al. describe two technologies for the spatially resolved co-mapping of epigenome and transcriptome at near single-cell resolution.

    • Kirsty Minton

  • 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 Cancer Cell reports genetic ancestry-associated differences in clinical outcomes when using tumour mutational burden as a biomarker in the context of immune checkpoint inhibitor therapy.

    • Linda Koch

  • Research Highlight |

    Two recent studies report microbial genome and gene catalogues that archive oceanic and glacial genomic and functional diversity at scale and yield insights into their biosynthetic potential.

    • Linda Koch

  • Research Highlight |

    A report in Cell takes single-cell CRISPR screens to genome scale and demonstrates how the transcriptional phenotypes can be used to resolve gene functions.

    • Lucia Brunello

  • Research Highlight |

    In six new studies published in Science, the Telomere-to-Telomere (T2T) Consortium reports the assembly and initial characterization of the final, previously unresolved 8% of the human genome.

    • Michael Attwaters

  • Review Article |

    This Review discusses the types of single and multiple human organ-on-a-chip (organ chip) microfluidic devices and their diverse applications for disease modelling, drug development and personalized medicine, as well as the challenges that must be overcome for organ chips to reach their full potential.

    • Donald E. Ingber

  • 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 |

    A recent paper in Nature describes how CRISPR-based engineering of wheat confers robust resistance to powdery mildew disease without negatively impacting crop growth and yields.

    • Xian Deng
    •  & Xiaofeng Cao

  • In Brief |

    Flotte et al. describe the first test of adeno-associated virus-based gene therapy for Tay-Sachs disease in humans. Delivery to the thalamus and cerebrospinal fluid was found to be broadly safe, providing a firm basis for future clinical trials.

    • Dorothy Clyde

  • In Brief |

    A report in Science describes a method to generate transient chimeric antigen receptor (CAR) T cells in vivo via lipid nanoparticle-mediated T cell-targeted delivery of a CAR-encoding nucleoside-modified mRNA.

    • Dorothy Clyde

  • Review Article |

    RNA therapies can be used to manipulate gene expression or produce therapeutic proteins. Here, the authors describe the growing number of RNA therapies and their molecular mechanisms of action. They also discuss the path from preclinical drug delivery research to clinical approval of these drugs.

    • Kalina Paunovska
    • , David Loughrey
    •  & James E. Dahlman

  • Review Article |

    Synthetic RNA devices integrate sensing, processing and actuation of signals into defined, programmable functions to control cell behaviour. This Review discusses the emerging applications of RNA devices in biomedical research and biomanufacturing, as well as progress in creating new ligand sensors and new mechanisms of action with engineered RNAs.

    • Peter B. Dykstra
    • , Matias Kaplan
    •  & Christina D. Smolke

  • Research Highlight |

    Rubin et al. report the development of a programmable organism- and locus-specific genome editing approach that can target microorganisms in their native community context, without the need for isolation.

    • Linda Koch

  • Research Highlight |

    Four new studies in Nature report multi-tissue analyses of somatic mutations from human donors, with insights into cell lineage commitment during embryonic development, as well as tissue-specific aspects of mutagenesis.

    • Darren J. Burgess

  • In Brief |

    A study in Current Biology reports the retrieval of genome-scale information for human, wolf (Canis lupus) and bison (Bison bonasus) by shotgun sequencing and genomic analysis of a sediment sample.

    • Linda Koch

  • Review Article |

    Synthetic biology has enabled the development of engineered cells that can serve as ex vivo or in vivo diagnostic tools or therapeutic delivery systems. This Review discusses preclinical and clinical applications of bacterial and mammalian theranostic cells as well as their underlying biological designs and remaining hurdles to their successful clinical application.

    • Monica P. McNerney
    • , Kailyn E. Doiron
    •  & Pamela A. Silver

  • Review Article |

    Long-read sequencing at the population scale presents specific challenges but is becoming increasingly accessible. In this Review, Sedlazeck and colleagues discuss the major platforms and analytical tools, considerations in project design and challenges in scaling long-read sequencing to populations.

    • Wouter De Coster
    • , Matthias H. Weissensteiner
    •  & Fritz J. Sedlazeck

  • Research Highlight |

    The Vertebrate Genomes Project, which aims to produce high-quality reference genomes for all 71,657 living and named vertebrate species, reports the generation of high-quality genome assemblies for the first 16 species and describes the biological findings that these genomes have informed.

    • Katharine H. Wrighton

  • Journal Club |

    Qifa Zhang describes how a 2008 publication in Nature Biotechnology on transgenic purple tomatoes inspired him to tackle food security by improving the nutrient and culinary value of black rice.

    • Qifa Zhang

  • Research Highlight |

    Two new studies in Cell report the use of CRISPR–Cas cytosine base editors (CBEs) in mammalian cells for high-throughput functional genomics screens.

    • Linda Koch

  • 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 Genetics applies whole-genome sequencing to monozygotic twins, their parents, partners and offspring to identify and characterize early developmental mutations, as well as the fate of mutated cells.

    • Linda Koch

  • Research Highlight |

    Two new papers in Nature Biotechnology report methods for targeted sequencing of complex DNA samples, achieved in real time during nanopore sequencing runs.

    • Darren J. Burgess

  • 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

  • In Brief |

    The CRISPR–Cas13 system can be used to knock down circular RNAs (circRNAs) without any impact on related mRNAs, reports a study in Nature Methods.

    • Linda Koch

  • Review Article |

    Haematopoietic stem and progenitor cell (HSPC) gene therapy using lentiviral or gammaretroviral vectors has now been approved for clinical use. In this Review, Ferrari, Thrasher and Aiuti discuss the history of HSPC gene therapy, the clinical promise of gene-editing HPSCs and the use of HSPC gene therapy to treat specific diseases.

    • Giuliana Ferrari
    • , Adrian J. Thrasher
    •  & Alessandro Aiuti

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