Experimental organisms articles within Nature Reviews Genetics

Featured

  • In Brief |

    Gene loss is followed by the rapid emergence of new phenotypes owing to compensatory evolution, finds a recent study using experimental evolution of budding yeast lineages.

    • Linda Koch

  • In Brief |

    A recent study in Cell describes a developmentally important liquid-to-solid phase transition involving oskar ribonucleoprotein granules in Drosophila melanogaster oocytes.

    • Dorothy Clyde

  • Research Highlight |

    New work studying the plant Arabidopsis thaliana shows that patterns of observed sequence variants are primarily influenced by biases in initial mutation occurrences rather than by the subsequent selective pressures.

    • Darren J. Burgess

  • Research Highlight |

    Attempts to understand the role of aneuploidy in tumorigenesis have been hampered by conflicting results. Now, two new mouse models described in Genes and Development provide evidence that chromosome instability-induced aneuploidy drives T cell lymphomagenesis.

    • Dorothy Clyde

  • Review Article |

    MicroRNAs (miRNA) exert essential functions in mammalian development and physiology. The authors review recent insights from the phenotypic analysis of miRNA knockouts in mice that emphasize roles for these non-coding RNAs at different developmental stages and in adults, and illustrate the importance of functional miRNA targets, miRNA dosage, miRNA interactions and cellular context.

    • Brian DeVeale
    • , Jennifer Swindlehurst-Chan
    •  & Robert Blelloch

  • Research Highlight |

    A recent study re-casts proteomic analyses as a DNA sequencing problem; by fusing in vivo-expressed proteins to their encoding mRNA, molecular interactions can be identified and quantified through high-throughput nucleic-acid sequencing.

    • Linda Koch

  • 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 |

    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

  • Research Highlight |

    A study in Science describes the generation of a lineage-resolved single-cell transcriptome atlas for Caenorhabditis elegans embryos. This resource provides insight into the transcriptional changes underlying cell fate decisions.

    • Dorothy Clyde

  • 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

  • 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

  • Research Highlight |

    Unlike most organisms, planaria maintain pluripotent stem cells (PSCs) beyond embryogenesis. A new study reports the prospective identification and isolation of a neoblast subpopulation containing adult PSCs, characterization of which should help uncover the mechanisms underlying pluripotency and tissue regeneration.

    • Dorothy Clyde

  • Research Highlight |

    A new study reveals that DNA methylation-mediated repression of gene expression regulates early eye development in blind cave morphs of Astyanax mexicanus.

    • Linda Koch

  • Research Highlight |

    Three new studies in Nature and Nature Biotechnology report methods for dissecting transcriptomic cell phenotypes and lineage history simultaneously by combining single-cell RNA sequencing (scRNA-seq) with CRISPR-based lineage tracing.

    • Darren J. Burgess

  • 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

  • Analysis |

    Characterizing the essentiality of human genes provides insights into gene function and genome evolution and facilitates the clinical interpretation of genetic variants. This article analyses essentiality metrics based on the statistical intolerance to loss-of-function mutations in human population sequencing studies and discusses commonalities and distinctions relative to data sets from knockout mice and functional genomics screens in human cell culture. Implications for disease genetics and extrapolation to non-coding regions are also discussed.

    • István Bartha
    • , Julia di Iulio
    •  & Amalio Telenti

  • Review Article |

    Despite being a single species, dogs represent nearly 400 breeds with substantial genetic, morphological and behavioural diversity. In this Review, Ostranderet al. discuss how genomics studies of dogs have enhanced our understanding of dog and human population history, the desired and unintended consequences of trait-based selective breeding, and potentially human-applicable insights into cancer, ageing, behaviour and neurological diseases.

    • Elaine A. Ostrander
    • , Robert K. Wayne
    •  & Brian W. Davis

  • Review Article |

    Saccharomyces cerevisiaehas become an important model organism in the field of evolutionary genomics. Comparative genomic analysis of laboratory, wild and domesticated yeast populations is generating insights into how new species form and how populations adapt to their environments.

    • Souhir Marsit
    • , Jean-Baptiste Leducq
    •  & Christian R. Landry

  • Review Article |

    Next-generation sequencing technologies have enabled the comprehensive characterization of human and mouse genomes, including at the transcriptional level. This article reviews the degree of conservation of human and mouse transcriptomes, along with the challenges of identifying when the mouse is a suitable model of human physiology.

    • Alessandra Breschi
    • , Thomas R. Gingeras
    •  & Roderic Guigó

  • 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 |

    In this Review, the author discusses current knowledge on the paramutations that occur in maize and contrasts these behaviours with potentially parallel examples in metazoans. He highlights the key role of small RNAs (sRNAs) in diverse paramutation mechanisms across eukaryotes and considers the evolutionary importance of these regulatory systems.

    • Jay B. Hollick

  • 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

  • Comment |

    Researchers should embrace differences in genetic background to build richer disease models that more accurately reflect the level of variation in the human population, posits Clement Chow.

    • Clement Y. Chow

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