Biological techniques articles within Nature Reviews Genetics

Featured

  • Journal Club |

    Mustafa Mir reflects on a 1976 paper by McKnight and Miller, in which they developed a technique to directly visualize gene regulatory dynamics.

    • Mustafa Mir

  • Review Article |

    Targeted genome modification using CRISPR–Cas genome editing, base editing or prime editing is driving base research in plants and precise molecular breeding. The authors review the technological principles underlying these methods, approaches for their delivery in plants, and emerging crop-breeding strategies based on targeted genome modification.

    • Boshu Li
    • , Chao Sun
    •  & Caixia Gao

  • Research Highlight |

    A publication in Nature reports the data release of around 245,000 clinical-grade whole-genome sequences as part of the NIH’s All of Us Research Programme. Several companion papers highlight the value of better capturing global genomic diversity.

    • Linda Koch

  • Research Highlight |

    A study in Nature Genetics identifies many regulators of genome-wide chromatin accessibility and then reports the mechanistic underpinnings for one of the identified transcription factors.

    • Henry Ertl

  • Research Highlight |

    The Farm Animal GTEx project introduces a new resource for pigs, in which they map genetic variation to differences in gene expression across thousands of samples.

    • Henry Ertl

  • 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 |

    Genomic technologies have greatly improved the diagnosis of rare genetic diseases. Here, the authors review emerging approaches for the identification of disease-causal genetic variants as well as omic technologies that show great potential for variant interpretation.

    • Kristin D. Kernohan
    •  & Kym M. Boycott

  • Review Article |

    In this Review, the authors summarize and discuss guidelines for omics benchmarking. They highlight common oversights and difficulties, offer guidance for frequently encountered issues and provide a structured form that can be used for comprehensive reporting of benchmarking studies.

    • Thomas G. Brooks
    • , Nicholas F. Lahens
    •  & Gregory R. Grant

  • Review Article |

    In this Review, Hwang and co-authors outline single-molecule fluorescence imaging techniques that can be used in living cells to visualize individual molecules involved in the spatiotemporal regulation of gene expression. This Review also delves into the biological insights gained through these methodologies.

    • Dong-Woo Hwang
    • , Anna Maekiniemi
    •  & Hanae Sato

  • 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 |

    Legnini et al. report in Nature Methods their new optogenetic method for controlling gene expression in organoids that can be coupled with single-cell and spatial transcriptomics.

    • Henry Ertl

  • 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 |

    In this Review, Zhang et al. discuss how recent advances in computational methods are helping to reveal the multiscale features involved in genome folding within the nucleus and how the resulting 3D genome organization relates to genome function.

    • Yang Zhang
    • , Lorenzo Boninsegna
    •  & Jian Ma

  • 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 |

    This Review summarizes the genetic and non-genetic factors that impact the transferability of polygenic risk scores (PRSs) across populations, highlighting the technical challenges of existing PRS construction methods for diverse ancestries and the emerging resources for more widespread use of PRSs.

    • Linda Kachuri
    • , Nilanjan Chatterjee
    •  & Tian Ge

  • 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 |

    In five new studies, the Human Pangenome Reference Consortium reports the generation and initial characterization of a draft human pangenome.

    • Michael Attwaters

  • Research Highlight |

    A study in Nature Biotechnology describes Scriabin, a highly scalable framework for inference of cell–cell communication from scRNA-seq data at the level of individual cells.

    • Dorothy Clyde

  • Journal Club |

    Roser Vento-Tormo highlights the synergy of single-cell omics and organoids by Camp et al., who used single-cell RNA sequencing to characterize the cell–cell communication events driving tissue formation in human liver organoids.

    • Roser Vento-Tormo

  • Journal Club |

    In this Journal Club, Celine Vallot discusses two 2015 papers that introduced the concept of high-throughput RNA barcoding, which paved the way for today’s plethora of single-cell omic approaches.

    • Céline Vallot

  • Research Highlight |

    A study in Molecular Cell reveals how CTCF and cohesin contribute to genome organization through their roles in forming and stacking chromatin loops.

    • Dorothy Clyde

  • Review Article |

    In this Review, the authors describe the emerging field of single-cell genetics, which lies at the intersection of single-cell genomics and human genetics. They review the first single-cell expression quantitative trait loci studies, which combine single-cell information with genotype data at the population scale and thereby link genetic variation to the cellular processes underpinning key aspects of human biology and disease.

    • Anna S. E. Cuomo
    • , Aparna Nathan
    •  & Joseph E. Powell

  • Research Highlight |

    A paper in Cell introduces the EN-TEx resource, a detailed catalogue of allele-specific activity that can be used to develop deep learning models that analyse the biological impact of genetic variants.

    • Linda Koch

  • Expert Recommendation |

    Practitioners in the field of single-cell omics are now faced with diverse options for analytical tools to process and integrate data from various molecular modalities. In an Expert Recommendation article, the authors provide guidance on robust single-cell data analysis, including choices of best-performing tools from benchmarking studies.

    • Lukas Heumos
    • , Anna C. Schaar
    •  & Fabian J. Theis

  • 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, the authors discuss the latest advances in profiling multiple molecular modalities from single cells, including genomic, transcriptomic, epigenomic and proteomic information. They describe the diverse strategies for separately analysing different modalities, how the data can be computationally integrated, and approaches for obtaining spatially resolved data.

    • Katy Vandereyken
    • , Alejandro Sifrim
    •  & Thierry Voet

  • Journal Club |

    Julio Collado-Vides recalls two 2005 publications that provide a conceptual framework based on a statistical thermodynamics approach to quantitatively model the regulatory activity at promoters subject to regulation by multiple transcription factors.

    • Julio Collado-Vides

  • Journal Club |

    Magda Bienko highlights a landmark paper by Lieberman-Aiden et al., which in 2009 reported the development of high-throughput chromosome conformation capture (Hi-C), revolutionizing the field of 3D genome biology.

    • Magda Bienko

  • 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

  • Review Article |

    The ability to map DNA and RNA modifications has improved our understanding of these marks, but in some cases inconsistent results have been problematic. Here, Kong et al. discuss how to recognize and resolve issues associated with commonly used sequencing-based approaches to minimize mapping errors.

    • Yimeng Kong
    • , Edward A. Mead
    •  & Gang Fang

  • Review Article |

    The vast combinatorial sequence space of RNAs has prohibited quantitative mapping from nucleotide sequence to structure and function. New biochemical methods in vitro, which carry out measurements on hundreds of thousands of molecules at the same time, are now beginning to solve this issue.

    • Emil Marklund
    • , Yuxi Ke
    •  & William J. Greenleaf

  • 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, the authors discuss our latest understanding of the spatial aspects of cancer evolution, including the roles of cancer subclonal structure, tissue architecture, and interactions between cancer cells and diverse cell types of the microenvironment at local and distant sites.

    • Zaira Seferbekova
    • , Artem Lomakin
    •  & Moritz Gerstung

  • Research Highlight |

    A new study in Nature Methods describes a computational method named UTAG (unsupervised discovery of tissue architecture with graphs) that aims to identify and quantify higher-level tissue domains from biological images without previous knowledge.

    • Linda Koch

  • Research Highlight |

    A microscopy-based pooled CRISPR screening approach described in Cell enables the cellular functions of thousands of genes to be assessed at remarkable phenotypic depth.

    • Dorothy Clyde

  • Research Highlight |

    A new study reports Epigenomic MERFISH, an imaging method that combines CUT&Tag and MERFISH to interrogate histone marks representing cis-regulatory elements in single cells while preserving spatial information.

    • Linda Koch

  • 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 new study in Cell describes how topologically associating domains (TADs) of chromosomes can restructure to resolve the regulatory conflict that arises when a new gene incorporates into an ancestral TAD.

    • Darren J. Burgess

  • Review Article |

    This Review discusses how chromosome tracing has deepened our understanding of the role of 3D chromatin topology in transcriptional regulation by helping to resolve open questions and opposing models rising from data generated by sequencing-based approaches, such as 3C and HiC.

    • Antonina Hafner
    •  & Alistair Boettiger

  • Research Highlight |

    A new study in Cell has characterized genome-wide dosage sensitivity for 54 human disorders, providing insight into the causal genes and disease mechanisms associated with rare copy-number variants.

    • Dorothy Clyde

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