Biological sciences articles within Nature Reviews Genetics

Featured

  • Journal Club |

    In this Journal Club, Jessica Tollkuhn discusses how a paper describing genome-wide application of chromatin immunoprecipitation (ChIP)-on-chip inspired her own research into oestrogen-based gene regulation in the brain.

    • Jessica Tollkuhn

  • Tools of the Trade |

    In this Tools of the Trade article, Vipul Singhal and Nigel Chou describe BANKSY, a machine learning tool that harnesses gene expression gradients from the neighbourhood of a cell for cell typing and domain segmentation.

    • Vipul Singhal
    •  & Nigel Chou

  • 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 |

    In this Review, Stanley summarizes the role of genetics in mammalian glycosylation, highlighting how advances in genetic and genomic technologies are helping to characterize the genes involved and contributing to the development of therapies for diseases related to glycosylation.

    • Pamela Stanley

  • Research Highlight |

    Logsdon et al. report the second complete sequence of all centromeres from a single human genome, enabling comparative analyses of the variation in tandemly repeating α-satellite DNA.

    • Kirsty Minton

  • Comment |

    In this Comment, Lamkin and Gymrek discuss recent results that suggest that the systematic incorporation of tandem repeats into complex trait analyses will yield a rich source of causal variants and new biological insights.

    • Michael Lamkin
    •  & Melissa Gymrek

  • Tools of the Trade |

    In this Tools of the Trade article, Samuel Gould explains how prime editing sensors can improve experimental efficiency and can be designed using a computational tool he created and named PEGG.

    • Samuel I. Gould

  • 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

  • Journal Club |

    In this Journal Club, Kirstyn Brunker highlights two papers published in 2017 that showcase how the emergence of portable sequencing capabilities improved the real-time response to infectious disease outbreaks on a global scale.

    • Kirstyn Brunker

  • Journal Club |

    In this Journal Club article, Olivia Rissland describes how a 1987 paper by Don Cleveland and colleagues provided insight into co-translational gene regulation of tubulin.

    • Olivia S. Rissland

  • 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

  • Review Article |

    In this Review, Li and Durbin discuss how to generate telomere-to-telomere assemblies for large haploid or diploid genomes using currently available data types and algorithms, and outline remaining challenges in resolving highly repetitive sequences and polyploid genomes.

    • Heng Li
    •  & Richard Durbin

  • Review Article |

    In this Review, the authors summarize our current understanding of nuclear pre-mRNA and mRNA decay pathways. They describe how aberrantly processed mRNAs are targeted for decay in the nucleus and how this process is regulated to finely control gene expression.

    • Xavier Rambout
    •  & Lynne E. Maquat

  • Perspective |

    In this Perspective, Werner and colleagues discuss the many potential mechanisms by which natural antisense transcripts (NATs) can regulate expression of their complementary sense transcripts, the biological implications of their regulatory effects and the potential of NATs for therapeutic applications.

    • Andreas Werner
    • , Aditi Kanhere
    •  & John S. Mattick

  • Research Highlight |

    A paper in Nature Genetics identifies a mechanism involving the transcription factor DUXBL that controls the development of early embryonic mouse cells past stages marked by totipotency.

    • Henry Ertl

  • 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

  • Review Article |

    Genetic variants acquired early during embryogenesis can affect numerous tissues. The authors review the phenomenon of embryonic mosaicism, with a focus on small variants, and discuss mechanisms of cell competition that allow mosaic clones to expand, as well as the functional consequences of mosaicism for embryo viability and the health of the organism.

    • Sarah M. Waldvogel
    • , Jennifer E. Posey
    •  & Margaret A. Goodell

  • Review Article |

    In this Review, Mackay and Anholt discuss how epistasis and pleiotropy contribute to the genetic architecture of quantitative traits and outline factors that might explain observed differences in their prevalence between model organisms and humans.

    • Trudy F. C. Mackay
    •  & Robert R. H. Anholt

  • Review Article |

    In this Review, the authors compare the characteristics and detection methods of germline and somatic variants. Furthermore, they outline how the interplay between the two types of genetic variation can affect human health.

    • Zhi Yu
    • , Tim H. H. Coorens
    •  & Pradeep Natarajan

  • Research Highlight |

    A paper in Nature reports a ‘Z-DNA-anchored’ model for the target specificity of the transcription factor AIRE, involving promoter poising at double-strand breaks.

    • Kirsty Minton

  • Journal Club |

    Reflecting on the importance of short tandem repeats (STRs) in population genetics, Ning Xie highlights a 2023 publication that characterized genome-wide STR variation in global human genomes to expand our understanding of STR genetic diversity within and across populations.

    • Ning Xie

  • 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

  • Journal Club |

    In this Journal Club, Yoav Ram recalls how he reconciled results from his own research with the reduction principle through the help of a paper published in PNAS by Altenberg et al.

    • Yoav Ram

  • Review Article |

    Plants have uniquely adapted to manage endoplasmic reticulum stress triggered by protein misfolding. The authors review the dynamics of gene expression regulation underlying the unfolded protein response in plants, highlighting recent insights provided by systems-level approaches and omics data.

    • Dae Kwan Ko
    •  & Federica Brandizzi

  • 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

  • Review Article |

    In this Review, Sayers et al. summarize findings from recent large-scale genetic epidemiology studies on the genetic underpinnings of chronic respiratory diseases. Furthermore, they outline how insights gained from such studies can improve treatment approaches.

    • Ian Sayers
    • , Catherine John
    •  & Ian P. Hall

  • Journal Club |

    Hajk-Georg Drost recalls a 2010 publication that used a phylotranscriptomic approach to estimate the age of genes that contribute to the developmental transcriptome across animal species and inspired a subsequent study on the embryonic hourglass in plants.

    • Hajk-Georg Drost

  • Journal Club |

    Kate Galloway highlights a paper by Kueh et al., who showed that the cell cycle indirectly influences concentrations of the transcription factor PU.1 to stabilize cell-fate trajectories in mice.

    • Kate E. Galloway

  • 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

  • Review Article |

    Therapeutics that target long non-coding RNAs (lncRNAs) are promising treatments for cancer. In this Review, the authors discuss how technological advances have helped improve drug discovery pipelines for lncRNAs and overview their strengths and challenges as oncological therapeutics.

    • Michela Coan
    • , Simon Haefliger
    •  & Rory Johnson

  • Journal Club |

    Carl G. de Boer highlights a recent paper by Lim et al. on the importance low-affinity transcription factor-binding sites for determining organismal phenotypes.

    • Carl G. de Boer

  • Review Article |

    Plant pangenomes have had a transformative impact on crop enhancement, biodiversity conservation and evolutionary research. This Review delves into the application of plant pangenomes for understanding trait diversity, aiding breeding, biodiversity classification and monitoring, and illuminating evolutionary innovations.

    • Mona Schreiber
    • , Murukarthick Jayakodi
    •  & Martin Mascher

  • Review Article |

    This Review discusses the evolutionary origin of Wnt signalling, its ancestral function and the characteristics of the primal Wnt ligand. It emphasizes the importance of genomic studies in pre-metazoan and basal metazoan species to understanding the evolutionary origin of signalling pathways.

    • Michaela Holzem
    • , Michael Boutros
    •  & Thomas W. Holstein

  • Review Article |

    This Review describes tools and approaches for characterizing short tandem repeats in the human genome from whole-genome sequencing data. Furthermore, the authors discuss how these recent developments have helped to better understand the effect of short tandem repeats on human health and disease.

    • Hope A. Tanudisastro
    • , Ira W. Deveson
    •  & Daniel G. MacArthur

  • Research Highlight |

    A study in Nature describes how single-cell expression data can be used to understand gene regulatory landscapes in bacteria.

    • Michael Attwaters

  • Journal Club |

    Amnon Koren recalls two papers from 2001 and 2002 that laid the foundations for a new field by using microarrays to measure DNA replication timing across the genome.

    • Amnon Koren

  • 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 |

    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

  • Perspective |

    Multiple mechanisms have evolved to prevent or trap deleterious unwanted transcripts. The unwanted transcript hypothesis proposes that selection at synonymous sites favours mutations that prevent the generation of unwanted transcripts or that make native transcripts appear ‘wanted’ by being GC-rich.

    • Sofia Radrizzani
    • , Grzegorz Kudla
    •  & Laurence D. Hurst

  • 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

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