• Article |

    Analysis of 97,691 high-coverage human blood DNA-derived whole-genome sequences enabled simultaneous identification of germline and somatic mutations that predispose individuals to clonal expansion of haematopoietic stem cells, indicating that both inherited and acquired mutations are linked to age-related cancers and coronary heart disease.

    • Alexander G. Bick
    • , Joshua S. Weinstock
    •  & Pradeep Natarajan
  • Article |

    Analysis of cis-regulatory chromatin interactions, open chromatin and transcriptomes for different cell types isolated from mid-gestational human cortex samples provides insights into gene regulation during development.

    • Michael Song
    • , Mark-Phillip Pebworth
    •  & Yin Shen
  • Article |

    Single-cell analysis of blood vessels in the alveolus, the site of chronic disease and virus-induced lung injury, reveals two intermingled endothelial cell types with specialized gas exchange and stem cell functions.

    • Astrid Gillich
    • , Fan Zhang
    •  & Ross J. Metzger
  • Article |

    A combination of clonal expansion and DNA amplification is used to sequence genetic material from individual melanocytes, shedding light on the mutational landscape of these cells and the development of melanomas.

    • Jessica Tang
    • , Eleanor Fewings
    •  & A. Hunter Shain
  • Article |

    Single-nucleus RNA-sequencing analyses of brain from humans, macaques, marmosets, mice and ferrets reveal diverse ways that interneuron populations have changed during evolution.

    • Fenna M. Krienen
    • , Melissa Goldman
    •  & Steven A. McCarroll
  • Article
    | Open Access

    Single-cell and single-nucleus RNA sequencing are used to construct a cellular atlas of the human heart that will aid further research into cardiac physiology and disease.

    • Monika Litviňuková
    • , Carlos Talavera-López
    •  & Sarah A. Teichmann
  • Article |

    Ancient DNA analyses reveal that Viking Age migrations from Scandinavia resulted in differential influxes of ancestry to different parts of Europe, and the increased presence of non-local ancestry within Scandinavia.

    • Ashot Margaryan
    • , Daniel J. Lawson
    •  & Eske Willerslev
  • Article |

    The building blocks of the nanostructures observed on Drosophila corneas are determined, and then used to create artificial nanostructures with anti-reflective and anti-adhesive properties.

    • Mikhail Kryuchkov
    • , Oleksii Bilousov
    •  & Vladimir L. Katanaev
  • Article |

    Exposing Caenorhabditis elegans to non-coding small RNAs from pathogenic Pseudomonas aeruginosa induces avoidance behaviours in treated worms and their progeny, which reveals how C. elegans discriminates between bacterial species in its microbial environment.

    • Rachel Kaletsky
    • , Rebecca S. Moore
    •  & Coleen T. Murphy
  • Article |

    Fission yeast grown in sublethal levels of caffeine develop heterochromatin-dependent epimutations conferring unstable heritable gene silencing that conveys resistance to caffeine, while remaining genetically wild type.

    • Sito Torres-Garcia
    • , Imtiyaz Yaseen
    •  & Robin C. Allshire
  • Article |

    A genome-wide association study shows that myocardial trabeculae are an important determinant of cardiac performance in the adult heart, identifies conserved pathways that regulate structural complexity and reveals the influence of trabeculae on the susceptibility to cardiovascular disease.

    • Hannah V. Meyer
    • , Timothy J. W. Dawes
    •  & Declan P. O’Regan
  • Article
    | Open Access

    The approximately 5-Gb tuatara (Sphenodon punctatus) genome assembly provides a resource for analysing amniote evolution, and highlights the imperative for meaningful cultural engagement with Indigenous communities in genome-sequencing endeavours.

    • Neil J. Gemmell
    • , Kim Rutherford
    •  & Haydn Edmonds
  • Article
    | Open Access

    ChIP–seq and CETCh–seq data are used to analyse binding maps for 208 transcription factors and other chromatin-associated proteins in a single human cell type, providing a comprehensive catalogue of the transcription factor landscape and gene regulatory networks in these cells.

    • E. Christopher Partridge
    • , Surya B. Chhetri
    •  & Eric M. Mendenhall
  • Perspective
    | Open Access

    The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

    • Federico Abascal
    • , Reyes Acosta
    •  & Richard M. Myers
  • Article |

    An experimental and analytical pipeline is used to assess, at the single-cell level, complex transcriptional and morphological mutant phenotypes that occur in mouse embryos during gastrulation.

    • Stefanie Grosswendt
    • , Helene Kretzmer
    •  & Alexander Meissner
  • Article |

    Genome-wide analysis of tandem DNA repeats in the genomes of individuals with autism spectrum disorder and control participants reveals a strong contribution of tandem repeat expansions to the genetic aetiology and phenotypic complexity of autism spectrum disorder.

    • Brett Trost
    • , Worrawat Engchuan
    •  & Ryan K. C. Yuen
  • Article |

    The chromatin protein MeCP2 is a component of dynamic, liquid-like heterochromatin condensates, and the ability of MeCP2 to form condensates is disrupted by mutations in the MECP2 gene that occur in the neurodevelopmental disorder Rett syndrome.

    • Charles H. Li
    • , Eliot L. Coffey
    •  & Richard A. Young
  • Article |

    The histone variant H3.3 is phosphorylated at Ser31 in induced genes, and this selective mark stimulates the histone methyltransferase SETD2 and ejects the ZMYND11 repressor, thus revealing a role for histone phosphorylation in amplifying de novo transcription.

    • Anja Armache
    • , Shuang Yang
    •  & Steven Z. Josefowicz
  • Article
    | Open Access

    Reference-quality genomes for six bat species shed light on the phylogenetic position of Chiroptera, and provide insight into the genetic underpinnings of the unique adaptations of this clade.

    • David Jebb
    • , Zixia Huang
    •  & Emma C. Teeling
  • Article |

    Chiquihuite Cave (Zacatecas, Mexico) provides evidence of human presence in the Americas between about 33,000–31,000 and 14,000–12,000 years ago, and expands the cultural variability known from sites of this date.

    • Ciprian F. Ardelean
    • , Lorena Becerra-Valdivia
    •  & Eske Willerslev
  • Article |

    Bulk RNA sequencing of organs and plasma proteomics at different ages across the mouse lifespan is integrated with data from the Tabula Muris Senis, a transcriptomic atlas of ageing mouse tissues, to describe organ-specific changes in gene expression during ageing.

    • Nicholas Schaum
    • , Benoit Lehallier
    •  & Tony Wyss-Coray
  • Article |

    The DNA modification N6-methyladenine regulates gene expression during mouse trophoblast development by depositing at the boundaries of active chromatin and preventing its spread by antagonizing the chromatin organizer SATB1.

    • Zheng Li
    • , Shuai Zhao
    •  & Andrew Z. Xiao
  • Article
    | Open Access

    High-coverage, ultra-long-read nanopore sequencing is used to create a new human genome assembly that improves on the coverage and accuracy of the current reference (GRCh38) and includes the gap-free, telomere-to-telomere sequence of the X chromosome.

    • Karen H. Miga
    • , Sergey Koren
    •  & Adam M. Phillippy
  • Article |

    Resequencing analyses of three species of wild sunflower identify large non-recombining haplotype blocks that correlate with ecologically relevant traits, soil and climate characteristics, and that differentiate species ecotypes.

    • Marco Todesco
    • , Gregory L. Owens
    •  & Loren H. Rieseberg
  • Article |

    Genomic analyses of DNA from modern individuals show that, about 800 years ago, pre-European contact occurred between Polynesian individuals and Native American individuals from near present-day Colombia, while remote Pacific islands were still being settled.

    • Alexander G. Ioannidis
    • , Javier Blanco-Portillo
    •  & Andrés Moreno-Estrada
  • Article |

    Structural cells implement a broad range of immune-regulatory functions beyond their roles as barriers and connective tissues, and they utilize an epigenetically encoded potential for immune gene activation in their rapid response to viral infection.

    • Thomas Krausgruber
    • , Nikolaus Fortelny
    •  & Christoph Bock
  • Article |

    Population-specific patterns of genomic mutations and selection of haematopoietic clones in Japanese and European participants predict the divergent rates of chronic lymphocytic leukaemia and T cell leukaemia in these populations.

    • Chikashi Terao
    • , Akari Suzuki
    •  & Yoichiro Kamatani
  • Article |

    Analysis of blood-derived DNA from participants in the UK Biobank demonstrates that clonal expansions of acquired copy-neutral loss of heterozygosity mutations act on inherited alleles along a chromosome arm by modifying their allelic dosages.

    • Po-Ru Loh
    • , Giulio Genovese
    •  & Steven A. McCarroll
  • Article |

    A method termed ac4C-seq is introduced for the transcriptome-wide mapping of the RNA modification N4-acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.

    • Aldema Sas-Chen
    • , Justin M. Thomas
    •  & Schraga Schwartz
  • Article |

    Skeletal remains from the Neolithic passage tomb at Newgrange (Ireland) represent the adult son of a first-degree incestuous union, suggesting that a politico-religious elite may have controlled the construction of Irish sites of this type.

    • Lara M. Cassidy
    • , Ros Ó Maoldúin
    •  & Daniel G. Bradley
  • Article |

    Thousands of sperm genomes have been analysed with a new method called Sperm-seq, revealing interconnected meiotic variation at the single-cell and person-to-person levels, and suggesting chromosome compaction as a way to explain the relationships between diverse recombination phenotypes.

    • Avery Davis Bell
    • , Curtis J. Mello
    •  & Steven A. McCarroll