Review Articles

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  • In this Review, the authors discuss our latest understanding of extrachromosomal DNA (ecDNA), a type of circular DNA element commonly found in cancers. They discuss ecDNA properties, including oncogene amplifications and transcriptional hub formation, as well as opportunities for therapeutic interventions.

    • Eunhee Yi
    • Rocío Chamorro González
    • Roel G. W. Verhaak
    Review Article
  • Spatial omics methods enable the charting of cellular heterogeneity, complex tissue architectures and dynamic changes during development and disease. The authors review the developing landscape of in situ spatial transcriptome, genome and proteome technologies and highlight their impact on basic and translational research.

    • Jeffrey R. Moffitt
    • Emma Lundberg
    • Holger Heyn
    Review Article
  • In this Review, Preissl, Gaulton and Ren discuss single-cell epigenomic methods and data analysis tools, their readiness for profiling cis-regulatory elements in human tissues and the insight they can provide into dynamic, context-specific gene regulation.

    • Sebastian Preissl
    • Kyle J. Gaulton
    • Bing Ren
    Review Article
  • Molecular measures of biological ageing based on high-throughput omics technologies are enabling the quantitative characterization of ageing. The authors review how epigenomic, transcriptomic, proteomic, metabolomic and other omics data can be harnessed using machine learning to build ‘ageing clocks’.

    • Jarod Rutledge
    • Hamilton Oh
    • Tony Wyss-Coray
    Review Article
  • In this Review, Kim and Kingston discuss the compositional and mechanistic diversity of Polycomb repressive complexes (PRCs) and how their context-dependent formation may be required for proper epigenetic regulation in development.

    • Jongmin J. Kim
    • Robert E. Kingston
    Review Article
  • tRNA function and gene expression profiles are dynamically regulated by post-transcriptional tRNA modifications. Here, Orellana et al. discuss the canonical role of tRNAs in mRNA translation, focusing on alterations in tRNA abundance or function implicated in human diseases.

    • Esteban A. Orellana
    • Elisabeth Siegal
    • Richard I. Gregory
    Review Article
  • Dupont and Wickström review the current understanding of how mechanical forces regulate chromatin state and gene expression and discuss the importance of this mechanosensitive gene regulation to physiology and disease.

    • Sirio Dupont
    • Sara A. Wickström
    Review Article
  • Publicly available sequencing data can be used as external common controls for rare variant analyses but cautious sample ascertainment and processing is needed to avoid bias and confounding. The authors review opportunities and challenges for the robust use of common controls in genetic studies, including study design, infrastructure and quality control considerations.

    • Genevieve L. Wojcik
    • Jessica Murphy
    • Audrey E. Hendricks
    Review Article
  • In this Review, the authors give an overview of age-related changes to the methylation landscape and the statistical tools used to quantify them. They also discuss the evidence for longevity strategies that aim to counter these changes, and the candidate mechanistic causes of epigenetic ageing.

    • Kirsten Seale
    • Steve Horvath
    • Sarah Voisin
    Review Article
  • In this article, Niemi, Daly and Ganna discuss how large-scale genomics studies are providing a rapidly maturing understanding of the influence of host genetics on coronavirus disease 2019 (COVID-19) susceptibility and severity. They also describe the implications for identifying causal mechanisms of pathology and potential therapeutic opportunities.

    • Mari E. K. Niemi
    • Mark J. Daly
    • Andrea Ganna
    Review Article
  • Rackham and Filipovska review our current understanding of mitochondrial genome organization and expression, and discuss how new technologies and animal models are providing insights into how its mis-regulation leads to diseases of impaired energy conversion.

    • Oliver Rackham
    • Aleksandra Filipovska
    Review Article
  • Histone post-translational modifications (PTMs) have been mainly regarded as instructing DNA-templated processes. In this Review, Gonzalo Millán-Zambrano and colleagues describe how histone PTMs both affect and are affected by these DNA processes and should be viewed as components of a complex genome-regulating network.

    • Gonzalo Millán-Zambrano
    • Adam Burton
    • Robert Schneider
    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
    Review Article
  • DNA methylation-based predictors of health aim to predict outcomes such as exposure, phenotype or disease on the basis of genome-wide levels of DNA methylation. The authors review applications of existing DNA methylation-based predictors and highlight key statistical best practices to ensure their reliable performance.

    • Paul D. Yousefi
    • Matthew Suderman
    • Caroline L. Relton
    Review Article
  • In this Review, Boulias and Greer provide an overview of current approaches for detecting and mapping N6-methyl-2′-deoxyadenosine (6mA or m6dA), and discuss the evidence for its presence and functional importance in the genomes of multicellular eukaryotes.

    • Konstantinos Boulias
    • Eric Lieberman Greer
    Review Article
  • In this Review, the authors describe technical and legal protection mechanisms for mitigating vulnerabilities in genomic data privacy. They also discuss how these protections are dependent on the context of data use such as in research, health care, direct-to-consumer testing or forensic investigations.

    • Zhiyu Wan
    • James W. Hazel
    • Bradley A. Malin
    Review Article
  • Single-cell transcriptomics is beginning to systematically define commonalities but also heterogeneity within and between organs for multiple human cell types. Here, the authors review emerging biological insights from cross-tissue single-cell transcriptomic studies into epithelial, fibroblast, vascular and immune cells.

    • Rasa Elmentaite
    • Cecilia Domínguez Conde
    • Sarah A. Teichmann
    Review Article
  • The reduction in individual and mean population fitness induced by novel deleterious genetic variation is known as the genetic load. Bertorelle et al. review the definition of the genetic load and its components as well as the impact of whole-genome sequencing on the theoretical and applied study of the genetic load.

    • Giorgio Bertorelle
    • Francesca Raffini
    • Cock van Oosterhout
    Review Article