Reviews & Analysis

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  • In this Viewpoint, five experts discuss our biological understanding of super-enhancers, how we can responsibly study their functions, and their opinions on whether names for enhancer clusters are an informative reflection of their functional properties.

    • Gerd A. Blobel
    • Douglas R. Higgs
    • Richard A. Young
    Viewpoint
  • Leigh and colleagues describe the potential of the emerging field of macrogenetics to improve conservation and biodiversity management. Challenges preventing the field from reaching its full promise are highlighted and possible solutions and a framework for future macrogenetic studies are proposed.

    • Deborah M. Leigh
    • Charles B. van Rees
    • Ivan Paz-Vinas
    Review Article
  • The evolutionary persistence of animal symbioses depends on both host and symbiont innovations. Perreau and Moran review how genome sequencing and related experiments have clarified how these innovations arise under different symbiont population structures, categorized here as open, closed and mixed.

    • Julie Perreau
    • Nancy A. Moran
    Review Article
  • In this Review, Ethan Bier discusses how several impactful technical advancements, particularly involving CRISPR-based methods, are providing a diverse toolkit of gene-drive systems for the control of populations such as insect vectors of disease.

    • Ethan Bier
    Review Article
  • In this Review, Senft and Macfarlan discuss the diverse ways by which transposable elements (TEs) contribute to mammalian development and evolution, including direct contributions through TE-derived regulatory elements, RNAs and proteins, as well as indirect effects through the evolution of a TE repression system, the Krüppel-associated box zinc finger proteins (KRAB-ZFPs).

    • Anna D. Senft
    • Todd S. Macfarlan
    Review Article
  • In this Review, the authors discuss computational methods for interpreting the molecular and clinical effects of genetic variants. They focus on methods leveraging machine learning, including those that characterize the effects on wider molecular networks.

    • Aaron K. Wong
    • Rachel S. G. Sealfon
    • Olga G. Troyanskaya
    Review Article
  • Genome-wide association studies (GWAS) have revealed important biological insights into complex diseases. The authors review approaches that leverage GWAS to identify opportunities for repurposing existing drugs, including single-loci mapping to drug targets, transcriptome-wide association studies, gene-set association, causal inference by Mendelian randomization and polygenic scoring.

    • William R. Reay
    • Murray J. Cairns
    Review Article
  • Synthetic biology has enabled the development of engineered cells that can serve as ex vivo or in vivo diagnostic tools or therapeutic delivery systems. This Review discusses preclinical and clinical applications of bacterial and mammalian theranostic cells as well as their underlying biological designs and remaining hurdles to their successful clinical application.

    • Monica P. McNerney
    • Kailyn E. Doiron
    • Pamela A. Silver
    Review Article
  • In this Review, Gelernter and Polimanti discuss how recent large-scale studies have provided insights into the genetics and biology of substance use and abuse. By considering a range of addictive substances (both legal and illegal), they describe the genetic commonalities and distinctions among use and dependency phenotypes for these substances.

    • Joel Gelernter
    • Renato Polimanti
    Review Article
  • McLaren and Fellay review our current understanding of the effects of human genetic variation on HIV infection and disease progression and how this knowledge is contributing to preventative and therapeutic approaches.

    • Paul J. McLaren
    • Jacques Fellay
    Review Article
  • Genome-scale sequencing data have revealed statistical properties of mutagenesis in humans. Statistical analyses that interpret these patterns and incorporate knowledge on DNA replication and repair pathways can provide mechanistic models that shed light on the origin of spontaneous human mutation in the germ line.

    • Vladimir B. Seplyarskiy
    • Shamil Sunyaev
    Review Article
  • Combining single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics can localize transcriptionally characterized single cells within their native tissue context. This Review discusses methodologies and tools to integrate scRNA-seq with spatial transcriptomics approaches, and illustrates the types of insights that can be gained.

    • Sophia K. Longo
    • Margaret G. Guo
    • Paul A. Khavari
    Review Article
  • Omics methods can be used to mine the genomes of diverse organisms, from microorganisms to plants and animals, for the discovery of natural products and their biosynthetic genes. In this Review, the authors review the why, what, where and how of genome mining.

    • Marnix H. Medema
    • Tristan de Rond
    • Bradley S. Moore
    Review Article
  • Differences of sex development (DSD) are under-diagnosed, partly because of the complexity of conditions included under this umbrella terminology. This Review discusses the potential of genomic approaches to improve variant detection, molecular diagnosis and outcomes for individuals with DSD.

    • Emmanuèle C. Délot
    • Eric Vilain
    Review Article
  • Long-read sequencing at the population scale presents specific challenges but is becoming increasingly accessible. In this Review, Sedlazeck and colleagues discuss the major platforms and analytical tools, considerations in project design and challenges in scaling long-read sequencing to populations.

    • Wouter De Coster
    • Matthias H. Weissensteiner
    • Fritz J. Sedlazeck
    Review Article
  • Silver, Bick and Savona discuss our latest understanding of clonal haematopoiesis (CH), which is an expansion of blood cell populations with shared somatic mutations. They focus on human germline risk variants and on how these are linked to different forms of CH and their associated disease pathologies.

    • Alexander J. Silver
    • Alexander G. Bick
    • Michael R. Savona
    Review Article
  • This Review outlines how approaches from physics can be used to simplify and understand complex patterning events during development. In particular, wavefronts, genetic oscillators and genetic timers are discussed in the context of illustrative developmental processes.

    • Jose Negrete Jr
    • Andrew C. Oates
    Review Article
  • Population-scale testing is an essential component of responses to the COVID-19 pandemic and is likely to become increasingly important in public health. Here, Mercer and Salit describe the roles of testing during the COVID-19 pandemic, including in genomic surveillance, contact tracing and environmental testing.

    • Tim R. Mercer
    • Marc Salit
    Review Article
  • In this Perspective article, Oh and Petronis discuss emerging evidence of time-dependent patterns of DNA modification and describe how incorporating this ‘chrono-epigenetic’ perspective could add value and interpretability in human disease studies.

    • Edward Saehong Oh
    • Art Petronis
    Perspective
  • In this Perspective, Teschendorff and Feinberg describe how single-cell analysis methods based on statistical mechanics can provide valuable insights into developmental phenomena, such as differentiation potency and lineage trajectories, as well as disruption of these processes in cancer.

    • Andrew E. Teschendorff
    • Andrew P. Feinberg
    Perspective