Reviews & Analysis

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  • The function of transposable elements present in mammalian genomes remains an enigma. In this issue, Bodega, Abrignani and colleagues show that LINE1-containing transcripts are key regulators of T cell effector function and exhaustion.

    • Marina Lusic
    • Musa M. Mhlanga
    News & Views
  • Complex disease definitions often represent descriptive umbrella terms of symptoms rather than mechanistic entities. A new study shows how network-based approaches can help identify the mechanisms that link genes, cells, tissues and organs in cardiovascular diseases.

    • Harald H. H. W. Schmidt
    • Jörg Menche
    News & Views
  • Although clear genetic connections to ALS were first established three decades ago, there has been negligible progress in the development of disease-modifying treatments for this disease. Despite tremendous unmet need, industry has often been largely baffled by a disease seemingly designed to thwart current effective drug development approaches. In the largest genetic study of ALS to date, van Rheenen and colleagues use sophisticated analyses to gain novel insights into its pathogenesis.

    • Sunil Sahdeo
    • David B. Goldstein
    News & Views
  • Oncogene amplification is a major driver of tumorigenesis; yet, the mechanisms generating amplification are only partially understood. New research reports on the identification of a new focal amplification pattern termed ‘seismic amplification’ that is hypothesized to originate from recombination between extrachromosomal DNA circles.

    • David Pellman
    • Cheng-Zhong Zhang
    News & Views
  • How somatic and germline mutations interact in cancer remains largely unexplored. A study of 17,152 patients with cancer suggests that the relative contribution of pathogenic germline mutations is governed by lineage and penetrance.

    • Stephen J. Chanock
    News & Views
  • A new study shows that re-expressing PKD genes early in the course of the disease can fully reverse polycystic kidney disease in mice. These results reveal an unexpected ability of the kidney to regenerate following genetic rescue of polycystin function.

    • Alessandra Boletta
    News & Views
  • The genomes of cells across human tissues are riddled by changes to their DNA13. Many of these mutations do not alter the properties of a cell, and are neutral passengers. However, a small proportion can change a cell’s fitness, and increase or decrease the progeny that originate from the mutated cell4. How many of these alterations under positive selection (drivers) exist in total is unknown. Whether the current list of drivers is almost complete, or whether large proportions of positively selected drivers in the human genome remain undetected is yet to be determined.

    • Benjamin Werner
    News & Views
  • Mutational signatures can shed light onto mechanisms of carcinogenesis and reveal the mutagenic impact of novel and established environmental risk factors. A new study examines the mutational spectra of esophageal squamous cell cancer together with exposure information in regions of high and low incidence of the disease, and demonstrates both the limitations and potential of mutational signature analyses.

    • Marios Giannakis
    • Ulrike Peters
    News & Views
  • Heterogeneity in brain tumors has been viewed through many lenses—from microscopes and experimental models to ‘omic’ analysis at the tissue and single-cell levels. Two studies now characterize patterns of DNA methylation and gene expression in single cells to reveal epigenomic underpinnings of cellular heterogeneity and plasticity in exquisite detail, including mechanistic insight into cellular transitions between stem-like and differentiated-like states.

    • Radhika Mathur
    • Joseph F. Costello
    News & Views
  • Metastable epialleles refer to loci with variable methylation states among individuals without underlying genetic differences. Although these loci have generally been assumed to be vulnerable to environmental influence, a new study reports their remarkable metastable epigenetic robustness toward a range of physiological, chemical and dietary disruptions in mammals.

    • Deborah Bourc’his
    News & Views
  • Genome-wide association studies have identified genetic variants in maternal and fetal genomes associated with early-life growth traits but have been limited by the paucity of large-scale family-based cohorts that would enable the resolution of informative transmissions between parents and their offspring. A new study uses extensive pedigree data from the Icelandic population to identify genetic effects on birth weight that differ according to parental origin and to demarcate distinct contributions from the maternal intrauterine environment and offspring genetics on fetal growth.

    • David M. Evans
    • Rachel M. Freathy
    News & Views
  • R-loops—nucleic acid structures composed of an RNA:DNA hybrid and displaced single-stranded DNA—are abundant in the genome and may impair progression of the replication fork, thus leading to accumulation of DNA damage and genome instability. A new study demonstrates that SWI/SNF chromatin-remodeling complexes are instrumental in resolving such R-loop-mediated transcription–replication conflicts, highlighting the importance of these chromatin remodelers in R-loop homeostasis and the maintenance of genome integrity.

    • Abdulkadir Abakir
    • Alexey Ruzov
    News & Views
  • Genome editing with CRISPR–Cas9 is beginning to be used clinically; promising results to date inspire hope for broad medical impact and mindfulness about safety. A new study shows that when Cas9 cuts its target, a fraction of the time, the target chromosome experiences a breakage process known as chromothripsis, thus prompting efforts to understand the potential negative consequences of this phenomenon and ways to mitigate them.

    • Fyodor D. Urnov
    News & Views
  • Single-cell and bulk transcriptomics of adult human microglia from a population of individuals reveals activated states across several brain disorders and maps Alzheimer’s disease variants to microglia-enriched genes.

    • Kevin W. Kelley
    • Sergiu P. Pașca
    News & Views
  • This Perspective on crop genomics discusses the promises of new technologies and approaches to help minimize food insecurity and to lay the foundation for sustainable agricultural systems needed to feed the world.

    • Michael D. Purugganan
    • Scott A. Jackson
    Perspective
  • Recent technologies allow experimental manipulation of chromatin conformation. This Perspective discusses the insights obtained from gain-of-function studies that engineer the three-dimensional genome.

    • Di Zhang
    • Jessica Lam
    • Gerd A. Blobel
    Perspective