Reviews & Analysis

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  • A new study uses single-cell and spatial transcriptomics to provide a systematic characterization of the recurrent gene-expression programs that control neoplastic cell states in diverse cancers.

    • Daniel Roden
    • Alexander Swarbrick
    News & Views
  • In the zebrafish heart, several transient fibroblast types appear after injury. High-throughput lineage tracing revealed that injury-responsive fibroblasts are derived from two distinct lineage origins: the epicardium and the endocardium. Targeted cell-type-specific depletion showed that at least one fibroblast type has a critical role in heart regeneration.

    Research Briefing
  • Assemblies of hexaploid cultivated oat, and of close relatives of its diploid and tetraploid progenitors, have revealed its polyploid formation and subgenome evolution. These high-quality oat reference genomes will facilitate the discovery of candidate genes that underlie beneficial traits such as hulless grain and disease resistance.

    Research Briefing
  • The impact of endogenous retrovirus silencing during mammalian development is poorly understood. A new study shows that their abnormal reactivation in pluripotent cells dismantles key gene regulatory networks by perturbing transcriptional condensates linked to super-enhancer function.

    • Edward J. Grow
    News & Views
  • Genetic and phenotypic analyses of data from over 400,000 participants in the UK Biobank identified 10 new loci associated with the development of clonal hematopoiesis and implicated DNA damage, oncogene signaling, telomere maintenance and blood cell homing in its pathogenesis. These findings can help to decipher the pathogenesis of clonal hematopoiesis and develop therapeutic approaches.

    Research Briefing
  • Systematic CRISPR screens in primary human T cells uncovered the upstream regulators of crucial immune genes — IL2RA, IL2 and CTLA4. Then, using RNA-seq and ATAC-seq in knockout T cells, we mapped the downstream target genes and non-coding cis-regulatory elements of key regulators, thereby revealing a regulatory network enriched for immune disease-associated genes.

    Research Briefing
  • A machine-learning model produces summarized sequence representations of genomic regulatory activity, and provides a functional view of regulatory DNA variation in the human genome, with the aim of better understanding the role of sequence variation in health and disease.

    • Anshul Kundaje
    • Wouter Meuleman
    News & Views
  • The boundaries of chromatin domains have an important role in genome organization and regulation. A comprehensive genetic dissection of a domain boundary in vivo provides insights into how boundary elements function and cooperate to mediate insulation between chromatin domains.

    • A. Marieke Oudelaar
    News & Views
  • In celebration of the 200th anniversary of Gregor Mendel’s birth, this Perspective discusses the historical context of Mendel’s discoveries and the importance of these insights in shaping the field of genetics.

    • Peter J. van Dijk
    • Adrienne P. Jessop
    • T. H. Noel Ellis
    Perspective
  • By integrating single-cell and bulk transcriptomic analyses, we found that malignant cells belong to two major intrinsic epithelial subtypes. We propose a refined, three-tiered classification of colorectal cancer subtypes based on intrinsic epithelial subtypes, microsatellite instability status and the presence of fibrosis.

    Research Briefing
  • A large-scale collaborative effort now provides a comprehensive annotation of functional non-coding elements in the zebrafish genome. This work serves as an essential foundation for future studies to understand how gene regulatory circuits control embryonic development.

    • Nathan D. Lawson
    News & Views
  • The largest GWAS for kidney function so far provided the starting point for integrated multi-stage annotation of genetic loci. Whole kidney and single-cell epigenomic information is crucial for translating GWAS information to the identification of causal genes and pathogenetic (and potentially targetable) cellular and molecular mechanisms of kidney disease.

    Research Briefing
  • The use of association studies to identify candidate genes for complex biological traits in plants has been challenging due to a reliance on single reference genomes, leading to missing heritability. Graphical pangenomes and the identification of causal variants help overcome this and provide an important advance for crop breeding.

    • David Edwards
    • Jacqueline Batley
    News & Views
  • A new study employs CRISPR–Cas9-based base editing for simultaneous mutagenesis of all copies of histone H3 genes in mammals, highlighting the functional importance of H3K27me3 for Polycomb-mediated gene silencing and the dispensability of H3K27ac in transcriptional activation.

    • Alessandro Scacchetti
    • Roberto Bonasio
    News & Views
  • A new study highlights a strategy to link SNPs implicated in human complex traits and diseases with probable causal genes. This method prioritizes genes for functional characterization and helps address questions about the architecture of human phenotypes.

    • Guillaume Lettre
    News & Views
  • A study using single-cell transcriptomics and mapping of expression quantitative trait loci (eQTLs) in a dynamic model of CD4+ T cell activation reveals novel, context-specific eQTLs linked to genes associated with immune diseases such as inflammatory bowel disease.

    Research Briefing
  • A large-scale single-nucleus chromatin accessibility profiling study in coronary artery samples from patients with coronary artery disease generated a landscape of the regulatory activity during the disease. These data highlight cell type-specific gene programs that can improve the interpretation of human genome-wide association studies findings for cardiovascular diseases.

    Research Briefing
  • The genome of the SunUp transgenic papaya cultivar includes a complex 1.64-Mb insertion that contains 3 transgenic fragments integrated with 61 nuclear genome fragments from the progenitor Sunset cultivar and 13 organelle genome fragments. Population genomic analyses yielded 147 selective sweeps during papaya domestication, which include essential genes that are involved in fruit flesh color formation and sugar content.

    Research Briefing
  • A new study demonstrates that the disordered N-terminal domain of DNMT3A1 binds PRC1-catalyzed H2AK119ub, targeting DNA methylation to bivalent promoters in mouse brain cortical cells. Methylation around bivalent genes is critical for mouse postnatal development, and could be equally important in other cell types and in disease.

    • Aled J. Parry
    • Wolf Reik
    News & Views