Reviews & Analysis

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  • 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
  • Defining the most appropriate phenotypes in genome-wide association studies of COVID-19 is challenging, and two new publications demonstrate how case-control definitions critically determine outcomes and downstream clinical utility of findings.

    • Tom H. Karlsen
    News & Views
  • Chromosomes are shaped by an interplay between loop extrusion and compartmentalization. Two new studies demonstrate that bromodomain and extraterminal domain (BET) proteins contribute to both processes, with BRD4 facilitating one process and surprisingly inhibiting the other.

    • Kyle P. Eagen
    News & Views
  • The largest genetic study of educational attainment (EA) so far combines gene mapping and family analyses to show that genetic associations with EA and its health benefits may be mostly indirect. As such, future genetic studies of human social and behavioral traits must include diversity in population, demographic and environmental contexts.

    • Andrew J. Schork
    • Roseann E. Peterson
    • Kenneth S. Kendler
    News & Views
  • A new study demonstrates that profiles of nascent RNA accurately predict genomic patterns of histone modifications and chromatin state. Consistent with that, active histone marks are revealed to reflect transcription activity, rather than preceding or directing gene output.

    • Karen Adelman
    News & Views
  • The gap between heritability estimates from twin studies and those from genotyping array data has puzzled researchers for over a decade. New research suggests that much of the ‘missing’ heritability is due to rare variants that can only be captured by whole-genome sequencing (WGS) data.

    • Alexander I. Young
    News & Views
  • Similar to CTCF, MAZ insulates repressed posterior Hoxa genes from the spreading of anterior active regulatory cues during motoneuron differentiation. This discovery provides new perspectives to understand chromatin organization and insulation.

    • Fabrice Darbellay
    • Raquel Rouco
    • Guillaume Andrey
    News & Views
  • Normal cellular processes can cause DNA breaks which become substrates for the cell’s DNA repair machinery. Focusing on neurons, this Perspective article explores the role of this ‘programmed’ DNA damage and its repair in health, ageing and neurodegenerative disease.

    • Keith W. Caldecott
    • Michael E. Ward
    • André Nussenzweig
    Perspective