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Microbiome epidemiology associates microbial community features with health outcomes, traits or exposures in human host populations. In this Review, the authors discuss ways in which various microbiome features at varying levels of resolution (community, strain, pathway or gene) influence human health using established examples of microbiome-associated changes linked with host outcomes.
In this Review, the authors describe advances in deep learning approaches in genomics, whereby researchers are moving beyond the typical ‘black box’ nature of models to obtain biological insights through explainable artificial intelligence (xAI).
Inducible protein degradation technologies enable the depletion of loop extrusion factors within short time frames, leading to the rapid reconfiguration of the 3D genome. Nora and de Wit review insights from degron approaches into the molecular factors controlling genome folding and how these findings have changed our understanding of genome organization, including its role in transcription.
Mendelian defects in genes encoding factors that regulate telomere length, structure and function cause telomeropathies, or telomere biology disorders (TBDs). The authors review confirmed as well as potential TBD-causing genes and their main functions in telomere biology. They also discuss genetic features that underlie the complex nature of these diseases.
This Review discusses how chromosome tracing has deepened our understanding of the role of 3D chromatin topology in transcriptional regulation by helping to resolve open questions and opposing models rising from data generated by sequencing-based approaches, such as 3C and HiC.
The circadian system and sleep physiology are linked to myriad biological processes, the disruption of which is detrimental to human health. Here, the authors review insights from genetic studies of human circadian and sleep phenotypes and disorders, with a focus on those with causal contributions to other complex diseases.
Sex-specific morphs exhibit phenotypes that differ between the sexes and typically include many different traits. Here, the author reviews recent genomic and transcriptomic studies that are yielding new insights into the evolutionary origin and development of sex-specific morphs in a wide range of animal species.
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.
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.
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.
In this Review, Isbel et al. describe our current understanding of how transcription factors navigate features of chromatin — particularly DNA methylation and nucleosomes — and how this contributes to specificity of genomic binding and, ultimately, transcriptional regulation.
In this Perspective, the authors discuss how regulated alternative splicing can generate phenotypic diversity and outline emerging evidence that alternative splicing contributes to adaptation and species divergence.
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’.
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.
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.
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.
Commemorating the 200th birthday of Gregor Mendel, Kim Nasmyth reflects on Mendel’s life and legacy and how his work has shaped and defined the field of modern genetics.
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.
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.
