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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.
A study in Nature describes ‘DNA Typewriter’, a prime-editing-based DNA recording technology that can capture the order of large numbers of distinct molecular events in mammalian cells.
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.
Two recent studies report microbial genome and gene catalogues that archive oceanic and glacial genomic and functional diversity at scale and yield insights into their biosynthetic potential.
Steiner highlights a study by Protacio et al., which has identified molecular mechanisms underlying the plasticity of meiotic recombination in Schizosaccharomyces pombe.
A report in Cell takes single-cell CRISPR screens to genome scale and demonstrates how the transcriptional phenotypes can be used to resolve gene functions.
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 Comment, the authors highlight caveats about using African ethnicities as population categories in genomics research and emphasize the need for an Africa-oriented humanities research agenda to inform genomics research.
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.
Somatic mutations accumulate with age in the genome of healthy individuals. Franco and Eriksson posit that recent sequencing data indicate a functional role for this increased mutational load in ageing and age-associated diseases.
In this Journal Club, Itay Tirosh highlights a 2011 publication by Gupta et al., which showed that cells undergo frequent stochastic transitions between distinct states in breast cancer cell lines.
Gegenhuber et al. now show that, in mice, a neonatal surge in oestradiol activates oestrogen receptor-α to drive a sustained male-typical gene expression programme that determines brain sexual differentiation.
