Reviews & Analysis

Genome instability can lead to a number of human diseases, including neurodegeneration and cancer. In this Review, Zong et al. discuss the various ways in which RNA can both promote genome instability and contribute to genome maintenance.

Gene expression is typically measured at the level of either mRNAs or proteins. In this Review, Buccitelli and Selbach discuss how large-scale comparative studies are characterizing the degree to which mRNA and protein levels correlate. They discuss technical and biological reasons why mRNA and protein levels may be particularly concordant or disconnected, as well as the different biological information provided by these non-redundant readouts of gene expression.

Data sharing can maximize the benefit and reach of genomics research. However, sharing must occur in a responsible manner, particularly when there are privacy risks to human participants. In this Review, the authors discuss the principles of data sharing, strategies for assessing and mitigating privacy risks, as well as practical guidelines for researchers and wider stakeholders.

In this Expert Recommendation, the authors review the definitions of classic concepts relating to bacterial gene regulation, with a focus on transcription initiation, and suggest up-to-date, precise definitions to provide a reference for knowledge representation, modelling and future research on bacterial gene regulation.

Increased capacities for sequencing and genotyping are enabling a more comprehensive understanding of the genetics of adaptation for diverse species. In this Perspective, Barghi, Hermisson and Schlötterer describe how polygenic adaptation can be studied using a framework of ‘adaptive architecture’ that unifies principles from the traditionally disparate fields of quantitative genetics and molecular population genetics.

Computational tools to analyse RNA sequencing data often disregard or even misinterpret reads derived from transposable elements. This Review highlights the main challenges associated with the detection of transposable element expression, including mappability, sequence polymorphisms and transcript diversity, and discusses the experimental and computational strategies to overcome them.

The development of successful anticancer therapies relies on identifying drug targets that are genuine cancer-specific vulnerabilities. In this article, Lin and Sheltzer discuss how the different genetic and pharmacological methods for identifying and characterizing cancer dependencies each have important strengths and limitations. Responsible and orthogonal use of these methods holds promise for maximizing the ability of preclinical research to translate into clinical benefit.

In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.

The role of DNA methylation in genomic imprinting and X-chromosome inactivation (XCI) is well documented, but other imprinting mechanisms exist. Here, the authors review the role of oocyte-derived histone H3 lysine 27 trimethylation in establishing autosomal imprinting and imprinted XCI.

Long-read sequencing is becoming more accessible and more accurate. In this Review, Logsdon et al. discuss the currently available platforms, how the technologies are being applied to assemble and phase human genomes, and their impact on improving our understanding of human genetic variation.

The capacity to regenerate tissue varies across different species and tissue types. The poor regenerative capacity of organs such as the heart and nervous system contributes to the aetiology of a number of serious diseases, including heart failure and Alzheimer disease. In this Review, Goldman and Poss discuss how genetic programmes of regeneration are regulated and how the control mechanisms might be adapted to treat human disease.

Genetic recombination is a fundamental biological process generating genetic variation by shuffling combinations of alleles. In this Review, Peñalba and Wolf focus on how sequencing-based approaches are providing diverse insights into recombination rate variation across levels of biological organization and timescales, from individual gametes of single individuals to populations through evolutionary history.

Wilkinson and colleagues discuss haematopoietic stem cell (HSC) self-renewal in mice and humans. Experimental techniques for assaying HSC self-renewal are addressed, along with biological mechanisms regulating HSC self-renewal in vivo and ex vivo, and the therapeutic implications of this understanding.

Understanding evolutionary relationships between species requires the generation of accurate phylogenetic trees. In this Review, Kapli, Yang and Telford discuss the principles, steps and computational tools for phylogenetic tree building. They describe the impact of burgeoning genomic datasets as well as the diverse sources of errors and how they can be mitigated.

Colour traits have been useful for studying the genetics underlying adaptive evolution. This Review discusses how genomic technologies are providing a deeper understanding of these traits, revealing fresh insights into their genetic architecture, evolvability and origins of adaptive variation.

A curated list of genes that are relevant to autism spectrum disorder (ASD) would greatly benefit clinical genetic testing. This Roadmap discusses the need for an evidence-based framework for gene curation that is based on the level of information supporting a clinically relevant relationship between a given gene and ASD.

Genetic improvement of production traits in aquaculture has great potential to help meet the rising seafood demands driven by human population growth. The authors review how genomics is being applied to aquaculture species at all stages of the domestication process to optimize selective breeding.

Improvements in DNA extraction methods and sequencing technologies have led to the successful sequencing of numerous whole ancient genomes. In this Review, the authors provide an overview of how ancient DNA has informed our understanding of the domestication of various animal species, including dogs, pigs, cattle, goats and chickens.

In this Perspective article, the authors discuss how Indigenous Peoples' desires for greater involvement and oversight when participating in genomic research projects can be balanced against calls for unrestricted data access. They provide practical recommendations for the handling and sharing of Indigenous genomic data, with the aim of achieving mutual benefit for the research community and participating Indigenous communities.

Understanding developmental trajectories has recently been enabled by progress in modern lineage-tracing methods that combine genetic lineage analysis with omics-based characterization of cell states (particularly transcriptomes). In this Review, Wagner and Klein discuss the conceptual underpinnings, experimental strategies and analytical considerations of these approaches, as well as the biological insights gained.