Review Articles

Chromothripsis, a complex genomic rearrangement of one (or a few) chromosomes, is frequently found in cancer genomes. The authors review methods to identify chromothripsis in cancer genomes and discuss its mechanisms of formation in micronuclei or chromosomal bridges as well as its consequences in cancer. They also highlight the link between chromothripsis and extrachromosomal DNA.

Species and communities can respond to global climate change by genetically adapting to new environmental conditions, by shifting their range or through phenotypic plasticity. This Review summarizes approaches that apply and integrate omics tools to experimentally investigate, monitor and predict these species responses.

This Review discusses the genetic architecture of inborn errors of immunity (IEIs), highlighting the role of common genetic variants, concepts related to their incomplete penetrance and the increasing incidence of IEIs affecting distal organ systems.

Antimicrobial resistance (AMR) is an important public health issue that affects human, animal and environmental sectors worldwide. The authors review the role of genomics in AMR surveillance using a One Health approach, and how genomic approaches can help mitigate the spread of AMR to improve global health.

Ancient DNA studies over the past decade have yielded a plethora of insights into the Denisovan archaic hominin group. The authors review our understanding of Denisovan population history and their interactions with other human groups, insights from studies of Denisovan ancestry in modern humans, what we know about the Denisovan phenotype and their impact on our own evolutionary history.

Native nucleotide modifications regulate RNA function and metabolism, the study of which has revealed disease mechanisms, offers therapeutic potential and enables innovative clinical strategies. Chemical modifications in RNA are harnessed for clinical use in stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules.

Genomic imprinting — the monoallelic expression of genes based on their parent of origin — may have evolved due to an intragenomic conflict between maternal and paternal genomes within an individual, with differential interests regarding the level of parental caregiving. Here, the authors review the influence of genomic imprinting on parenting behaviour in mammals, with a focus on studies in mice.

In this Review, Zhang et al. discuss how recent advances in computational methods are helping to reveal the multiscale features involved in genome folding within the nucleus and how the resulting 3D genome organization relates to genome function.

Applying deep learning to large-scale genomic data of species or populations is providing new opportunities to understand the evolutionary forces that drive genetic diversity. This Review introduces common deep learning architectures and provides comprehensive guidelines to implement deep learning models for population genetic inference. The authors also discuss current opportunities and challenges for deep learning in population genetics.

This Review summarizes the genetic and non-genetic factors that impact the transferability of polygenic risk scores (PRSs) across populations, highlighting the technical challenges of existing PRS construction methods for diverse ancestries and the emerging resources for more widespread use of PRSs.

In this Review, the authors discuss recent advances in our understanding of Mediator and TFIID, coactivators associated with the RNA polymerase II (Pol II) pre-initiation complex (PIC), focusing on their structure, interactions with activators and impact on the function of the PIC.

In this Review, Zhou et al. discuss our current understanding of the genetic control of key steps involved in human brain development and diseases, and they describe current and emerging approaches for investigating the underlying genetic architecture.

This Review explores the use of non-mammalian model organisms in the genetic diagnosis of rare diseases, focusing on the use of worms, flies and zebrafish. The strategies, genetic technologies and approaches to using these models are discussed, as well as how they can provide insight into more common disease mechanisms.

Control can be applied to alter the ecological or evolutionary trajectory of a target system towards a predefined objective. In this Review, the authors discuss the aims, applications, mechanisms and dynamics of eco-evolutionary control across different biological systems.

In this Review, the authors summarize the current evidence for the use of genomic sequencing in newborn screening for rare diseases. As several large-scale studies launch internationally, the authors discuss major challenges and opportunities that lie ahead and identify key research priorities.

In this Review, the authors describe how the application of new technologies to the microRNA (miRNA) field has yielded key insights into miRNA biology. The authors summarize our current understanding of miRNA biogenesis, function and processing, and highlight challenges to address in future research.

Incongruence occurs when phylogenetic trees show conflicting evolutionary histories such as patterns of branching or relationships among taxa. This Review discusses the biological and analytical factors that lead to incongruence, methodological advances to identify and resolve incongruence, and avenues for future research.

Regulatory circuits of gene expression can be represented as gene regulatory networks (GRNs) that are useful to understand cellular identity and disease. Here, the authors review the computational methods used to infer GRNs — in particular from single-cell multi-omics data — as well as the biological insights that they can provide, and methods for their downstream analysis and experimental assessment.

This Review discusses the range of methods used for assessing the growth and fitness of SARS-CoV-2 variants, from classic population genetics to phylogenetics and epidemiological data, and describes future perspectives for surveillance of SARS-CoV-2.

This Review discusses how transposable elements contribute to mammalian genome evolution and gene regulation through their ability to both maintain and reshape 3D genome structure.