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Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype can be rescued by mutations in the retrotransposon coding sequence.

Dubois and colleagues assemble a large cohort of human pediatric high-grade glioma samples, identifying patterns of simple and complex structural variants and characterizing their role in tumor development and evolution.

Single-nucleus RNA sequencing from the dorsolateral prefrontal cortex of 424 aging individuals, and mapping the effect of genetic variation on gene expression, identified a large number of cis-expression quantitative trait loci at the level of cell types and cell subtypes.

A large-scale single-cell transcriptomic atlas of the non-human primate Macaca fascicularis encompasses over 1 million cells from 45 adult tissues.

This work presents NeoLoopFinder, a computational method, for identifying chromatin interactions of structurally rearranged genomes. NeoLoopFinder was applied in 50 cancer datasets and identified genes associated with enhancer-hijacking events.

Technological advances over the past decade have revolutionized many areas of rheumatology, ranging from diagnosis, prognosis and therapeutic development to the mechanistic understanding of rheumatic diseases. This overview highlights key technological innovations and discusses the major impact that these developments are having on research and clinical practice.

Using a transposon-based approach to create a set of large genomic rearrangements, Dauban et al. demonstrate that interactions of lamina-associated domains with the nuclear lamina involve multiple contacts of varying strength.

The spatial and frontal QRS-T angles are electrocardiographic (ECG) predictors for arrhythmia. This work used genetic analyses to identify associated loci and pathways, and explore their relationships with other ECG traits and cardiovascular disease.

The genomic characterisation of nasopharyngeal carcinoma (NPC) remains crucial. Here, the authors perform whole-genome sequencing for 70 NPCs with EBV gene expression, report the somatic alterations and EBV-mediated effects converging on NF-κB activation and immune escape and identify targetable homozygous MTAP deletions.

DNA methylation is efficiently profiled in non-coding regulatory sequences in single cells.

As part of Myeloid Cells in Neurodegenerative Disease (MyND) initiative, the authors profiled the transcriptome of primary monocytes and microglia from patients with Parkinson’s disease and controls, revealing the pathways and genes that are altered in the immune system of patients with Parkinson’s disease.

The authors study the cis-regulatory evolution of the Shh locus in vertebrates. Using genomic editing and chromatin profiling, they conclude that paired fins emerged through the co-option of developmental programs for the median fins of gnathostomes.

Predicting chromatin loops from genome-wide interaction matrices such as Hi-C data provides insight into gene regulation events. Here, the authors present Peakachu, a Random Forest classification framework that predicts chromatin loops from genome-wide contact maps, and apply it to systematically predict chromatin loops in 56 Hi-C datasets, with results available at the 3D Genome Browser.

The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.

Biocompatible nanoparticles for targeted drug delivery, imaging and tracking of therapeutic agents are sought-after. Here, the authors report cyclic peptide nanoparticles with structure induced fluorescence that can conjugate with biomarkers and carry drugs for application in esophageal cancer.

A transcriptome-wide association study integrating genome-wide association data with expression data from brain, blood and adipose tissues identifies new candidate susceptibility genes for schizophrenia, providing a step toward understanding the underlying biology.

This protocol provides guidelines for performing single-cell combinatorial indexing cleavage under targets and tagmentation. This method builds on the existing cleavage under targets and tagmentation method and uses a combinatorial indexing step to allow single-cell profiling of chromatin modifications.

A scalable barcoding method measures multiple chromatin-associated proteins in single cells.

An epigenome-focused CRISPR screen in enzalutamide-resistant prostate cancer identified a unique dependency against SWI/SNF complexes that is potentially mediated by an expansion of their binding regions.

Chromatin run-on and sequencing (ChRO-seq) is a new method that maps the location of RNA polymerase using virtually any input sample. Here, ChRO-seq is used to study nascent transcription in human glioblastoma, and to identify regulators of tumor subtype.

Combining 32 genome-wide association studies with high-density imputation provides a comprehensive view of the genetic contribution to type 2 diabetes in individuals of European ancestry with respect to locus discovery, causal-variant resolution, and mechanistic insight.

In a genome-wide association study for traits related to pancreatic beta-cell function in 26,000 individuals, 55 independent associations mapping to 44 genetic loci are identified.

Systemic sclerosis (SSc) is a heterogeneous chronic autoimmune disease that affects the connective tissue. Here, López-Isac et al. identify 13 new risk loci for SSc as well as loci specific for limited cutaneous and diffuse SSc and, defining credible sets and performing functional annotation, highlight key pathways and cell types for SSc.

The authors describe how aging rewires the cellular composition of mouse mammary tissues and impacts the transcriptomic and epigenomic programs of mammary epithelial, fibroblast and immune cells, identifying shared signatures of aging and cancer.

Sequencing and assembly of the 32-Gb genome of the Mexican axolotl reveals that it lacks the developmental gene Pax3, which is essential in other vertebrates; the genome sequence could improve our understanding of the evolution of the axolotl’s remarkable regenerative capabilities.

The integration of omics technologies, genome editing and protein design with artificial intelligence (AI) promises rapid advances in the field of crop improvement that will improve global food security.

The Perturb-Tracing approach represents a significant step forward in our ability to perform pooled loss-of-function perturbations to identify regulators of 3D genome organization across multiple length scales.

In this Review, Butterfield and Najjar discuss the rationale for combination strategies in cancer, including combinations of different immunotherapies and combinations of immunotherapies with other types of therapies. Moreover, they examine the evolution of biomarker approaches to guide such therapies.

The International Strawberry Sequencing Consortium reports the draft genome of the woodland strawberry (Fragaria vesca). The genome of this diploid species should serve as a reference genome for the Fragaria genus, as the cultivated strawberry (Fragaria × ananassa) is an octoploid where F. vesca is predicted to be a subgenome donor.

The BRAIN Initiative Cell Census Network has constructed a multimodal cell census and atlas of the mammalian primary motor cortex in a landmark effort towards understanding brain cell-type diversity, neural circuit organization and brain function.

A number of core pathways and mechanisms of fibrosis, outlined in this Review, are shared across different tissues and might therefore present targets for general antifibrotic strategies. Organ-specific and disease-specific differences in fibrotic diseases could also provide insights for drug development efforts.

A technique using barcoded beads for DNA sequencing within tissue sections enables spatial resolution of tumour clonal heterogeneity and can be multiplexed with other analytical techniques for analysis of complex cellular phenotypes.

The authors introduce CausalBench, a benchmark suite that enhances network inference evaluation with real-world, large-scale single-cell perturbation data.

Genome-wide analyses identify eight independent loci associated with anorexia nervosa. Genetic correlations implicate both psychiatric and metabolic components in the etiology of this disorder, even after adjusting for the effects of common variants associated with body mass index.

In this Expert Recommendation, Faupel-Badger and colleagues present a conceptual framework to define precancer and advance our understanding of the earliest changes that occur in the progression to overt cancer, providing novel opportunities to intervene to prevent or treat their emergence.

Studies using mouse models of lung adenocarcinoma identify an association between age, iron homeostasis and tumour initiation potential that involves NUPR1 and lipocalin-2.

Regenerative tissue engineering aims to functionally restore damaged tissues. This Review discusses how advances in single-cell RNA sequencing techniques and analysis methods can expand our understanding of tissue injury responses to inform the design of new regenerative biomaterials and therapeutics.