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A deep-learning framework interprets multiomic data across epidermal differentiation, identifying cooperative DNA sequence rules that regulate gene modules. Massively parallel reporter assay analysis validates temporal dynamics and cis-regulatory logic.
Re-expression of Pkd genes in cystic kidneys results in rapid reversal of autosomal dominant polycystic kidney disease phenotypes in mice, revealing an unexpected capacity for renal plasticity under the control of Pkd gene function.
Depletion of BRD4 reduces the chromatin occupancy of NIPBL, resulting in aberrant genome folding. Loss of BRD4 impedes neural crest differentiation, which can be rescued by depletion of WAPL.
Genome-wide association and Mendelian randomization analyses in the UK Biobank identify genetic variants associated with leukocyte telomere length and highlight putative causal links between telomere length and biomedical phenotypes.
A high-resolution reference panel based on whole-genome sequencing data enables accurate imputation of HLA alleles across diverse populations and fine-mapping of HLA association signals for HIV-1 host response.
Multimodal DNA methylation and transcriptome profiling of single glioma cells links tumor cell transcriptional states to epigenetics via interaction with PRC2 and shows that these states are heritable and important for tumor plasticity.
Healthy tissues from individuals with germline mutations in POLE or POLD1 show increased mutational burden, suggesting that normal cells are capable of tolerating high mutation rates.
Single-cell DNA methylation and transcriptomic glioma analyses link local DNA methylation disorder and cellular plasticity. Increases in disorder are associated with stress and disease progression, suggesting a role in shaping the therapeutic response.
Genome-wide analyses in BioBank Japan, UK Biobank and FinnGen identify ~5,000 new loci associated with 220 human traits. Statistical decomposition of matrices of phenome-wide summary statistics further highlights variants underpinning diseases across populations.
Analysis of 2,170 SARS-CoV-2 sequences from the first wave of the COVID-19 epidemic in Spain provides insights into transmission patterns and the effects of lockdown on the emergence of new variants.
Mice bearing mutations in Flt3-ITD and Npm1c, which are commonly found in acute myeloid leukemia, are used to characterize the cooperative effects of these cancer drivers on the cellular epigenome and three-dimensional genome conformation during tumor development.
A genome-wide association study performed in 1,126,563 individuals identifies seven new loci associated with Alzheimer’s disease and implicates microglia and immune cells in late-onset disease.
Sex-stratified GWAS analyses for 530 traits within 452,264 individuals of European ancestry from the UK Biobank provide insights into the scope of genotype by sex (GxS) interactions and the genetics of sex differences.
Whole-genome sequencing of lung cancer in never smokers identifies different copy number subtypes and shows a lack of tobacco smoking signatures, even in cases exposed to secondhand smoke.
A multi-omic atlas of breast cancers, integrating single-cell RNA sequencing, spatial transcriptomics and immunophenotyping, identifies nine ecotypes associated with cellular heterogeneity and prognosis.
DNA methylation quantitative trait locus (mQTL) analyses on 32,851 participants identify genetic variants associated with DNA methylation at 420,509 sites in blood, resulting in a database of >270,000 independent mQTLs.
The eQTL Catalogue provides uniform processing of 21 eQTL studies, allowing the identification of highly reproducible eQTLs affecting whole gene and transcript expression levels.
A chromosome-scale de novo assembly of a yellow-seeded Brassica juncea genome and population analyses of 480 accessions from 38 countries provide insights into the origin, domestication history and morphological diversification of B. juncea.
Analyses of expression profiles from whole blood of 31,684 individuals identify cis-expression quantitative trait loci (eQTL) effects for 88% of genes and trans-eQTL effects for 37% of trait-associated variants.