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Population analysis of 516 wild and domesticated broomcorn millet genomes and a graph-based pangenome based on de novo assemblies of 32 representative accessions identify genomic variations associated with domestication traits.
Roulette enables the estimation of germline mutation rates at basepair resolution from humans. Genes encoding small nuclear RNA showed significant deviations from the mutation rate predicted by Roulette, highlighting RNA polymerase III (Pol III)-dependent transcription as a potent source of mutations in the human genome.
A multivariate framework for isoform-resolution transcriptome-wide association studies enables modeling of a greater number of genes, with the benefit of identifying isoform-specific associations with psychiatric traits not observed at the gene level.
Genome-wide analyses yield insights into the polygenic effects contributing to clinical heterogeneity in attention deficit hyperactivity disorder, advancing understanding of its genetic etiology and serving as a model for future studies in other complex disorders.
Multi-ancestry genome-wide association meta-analyses identify risk loci for cannabis use disorder. Genomic structural equation modeling and genetic correlation analyses show overlap with several other traits, including impulsivity and psychopathology.
Phenotype imputation increases the effective sample size of major depressive disorder cases in UK Biobank, enhancing study power and polygenic risk score (PRS) accuracy. A new pleiotropy metric enables assessment of PRS specificity and comparison among different PRS models.
In pancreatic duct adenocarcinoma, super-enhancer RNAs (seRNAs) have higher N6-methyladenosine (m6A) levels than in adjacent normal tissue due to upregulation of the METTL3 cofactor CFL1. Aberrant m6A seRNAs promote oncogene expression via the YTHDC2–MLL1 complex.
Circular extrachromosomal DNA in high-risk medulloblastoma contributes to tumor heterogeneity and associates with relapse and survival. Enhancer rewiring events involving known oncogenes are frequent events, affecting transcription and proliferation.
CRISPR activation/interference screens identify transcriptional regulators of human CD8+ T cells, including BATF3. BATF3 overexpression counteracts T cell exhaustion and enhances cancer immunotherapy in in vivo models.
JaBbA v1 pinpoints the ‘loose ends’ of large (>10-kb) unmapped structural variants in short-read DNA sequencing, suggesting that about 90% of cancer chromosomal alterations outside centromeres are resolvable with short reads and that long reads will primarily improve calling of smaller somatic variants.
A barcode-based approach applied to UK Biobank and an Icelandic cohort identifies drivers of clonal hematopoiesis (CH) and finds associations between CH and multiple diseases. Genome-wide association analyses identify 25 loci associated with CH susceptibility.
Chromosome-level genome assemblies of three Allium crops (onion, garlic and Welsh onion) and spatial RNA sequencing provide insights into Allium trait evolution and gene expression patterns during onion bulb formation.
Homozygous loss-of-function variants in phospholipase A/acyltransferase 3 (PLAAT3) underlie a new lipodystrophy syndrome. Functional studies link PLAAT3 loss with peroxisome proliferator-activated receptor gamma (PPARγ)-mediated defects in white adipose tissue differentiation and function.
Single-haplotype genome assemblies from five cat species shed light on the dynamics of structural variations during felid radiation and resolve sensory gene repertoires associated with adaptation and domestication.
Genome-wide analyses identify 43 loci associated with forearm fracture, including some influencing bone quality parameters. Follow-up work shows that Tac4 knockout mice exhibit reduced mechanical bone strength with no effect on bone mineral density.
Analysis of GTEx RNA-seq samples identifies hundreds of mosaic chromosomal alterations (mCAs). Considerable inter-tissue variability and excess incidence of mCAs across malignancies suggest a complex relationship with tumorigenesis.
A method that allows for the detection of mosaic chromosomal alterations from blood whole-genome sequencing data highlights ancestry-specific differences in the distribution of common and rare germline susceptibility variants.
Genome-wide association analyses of migraine and its subtypes identify new susceptibility loci, including rare variants with large effects implicating PRRT2, SCN11A and KCNK5.
Analysis of the somatic mutations landscape of 111 patients with psoriasis vulgaris shows that the disease is unlikely to be driven by clonal expansions caused by somatic mutations in keratinocytes. A mutational footprint associated with psoralen treatment was observed and characterized.