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Chromosome-level genome sequences of 69 diverse Arabidopsis thaliana strains reveal a quasi-fixed genome structure worldwide, in which large rearrangement is limited almost exclusively to the centromeric regions. Pan-genome analysis uncovered substantial diversity in gene content that, together with the genome assemblies, will fuel future genetic research.
Multi-ancestry genome-wide analyses identify 95 loci associated with post-traumatic stress disorder and implicate candidate genes, pathways and neurobiological systems underlying its pathophysiology.
Analysis of genetic modifiers of 599 developmental disorder genes in the UK Biobank found that rare variant burden within this set, as well as the common polygenic background, can alter the expressivity of cognitive and socioeconomic traits in an additive manner.
A multi-ancestry genome-wide association study of liver cirrhosis and its associated endophenotypes identifies and validates 14 risk variants. Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis.
A single-cell-based approach allows the daughters of a damaged cell to be separately tracked following single mitotic events. This technique highlights the different ways in which ultraviolet light and reactive oxygen species cause mutagenesis.
A comprehensive time series characterization of a mouse model of cholestatic liver injury with spatial enhanced resolution omics sequencing and single-cell RNA sequencing identifies zonal responses to insult, such as cholangiocyte signaling recruiting lipid-associated macrophages.
A Stereo-seq and scRNA-seq atlas of mouse liver in homeostasis and regeneration after partial hepatectomy identifies zonated genes, pathways, cell–cell interactions and gene regulatory networks. Functional validation finds that cooperation between TBL1XR1 and β-catenin activates hepatocyte proliferation.
Chromosome-level genome assemblies of allotetraploid Coffea arabica and representatives of its diploid progenitors, Coffeaeugenioides and Coffeacanephora, provide insights into Arabica’s diversification history.
A pan-genome of Arabidopsis thaliana constructed using chromosome-level genome assemblies of 69 diverse accessions reveals a conserved genome structure throughout the global species range.
SCENT is a nonparametric method that models association between chromatin accessibility and gene expression in single-cell multimodal datasets, enabling construction of cell-type-specific enhancer–gene maps to aid mapping of candidate causal variants and genes for common diseases.
Analyses of whole-exome sequencing data identify rare loss-of-function variants in BSN associated with adult-onset obesity, type 2 diabetes and fatty liver disease, with stronger effect sizes than those observed for variants in known obesity risk genes such as MC4R.
Using single-cell RNA-sequencing (scRNA-seq) of lung tissue, expression quantitative trait loci (eQTLs) were mapped across 38 cell types, revealing both shared and cell-type-specific effects. Highly cell-type-specific disease-interaction eQTLs were linked to cellular dysregulation in lung disease and lung disease risk variants were connected to their regulatory targets in relevant cell types.
This study of Chinese endometrioid endometrial carcinomas describes the proteogenomic differences between early-onset and late-onset tumors, finding that SIGLEC10 mutation may contribute to tumorigenesis and progestin resistance in early cases.
We have curated a comprehensive single-cell reference map of the human breast. Our data explore how age, parity and germline mutations might influence cellular dynamics, revealing unexpected signs of immune exhaustion in healthy tissues from carriers of BRCA1 or BRCA2 germline mutations.
Whole-genome sequencing in a Canadian cohort of 327 children with cerebral palsy compared to pediatric controls identifies novel pathogenic single-nucleotide variants/indels and copy number variations. In addition, mitochondrial variants in known disease genes were identified. This highlights the importance of genomic testing for individuals with cerebral palsy.
Incorporating protein-altering copy number variants ascertained from UK Biobank whole-exome sequencing data into analyses of rare predicted loss-of-function variants identifies complex trait associations not detectable using standard analysis methods.