Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
and JavaScript.
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.
Single-cell transcriptomics and expression quantitative trait locus mapping in 114 lung tissue samples, including 66 with interstitial lung disease, highlight the cell-type-specific functions of risk variants contributing to disease pathobiology.
Single-cell RNA sequencing analysis of over 800,000 human adult breast cells from 55 female donors identifies 41 cell subtypes and highlights age- and parity-dependent effects. Samples from healthy women with germline mutations in BRCA1 or BRCA2 showed signs of T cell exhaustion.
The exact relationship between 3D chromatin interactions and enhancer function is unclear. By probing three-dimensional enhancer interactions in developing embryos, two studies now show nuanced dynamics in tissue-specific contexts and reveal how moderately increased enhancer–promoter interactions coincide with functionality.
In mice, zygotic genome activation occurs at onset of the two-cell stage in embryonic development and coincides with the exit from totipotency. Our work shows that the transcription factor DUXBL participates in silencing part of the stage-specific two-cell-associated transcriptional program and is required for development to proceed.
Single-cell ATAC + RNA linking (SCARlink) predicts gene expression by jointly modeling local tiled chromatin accessibility using regularized Poisson regression on multi-ome data. SCARlink predictions can be used to identify cell-type-specific enhancers and perform chromatin potential analysis.
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 catalog of enhancer–promoter (E–P) interactions across ten mouse embryonic tissues, supported by in vivo functional experiments, shows that E–P proximity increases upon enhancer activation during development.