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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.
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.
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.
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.
The transcription factor double homeobox protein (DUX) induces a totipotency-specific regulatory program, including the upregulation of DUXBL. DUXBL subsequently accesses DUX-bound regions and interacts with TRIM24 and TRIM33, thus contributing to totipotency exit.
Chromosome-level genome assemblies of 11 bamboo species comprising lineages from diploid (herbaceous) to tetraploid and hexaploid (woody) provide insights into dynamic subgenome dominance in bamboos.
Analysis of enhancer–promoter (E–P) interactions during Drosophila embryogenesis suggests that the relationship between E–P proximity and activity depends on the developmental stage. Increased E–P proximity is associated with activity during differentiation but not specification.
This paper highlights the mechanisms underlying MYC-dependent gene regulation from transcriptional enhancers, which are distinct to the function of MYC at promoters. This process takes place in a cancer type-specific way, and the resulting transcriptional programs can predict prognosis.
Digenic inheritance of deleterious variants in serine/arginine protein kinase 3 (SRPK3) and titin (TTN) leads to a progressive early onset skeletal muscle myopathy. Zebrafish double mutants exhibit a similar myopathy phenotype accompanied by myofibrillar disorganization.
Epigenetic profiles can be predictive of macrophage transcriptional responses to influenza A virus infection in individuals of European and African ancestry. Ancestry-linked epigenetic differences appear to be genetically controlled.
An approach combining infection of primary human epithelial cells with a barcoded lentiviral-based library followed by engraftment into mice yields biologically relevant models of bladder and prostate cancer harboring complex genetic perturbations.
BANKSY is an algorithm with R and Python implementations that identifies both cell types and tissue domains from spatially resolved omics data by incorporating spatial kernels capturing microenvironmental information. It is applicable to a range of technologies and is scalable to millions of cells.