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Clones expressing variants of the X-chromosome-linked STAG2 gene only form lymphocytes in the absence of Stag2WT clones. Interactions between epigenetic clones can thus modulate the impact of X-chromosome-linked genetic diversity in a cell-type-specific manner.
Genomic analysis identifies an SVA retrotransposon insertion in an intron of ASIP as a likely causal variant influencing human pigmentation. This insertion appears to mitigate the effects of an older, nonpolymorphic SVA insertion in the same intron.
Allele-specific DNA methylation data in whole blood from 7,179 individuals sequenced by Nanopore, and gene expression profiles from 896 samples, show that DNA sequence variability accounts for most of the correlation between CpG methylation and gene expression.
A spatial transcriptomic analysis of healthy kidneys and those from individuals with chronic kidney disease characterizes the fibrotic microenvironment and highlights features that could be used to predict prognosis.
Single-cell analyses in RAD21-depleted mouse embryonic stem cells show that cohesin limits the coexpression of genes located in different accessible chromatin domains on the same chromosome by preventing co-bursting and blocking spatial mixing of different transcriptional hubs.
Inactivation of somatic SMC complexes in Caenorhabditis elegans shows that condensin I is the major long-range genome loop extruder, while cohesin forms small loops. Inactivation of cohesin, condensin II and condensin I/IDC causes minor transcriptional changes in autosomes.
Analysis of 2,096 single-cell clones from three tissues of 31 healthy donors characterizes mitochondrial DNA mosaicism and highlights the following two origins of mtDNA variants: heteroplasmy in the fertilized egg and postzygotic mutations.
Exome sequencing within a structured diagnostic process for rare diseases in Germany shows how facial image analysis and machine learning can guide variant prioritization and uncover many ultrarare diseases.
A European ancestry genome-wide meta-analysis of pregnancy-associated bleeding traits identifies five novel loci associated with postpartum hemorrhage, but none with early bleeding. Functional analysis highlights a role for progesterone receptor-mediated signaling.
A multiomic approach profiles the three-dimensional, epigenetic and mutational landscapes of 80 metastatic prostate cancer biopsies. Hi-C experiments identify an extrachromosomal circular DNA at the AR locus associated with therapy resistance.
GeneBayes is a Bayesian approach incorporating a Wright–Fisher population model with machine learning of gene features to infer an interpretable gene constraint metric that has a broad range of uses in downstream analysis.
Citrullus super-pangenome constructed using 27 telomere-to-telomere assemblies encompassing all seven Citrullus species highlights genomic diversity across wild and cultivated watermelons and the potential for crop improvement.
Representation Learning for Genetic Discovery on Low-Dimensional Embeddings (REGLE) uses machine learning to generate low-dimensional representations of healthcare data. Applied to lung spirograms and blood volume photoplethysmograms, REGLE factors capture additional information beyond expert-defined features, suggesting the utility of this approach.
This study presents a multiomic Gene–Metabolite Association Prediction (GeneMAP) platform for discovery of metabolic gene function and identifies SLC25A48 as a mediator of mitochondrial choline import.
Saturation genome editing characterizes von Hippel–Lindau (VHL) coding variants and their associations with diseases. Function scores for 2,268 VHL single-nucleotide variants (SNVs) classify pathogenic alleles driving renal cell carcinoma and suggest new mechanisms by which variants impact function.
Saturation genome editing characterizes BAP1 variants and their association with disease presentation. A phenome-wide association analysis in the UK finds that BAP1 variants identified as deleterious in the study are associated with higher serum IGF-1 levels.
Mismatch repair-deficient colorectal cancer clones adapt their mutation landscape by toggling homopolymer sequences in MutS homolog 3 (MSH3) and MutS homolog 6 (MSH6). This increases the subclonal mutation rate and clonal diversity, favoring immune escape and tumor growth.
Spatially resolved transcriptome analysis of human and mouse idiopathic pulmonary fibrosis identifies disease-associated niches and a role for aberrant alveolar epithelial cells in human disease pathogenesis.
A multi-ancestry genome-wide association study for age at menarche followed by fine mapping and downstream analysis implicates 665 pubertal timing genes, such as the G-protein-coupled receptor 83 (GPR83) and other genes expressed in the ovaries involved in the DNA damage response.
Analysis of the FGF14-SCA27B repeat locus identifies a common 5′-flanking insertion that represents the major allele, is present exclusively on nonpathogenic alleles, enhances repeat stability and increases chromatin accessibility.