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SOX9 titration in neural crest cells identifies regulatory elements and genes with sensitive or buffered responses. Sensitive genes are enriched for craniofacial disorder genes phenocopying SOX9, suggesting differential sensitivity contributes to phenotypic specificity.
A tomato super-pangenome constructed using chromosome-scale genomes of nine wild species and two cultivated accessions highlights genomic diversity and structural variation across wild and cultivated tomatoes.
Histone H2B N-terminus multisite lysine acetylation (H2BNTac) is identified as a signature of active enhancers. H2BNTac-positive putative enhancers are validated using orthogonal enhancer activity assays.
Genomic and transcriptomic analysis of 393 non-small cell lung cancer patients treated with checkpoint inhibitors identifies molecular features associated with response.
Disruption of MLL3/4 enzymatic activities prevents gastrulation and leads to early embryonic lethality in mice. This is largely due to defects in extraembryonic lineages, which compromise developmental progression.
Single-cell analysis of head and neck squamous cell carcinoma (HNSCC), specifically from human papillomavirus (HPV)-positive and HPV-negative oropharynx tumors, reveals high levels of inter- and intratumoral heterogeneity. Patterns of HPV gene expression were divergent within HPV-positive tumors, with corresponding functional effects on treatment resistance.
High-resolution Micro-C is applied to characterize the effect of RNA polymerase II (RNAPII) loss on chromosome looping, finding that the formation of enhancer–promoter, but not promoter–promoter, loops are dependent on RNAPII binding to their anchors.
Analysis of multiple tumor types, cancer cell lines and adult tissues identifies tumor-specific transposable-element-chimeric transcripts. Mass spectrometry data confirm that many are translated and subsequently located on the extracellular surface of cancer cells, highlighting potential immunogenic therapies.
Somatic evolutionary analysis of neuroblastoma, a pediatric tumor, proposes a common fetal time of origin. Notably, high-risk tumors exhibit early genomic instability and prolonged evolution, and this evolutionary duration predicts clinical outcomes.
Genome-wide CRISPR screening identifies thymidine nucleotide metabolism as a key regulator of human telomere length. Thymidine supplementation promotes telomere elongation in cells derived from patients with telomere biology disorders.
Genetic lineage tracing in mice shows that endocardium-derived fibroblasts preferentially proliferate in response to pressure overload. Ablation of these cells alleviates cardiac fibrosis and reduces functional decline after pressure overload injury.
Adjusting for common variant polygenic scores improves yield in gene-based rare variant association tests for quantitative traits, particularly when using sparse mixed models or simple linear models as an alternative to dense mixed-model approaches.
This analysis of individuals of admixed genetic ancestries suggests that complex trait causal variant effect sizes are, by and large, similar across ancestries, and discusses the implications for the study of these and other diverse populations.
Meta-analyses of genome-wide association studies for endometriosis identify 49 distinct association signals. Fine-mapping of causal variants explores functional effects across various tissues. Genetic correlations between endometriosis and other pain conditions are also highlighted.
Multi-ancestry genome-wide association analyses and systematic variant-to-gene mapping strategies implicate new genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.
Transitional liver progenitor cells (TLPCs), which derive from biliary epithelial cells (BECs), differentiate into hepatocytes after serious liver damage. Notch and WNT/β-catenin signaling regulate BEC-to-TLPC and TLPC-to-hepatocyte conversions, respectively.
Premalignant stromal cells from women with germline BRCA1 mutations exhibit increased expression of secreted factors regulating epithelial homeostasis in a paracrine fashion. These secreted factors, such as MMP3, promote premalignant epithelial changes including elevated proliferation and altered differentiation of a subpopulation of luminal progenitor cells.
Targeted sequencing finds a higher burden of rare protein-truncating variants in constrained genes among schizophrenia cases of diverse ancestries. Meta-analyses with existing datasets show that this excess burden is consistent across five ancestral populations.