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Co-deletion of all proteins with a functional methyl-CpG-binding domain does not impact genes or repeats silenced by DNA methylation. Analysis of chromatin accessibility and sequence motifs identifies transcription factors that appear sensitive to DNA methylation.
A genomic and transcriptomic analysis identifies molecular features associated with long-term survival in ovarian cancer. Exceptional survival was heterogeneous across the cohort, suggesting that it is likely the function of multiple cell-intrinsic and microenvironmental factors working in combination.
Prrx1-expressing can act as stem cells for bone, white adipose tissue and dermis in adult mice. These cells have a key role in tissue homeostasis and repair and are regulated by Wnt signaling.
Reanalysis of the immunotherapy-treated MSK-IMPACT cohort finds that chromosomal arm-level aneuploidy scores are an independent predictor of survival for patients with low tumor mutational burden.
Multiancestry genome-wide association analyses in the Million Veteran Program and UK Biobank identify new risk loci for osteoarthritis. Drug repurposing analyses yield potential insights into the effects of antiepileptics on osteoarthritis pain.
Multistage gene burden analysis in exome sequencing data from 32,558 individuals identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s disease.
Expression of mdg4 retrotransposons during Drosophila metamorphosis activates the antiviral NF-κB factor Relish. Silencing of mdg4 or Relish at the pupal stage leads to an inability to clear exogenous viruses in adulthood.
EGLN2 hydroxylates histone H3 at proline 16, enhancing the binding of KDM5A to H3K4me3. Genome- and transcriptome-wide analyses show that the EGLN2–KDM5A axis regulates target gene expression in mammalian cells.
De novo variants altering a conserved region in an intron of HK1 cause congenital hyperinsulinism by perturbing the activity of a putative cell type-specific regulatory element.
Whole-genome sequencing of chronic lymphocytic leukemia from 485 patients identifies putative coding and noncoding drivers of disease. Genomically defined subgroups show distinct clinical and biological characteristics.
Ectopic imprinting control regions (ICRs) recapitulate chromatin states of endogenous imprinted loci in mouse embryonic stem cells. ATF7IP and ZMYM2 regulate epigenetic memory at ICRs.
Multi-ancestry genome-wide association analyses identify 124 risk loci for rheumatoid arthritis, of which 34 are novel. A polygenic risk score based on multi-ancestry data showed comparable performance between populations of European and East Asian ancestries.
Adult kidney organoids, or tubuloids, originate from CD24+ epithelial cells. Tubuloids represent a functional kidney tubule and can be used to model autosomal dominant polycystic kidney disease and study drug response.
This study presents a method for constructing complex trait polygenic scores from rare variants and shows that a polygenic score combining common and rare variants improves the accuracy of diagnosis for type 2 diabetes based on hemoglobin A1C levels.
Common polygenic variation at chromosome 16p and rare recurrent deletions of 16p11.2 influencing autism risk are associated with reduced expression of genes throughout the 16p region, suggesting functional convergence of rare and common variant effects.
Genome-wide analyses identify loci associated with nonalcoholic fatty liver disease, including rare, protective loss-of-function variants in MTARC1 and GPAM. Plasma proteomic analyses provide insight into proteins involved in disease pathogenesis.
Genome-wide analysis of self-reported dyslexia identifies 42 associated loci, including 27 not previously associated with cognitive traits. Dyslexia shows genetic correlation with ambidexterity but not neuroanatomical measures of language-related circuitry.
A high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea reveals evidence of adaptive variation and provides a genus-wide resource of genetic diversity in Zea.
CRISPR-CATCH is used to isolate extrachromosomal DNA (ecDNA) molecules containing oncogenes from human cancer cells. CRISPR-CATCH followed by nanopore sequencing allows for methylation profiling, highlighting differences from the native chromosomal loci.
Microwell-seq is used to generate single-cell, whole-body expression landscapes of zebrafish, Drosophila and earthworm. A deep-learning model, Nvwa, predicts gene expression from DNA sequence and identifies regulatory programs shared across eight species.