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Common mutational analyses assume that every base in the genome can only mutate once. Here, the authors report multiple violations of this infinite sites model in whole-genome data across a range of tumor types.
PHYTOCHROME-INTERACTING FACTORs reshape the H2A.Z epigenetic landscape in response to light quality changes in Arabidopsis thaliana, through an interaction with the INO80 chromatin remodeling complex.
An association model that estimates dominance and additive effects applied to imputed whole-genome data from cattle allows for the mapping of recessive syndromes in the absence of disease classification by using proxy phenotypes such as body weight.
DNMT3A PWWP domain mutations promote localization of DNMT3A to CpG islands in a PRC1-dependent manner. DNMT3A interacts with H2AK119ub-modified nucleosomes.
Analysis of long-read sequencing data from 3,622 Icelanders identifies a set of high-confidence structural variants and provides insights into their effect on human traits and diseases.
A genome-wide survival study identifies variants at RIMS2 associated with progression of Parkinson’s disease to dementia and highlights divergence in the genetic architecture of disease onset and progression.
Analysis of the three-dimensional architecture of the dinoflagellate Breviolum minutum genome identifies large topological domains (dinoTADs) demarcated by convergent gene array boundaries. Transcriptional inhibition disrupts dinoTADs.
Chemical inhibition of the SWI/SNF remodeling complex shows decreased accessibility and transcription factor binding within minutes. These changes are rapidly restored on inhibitor removal suggesting that accessible chromatin is regenerated continuously.
Integrating human brain proteomes with genome-wide association data followed by Mendelian randomization identifies 11 genes with potentially causal roles in Alzheimer’s disease pathogenesis.
Chromosomal inversions at the mimicry locus of Heliconius numata butterflies accumulate deleterious variants. This leads to selection against homozygosity, in opposition to positive selection for mimicry, resulting in intermediate allele frequency.
Genome-wide analyses identify multiple loci associated with hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM) and left ventricular (LV) traits. Cardiomyopathies exhibit strong genetic correlations with LV traits, with opposing effects in HCM and DCM.
Genome-wide association analyses identify 12 susceptibility loci for hypertrophic cardiomyopathy (HCM). A genetic risk score for HCM was associated with disease status in a validation study and influenced phenotypic severity in carriers of risk variants in sarcomere genes.
Genome-wide association analysis of 8,956 German individuals identifies 38 genetic loci associated with single bacteria and overall microbiome composition.
A high tumor mutational burden (TMB) is associated with improved immunotherapy response in many tumor types. This analysis of 10,233 individuals shows that, in contrast, high TMB is associated with poorer survival in patients that have not been treated with immune checkpoint inhibitors.
Super-resolution microscopy identifies sub-topologically associating domain (TAD) nanodomains and intercellular heterogeneity in TAD conformation and insulation. Cohesin or CTCF depletion regulates distinct types of chromatin contacts at the TAD but not nanodomain level.
Analysis of two independent cohorts of patients with Bardet–Biedl syndrome (BBS) with known recessive biallelic pathogenic mutations in one of 17 BBS genes shows an enrichment of rare nonsynonymous secondary variants in the same gene set, with significant over-representation of secondary alleles in chaperonin-encoding genes.
Haplotype-resolved assembly of a heterozygous diploid potato, RH89-039-16, and identification of deleterious mutations provide insights into the genome organization and breeding of a clonally propagated diploid species.
LSD1 promotes FOXA1 chromatin binding by demethylating lysine 270 of FOXA1 in prostate cancer cells. LSD1 inhibition decreases growth of prostate cancer cells.