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Analysis of a chromosome-level bowfin genome assembly sheds light into neopterygian fish evolution. Chromatin accessibility and gene expression profiling provides insight into bowfin embryonic development.
Sequence analysis identifies gain-of-function somatic mutations in GNA11 or GNAQ in CTNNB1-mutant aldosterone-producing adenomas. Most patients with these mutations presented during puberty, pregnancy or menopause, with elevated LHCGR expression.
Cell-type-specific eQTL maps in the human kidney generated from the analysis of over 600 microdissected kidney samples, together with single-cell RNA sequencing and single-nucleus ATAC-seq, prioritize cell types influencing kidney function, hypertension and other traits.
High-quality genomes of two cultivated tetraploid cottons Gossypium hirsutum cv. NDM8 and Gossypium barbadense acc. Pima90 and resequencing of 1,081 G. hirsutum accessions provide insights into the role of structural variations.
Introduction of hereditary persistence of fetal hemoglobin variants into the γ-globin promoter by using CRISPR mutagenesis and editing provides insights into transcription factor interplay, with implications for gene therapies targeting this element.
Fourier Mixture Regression (FMR) is a method for estimating common-variant effect-size distributions. Applying FMR to summary statistics for complex traits from the UK Biobank shows that heritability is spread across a wide range of effect sizes.
HCR–FlowFISH is a new approach to characterize CRISPR-perturbed cis-regulatory elements (CREs) via accurate quantification of native transcripts, alongside CRISPR activity screen analysis (CASA), a hierarchical Bayesian model to quantify CRE activity.
Variably methylated intracisternal A particle (VM-IAP) retrotransposons are stable across the murine lifespan. VM-IAP retrotransposons are unaffected by maternal exposure to the endocrine disruptor bisphenol A, an obesogenic diet or methyl donor supplementation.
Analysis of whole-genome sequence data from 3,474 families finds an excess of private, likely gene-disrupting variants in individuals with autism. These variants are under purifying selection and suggest candidate genes not previously associated with autism.
The oncohistone H3.3-K27M decreases chromatin accessibility and H3K27ac at some active enhancers and downregulates nearby neurodevelopmental genes, while increasing transcriptional repression of a subset of PRC2-bound neurodevelopment genes.
Genome-wide association analyses using parental and offspring genotypes provide insights into fetal and maternal genetic effects on fetal growth. The results show that maternal and fetal genomes influence birth weight through distinct mechanisms.
Haplotype-resolved genome assembly of an Oolong tea cultivar Tieguanyin and population genomic analyses of 190 Camellia accessions provide insights into the evolutionary history of the tea plant Camellia sinensis.
The use of natural killer (NK) cells in immunotherapy as an alternative to allogeneic T cells is gaining ground. Here, two genome-scale high-throughput platforms are used to identify genes that modulate the sensitivity of multiple solid tumor cell lines to NK-mediated killing.
An integrative analysis of single-nucleus assay for transposase-accessible chromatin with sequencing and RNA sequencing in normal and Alzheimer’s disease brain tissue identifies cell-type-specific cis-regulatory elements and candidate target genes at disease-associated loci.
Imputation of rare coding variants in the UK Biobank enables association and fine-mapping analyses of rare (minor allele frequency (MAF) = 0.00005) genotypes, identifying 600 new variant–trait associations, including long allelic series in individual genes.
Analysis of 129 N6-methyladenosine (m6A) profiles across 4 tissues (brain, lung, muscle and heart) identifies 8,843 tissue-specific and 469 tissue-shared m6A quantitative trait loci (QTLs). Of these, 184 m6A QTLs colocalize with GWAS signals.
SPTBN1 mutations cause a neurodevelopmental syndrome characterized by intellectual disability, language and motor delays, autism, seizures and other features. The variants disrupt βII-spectrin function and disturb cytoskeletal organization and dynamics.
Analysis of live-cell imaging and single-cell genome sequencing data of colorectal cancer organoids identifies temporal dynamics of sub-chromosomal copy-number amplifications.
Genetic manipulation of poised enhancers (PEs) shows that orphan CpG islands promote physical and functional communication between PEs and distally located developmental genes.