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The histone H3K4 methyltransferase SET1B is recruited to a subset of hypoxia-inducible genes by the HIF complex. Loss of SET1B reduces HIF transcriptional activity in hypoxia and impairs tumor formation in xenograft models.
An analytical framework based on transcriptome-wide association and electronic medical records provides insights into the relationship between plasma lipids and complex diseases on a phenome-wide scale.
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.
A large-scale genetic analysis of type 1 diabetes identifies new susceptibility variants, highlights potential regulatory mechanisms and provides genetic support for therapeutic targets for immune intervention.
Hi-C and single-molecule sequencing analysis provide an improved assembly of the Xenopus tropicalis genome and insights into three-dimensional genome dynamics throughout embryogenesis.
QUILT is a method for rapid genotype imputation and phasing from low-coverage whole-genome sequence data using a large haplotype reference panel. QUILT enables highly accurate imputation across a range of coverages and data types.
A population-scale map of gene expression in primary human microglia provides a systematic exploration of microglia diversity and how age, sex, pathology, cortical anatomy and common germline genetic variation influence the microglia transcriptome.
A trans-ancestry meta-analysis of GWAS of glycemic traits in up to 281,416 individuals identifies 99 novel loci, of which one quarter was found due to the multi-ancestry approach, which also improves fine-mapping of credible variant sets.
Radiotherapy induces small and large deletions as well as inversions across the genome in multiple cancer types. The genomic changes associated with radiotherapy correlate with poorer clinical outcomes.
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.
REGENIE is a whole-genome regression method based on ridge regression that enables highly parallelized analysis of quantitative and binary traits in biobank-scale data with reduced computational requirements.
Genome-wide association analyses of 41,917 bipolar disorder cases and 371,549 controls of European ancestry provide new insights into the etiology of this disorder and identify novel therapeutic leads and potential opportunities for drug repurposing.
An analysis of the UK Biobank identifies 227 new associations between mitochondrial DNA (mtDNA) variants and phenotypes. mtDNA genetic architecture reflects regional UK nuclear genome ancestry.
The insulation potency of CTCF depends on the number of binding sites in tandem and on upstream flanking sequences. Insulators form local chromatin domain boundaries and weaken enhancer–promoter contacts.
A multi-tissue atlas of alternative polyadenylation (APA) quantitative trait loci (3′aQTLs) identifies approximately 0.4 million common genetic variants associated with the APA of target genes. Approximately 16% of trait-associated variants colocalize with 3′aQTLs.
The SWI/SNF complex helps resolve R-loop-mediated transcription–replication conflicts, as depletion of SWI/SNF complex member BRG1 increases R-loops, R-loop-dependent DNA breaks and transcription–replication conflicts.
DNMT3A PWWP domain mutations promote localization of DNMT3A to CpG islands in a PRC1-dependent manner. DNMT3A interacts with H2AK119ub-modified nucleosomes.
Enhancer–promoter three-dimensional interactions at oncogenic loci are modulated by H3K27ac dynamics. Enhancer hijacking mediated by chromosomal translocations leads to distinct chromatin states, intrachromosomal interactions and allele-specific gene expression.
Ultrafast Sample placement on Existing tRees (UShER) is an efficient method that facilitates the addition of new SARS-CoV-2 genome sequences onto the existing phylogeny, aiding in real-time analysis of viral evolution during the COVID-19 pandemic.
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.