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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.
Single-cell and bulk transcriptomics of adult human microglia from a population of individuals reveals activated states across several brain disorders and maps Alzheimer’s disease variants to microglia-enriched genes.
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.
Numerous statistical models have been used to analyze single-cell RNA sequencing data. This Perspective proposes that a Poisson measurement model is sufficient and suitably flexible for this task, and its use would resolve current controversies.
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.
The transition from normal esophageal tissue to squamous carcinoma is characterized by an altered SOX2 cistrome. This transcriptional reprogramming activates endogenous retroviruses and double-stranded RNA expression, creating a dependency on the RNA editing enzyme ADAR1.
