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Bottom-up in vitro reconstitution of ~10-kb chromatin domains shows that nucleosome positioning, rather than loop extrusion or transcription, determines domain formation in yeast.
Multi-omic analysis of single nuclei from 12 human placentas collected during early-stage and late-stage pregnancy characterizes syncytiotrophoblast diversity. Gene regulatory network analysis implicates candidate lineage regulators such as STAT5A and CEBPB.
A combination of single-cell imaging and dynamic polymer simulation shows that stacked boundary conformation facilitates cis-regulatory elements communication across topologically associating domain (TAD) borders at the Pitx1 locus in developing mouse limbs.
ZmWAKL, which encodes a cell-wall-associated receptor kinase-like protein, regulates quantitative disease resistance to gray leaf spot in maize through the ZmWAKL–ZmWIK–ZmBLK1–ZmRBOH4 module.
Inherited polygenic scores for blood cell traits are associated with an increased risk of JAK2V617F clonal expansion and influence clinical phenotypes in individuals with myeloproliferative neoplasms.
Genome-wide association analysis of triglycerides to high-density lipoprotein cholesterol (TG:HDL-C) ratio within the UK Biobank identifies candidate insulin resistance-associated loci linked to metabolic pathways and insulin biology. A polygenic risk score derived from these results shows an association with multiple cardiometabolic traits.
Massively parallel reporter assays identify 165 functional variants associated with skin pigmentation in ethnically diverse Africans. Functional characterization of eight variants demonstrates their impact in regulating melanin levels and validates CYB561A3 as a novel gene involved in melanogenesis and pigmentation.
A new computational method coupled with a CRISPR–Cas12a screen identifies human long noncoding RNAs (lncRNAs) that lead to cell proliferation defects, which can be rescued by zebrafish homologs. Knockdown of four zebrafish lncRNAs that perturb embryonic development can be rescued by human homologs.
Multi-ancestry genome-wide association meta-analysis of major depression identifies new risk loci, assesses the transferability of risk loci across ancestry groups, and improves fine-mapping resolution and prioritization of candidate effector genes.
The pilot phase of PigGTEx, re-analyzing 5,457 published RNA-seq samples, presents a pan-tissue catalog of molecular quantitative trait loci. Cross-species comparisons identify traits with shared genetic regulation in humans.
A human genetics-informed drug prioritization tool, genetic priority score (GPS), combines genetic features and drug datasets. GPS-supported indications are more likely to progress through clinical trials, suggesting the utility of this score for target prioritization.
Multi-ancestry genome-wide association analyses identify new risk loci for Parkinson’s disease, and fine-mapping and co-localization analyses implicate candidate genes whose expression is associated with disease susceptibility.
ancIBD identifies identity-by-descent regions in ancient DNA using a hidden Markov model optimized for these low-coverage data. Analysis of 4,248 individuals demonstrates that ancIBD can identify up to sixth-degree relatives and provides genealogical insights into ancient populations.
The long noncoding RNA AMANZI downregulates IL-1β expression and trained immunity by inducing IL-37 transcription via long-range chromatin contacts. The common variant rs16944 present in AMANZI modulates proinflammation or immunosuppression risk.
Chromosome-scale genome assemblies of triploid Cavendish and Gros Michel reveal the banana cultivars’ origins, disease resistance and fruit ripening mechanism.
DeepFlow uses deep learning to extract cardiac flow phenotypes from phase-contrast magnetic resonance images. Genome-wide analyses of cardiac flow traits in UK Biobank highlight the contribution of connective tissue genes to aortic valve function.
CellCharter is a flexible, platform-agnostic method for identifying cell niches in spatially resolved data. Analysis of lung cancers demonstrates the importance of considering spatial information, exemplified by a neutrophil-associated niche that correlates with an aggressive cancer cell state and patient prognosis.
A strategy for inferring phase for rare variant pairs is applied to exome sequencing data for 125,748 individuals from the Genome Aggregation Database (gnomAD). This resource will aid interpretation of rare co-occurring variants in the context of recessive disease.
Genome-wide analyses of blood cell phenotypes derived from perturbations coupled with flow cytometry-based functional readouts identify loci associated with latent cellular traits, yielding insights into biological mechanisms underlying common diseases.