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We identify an elite haplotype of the transcription factor gene OsGATA8 in rice that is associated with enhanced nitrogen uptake and a higher proportion of productive tillers. Revealing how OsGATA8 regulates nitrogen use efficiency (NUE) enables insights into coordination of nitrogen uptake and productive tiller formation to achieve high NUE in rice.
Kaiser et al. propose a nuanced and inclusive definition of genetic discrimination that reflects its multifaceted impact. This adaptive definition is intended to remain relevant in the face of an evolving social context and advancing genomic science.
Upon inflammation and targeted gene mutation, some fully differentiated secretory and postmitotic intestinal epithelial lineages dedifferentiate to acquire stem-like features and promote tumor formation.
Analysis of whole-genome sequencing data from over 10,000 tumor samples spanning 35 cancer types identifies putative driver genes and highlights new therapeutic opportunities.
CalPred is a framework that adjusts polygenic score (PGS) prediction intervals based on joint modeling of multiple contexts, such as age, sex and genetic ancestry. PGS show pervasive context-specific accuracy, suggesting that accounting for this will improve portability across contexts.
Marker-based CRISPR screens in pancreatic cancer cells followed by functional validation highlight a role for MED12 in bridging ΔNp63 and components of the Mediator family. This interaction helps drive basal cell identity in pancreatic ductal adenocarcinoma.
The study identifies transcription factor OsGATA8 as a negative regulator of nitrogen uptake and tiller formation in rice and OsGATA8-H as an elite haplotype with reduced expression and enhanced nitrogen use efficiency.
This study presents a synthetic surrogate (SynSurr) method for imputing missing phenotypes in biobank datasets. Joint analysis of the partially observed and imputed surrogate phenotype improves power in genome-wide association studies while being robust to imputation errors.
Microbats utilize ultrasonic echolocation to navigate and locate prey, whereas megabats primarily perceive human-audible sound in daily life. High-quality genomes and single-cell atlases of auditory cortices from microbat and megabat species identify parvalbumin-positive inhibitory neurons and the complexin-1 gene to be crucial in mammalian ultrasound perception.
A machine learning-based, continuous in silico coronary artery disease (CAD) score built using electronic health record data is applied to rare variant association analysis of CAD, implicating novel candidate genes and biological mechanisms.
Analyses in BioBank Japan, UK Biobank and Tohoku Medical Megabank show that polygenic scores constructed from subgroups stratified by body mass index (BMI) can optimize type 2 diabetes risk prediction, particularly among individuals with low BMI.
Genotype × environment interactions are a key mechanism underlying human phenotypic variation and contribute to our understanding of the genetic architecture of human traits, with possible applications in personalized medicine.
Analysis of exome sequencing data identifies a missense variant in RAB32 associated with high risk of familial Parkinson’s disease. Functional studies show that this risk variant increases LRRK2 kinase activity.
We used high-throughput transposon screens to examine the responses of generalist and host-adapted Salmonella enterica serovars to 25 stress conditions that recapitulate key stages of human infection. We identified and characterized numerous typhoid-specific gene networks, revealing a role for specific pseudogenes in shaping bacterial fitness outcomes.
A CRISPR–Cas9 screen identifies genes that modulate long interspersed nuclear element-1 (LINE-1) expression in human cells. LINE-1 5′ UTRs have enhancer features and can activate long-range gene expression, including during zygotic genome activation.
Our study explored cell-specific functional consequences and clonal expansions of mosaic structural variants in distinct hematopoietic stem and progenitor cells by utilizing advanced single-cell sequencing techniques. Our single-cell multi-omics approach paves the way for future studies to focus on the roles of somatic structural variants in aging and disease.
