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GAGE-seq is a joint assay for 3D genome and transcriptome in single cells using combinatorial indexing to increase throughput. Applied to complex tissues, GAGE-seq enables the analysis of links between 3D organization and gene expression in rare cell types.
Analysis of EZH2 separation-of-function mutants indicates that part of the RNA-binding surface of EZH2 is necessary for histone modification independently of RNA. A specific RNA-binding-defective mutant shows normal enzymatic activity in vitro and in lineage-committed cells.
Fitness-based analysis of 200,618 UK Biobank exomes and single-cell-derived hematopoietic clones identifies 17 genes under positive selection, including novel drivers of clonal hematopoiesis.
Genome-wide association analyses identify risk loci for breast cancer in women of African ancestry. Polygenic risk scores derived from these data improve ancestry-specific risk prediction.
Amplification-free single-cell whole-genome sequencing shows that genomic, evolutionary and biophysical factors collectively drive cell-to-cell variation in mitochondrial DNA copy number.
Joint likelihood mapping across six autoimmune diseases identifies shared and distinct association signals and improves fine-mapping resolution at loci with shared effects, yielding insights into the underlying biological mechanisms.
The authors develop and harness a suite of epigenome editing tools to explore the role of different epigenetic marks in modulating transcription. In particular, H3K4me3 deposition on promoter sequences is shown to directly promote transcription activation in mouse embryonic stem cells.
Short tandem repeat mutations in a primate Alu element on chromosome 15q cause activation of a thyroid-specific enhancer, upregulating MIR7-2/MIR1179. This results in defective thyroid proliferation and thyrotropin resistance.
A high-quality reference genome assembly of cauliflower C-8 (V2) and genomic analyses of 971 diverse accessions and their relatives reveal the stepwise domestication and the genetic mechanism of curd biogenesis.
Noncoding variants in a TTTG microsatellite on 15q26.1 are identified in Japanese patients with childhood and adult-onset thyroid abnormalities. Functional analyses suggest that these variants affect the role of the microsatellite as a potential regulator of thyroid cell growth.
Genome assemblies of four filamentous Zygnematophyceae and co-expression network analyses shed light on the evolutionary roots of the mechanism for balancing environmental responses and multicellular growth.
Genome-wide association analysis in over one million individuals of European ancestry identifies 2,103 independent genetic signals (including 113 new loci) associated with blood pressure traits.
SBayesRC integrates genome-wide association summary statistics with functional annotations to improve polygenic prediction of complex traits. Functional partitioning highlights a major contribution of evolutionarily constrained regions to prediction accuracy.
Multiple domestication-related traits in cultivated soybeans are pleiotropic effects of a locus composed of two tandemly duplicated long noncoding RNAs that act via sRNA repression of MYB transcription factors.
A multi-ancestry genome-wide association meta-analysis of kidney cancer identifies 63 regions associated with disease susceptibility including one locus that was associated with increased risk in individuals with African ancestry.
BEAN is a Bayesian approach for analyzing base editing screens with improved effect size quantification and variant classification. Applied to low-density lipoprotein (LDL)-associated common variants and saturation base editing of LDLR, BEAN identifies new LDL uptake genes and offers insights into variant structure–pathogenicity mechanisms.
A comprehensive variation map constructed by deep sequencing 1,904 accessions of weedy and cultivated broomcorn millet sheds light on the genetic architecture of agronomic traits during domestication.
A new acorn barnacles genome assembly, together with transcriptomic and proteomic datasets and functional experiments, identify bcs-6 and bsf, as new genes involved in the settlement process by facilitating energy metabolism and stabilizing the alternating layers of chitin and calcites, respectively.
High-quality genome assemblies of grain and vegetable cowpeas and re-sequencing of 344 accessions characterize genomic variations between cowpea subspecies and their domestication and improvement under selection.
DNA methylation data of whole blood from Han Chinese individuals are used to map mQTLs, finding that cis- and trans-mQTLs show distinct patterns of East Asians (EA) ancestry-specific colocalization with complex trait variation.