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This study examines karyotypic selection and evolution in vitro using immortalized mammary and kidney epithelial cell lines, observing aneuploidy patterns specific to each origin tissue that are correlated with frequencies in patient tumors and independent of drivers such as TP53 mutation.
Resequencing of 390 peanut accessions provides insights into peanut migration and diversity in China. Genome-wide association analysis identifies loci associated with 28 agronomic traits.
Lentiviral massively parallel reporter assay (lentiMPRA) analysis of cardiac cis-regulatory elements characterizes the effects of noncoding de novo variants identified in congenital heart disease. EpiCard is a model for variant prioritization.
Multi-omic analysis of 100 clear cell renal cell carcinomas identifies four transcriptomic subgroups (IM1–IM4). IM4 is a high-risk subtype characterized by specific metabolic changes and a loss of lipid droplets.
A genome-wide CRISPR knockout screen in eHAP cells using ATAC-see to fluorescently label chromatin identifies novel regulators of accessibility, such as the transcription factor TFDP1 via regulation of canonical histone expression.
MuSiCal is a mutational signature analysis tool combining minimum-volume nonnegative matrix factorization with other algorithmic innovations. Applied to PCAWG data, MuSiCal gives more accurate results, including resolving ambiguous flat signatures.
In vivo tracing of the single-cell 3D structure at the Hoxa cluster shows that Polycomb-associated domains in individual cells are flexible and often decompact while maintaining a repressive transcriptional state.
Analysis of colorectal cancer bulk gene expression data at the pathway level identifies a poor-prognosis subtype associated with cell differentiation. The subtypes are reproducible in single-cell data and offer biological insights beyond existing stratification strategies.
De novo genome assemblies of 22 Brassica oleracea accessions and pan-genome analyses highlight the effects of structural variations on gene expression and their contributions to morphotype diversification.
Near-gapless and haplotype-resolved genome assemblies of the dwarfing ‘M9’ and semi-vigorous ‘MM106’ rootstocks and a major apple cultivar ‘Fuji’ provide insights into the genetic basis of rootstock-induced dwarfing traits.
Fluorescence-activated nuclear sorting combined with deep profiling shows that Huntington’s disease repeat expansions arise in specific cell types and are associated with elevated MSH2 and MSH3, which promote expansions in vitro by inhibiting excision of CAG slip-outs by FAN1.
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.
Causal-TWAS (cTWAS) is a statistical framework that adjusts for genetic confounders in transcriptome-wide association studies. Application of cTWAS on common traits leads to reliable detection of candidate causal genes.
GIFT fine-maps candidate causal genes in a transcription-wide association study by conditioning on predicted expression of nearby genes, leading to improved statistical power and enhanced mapping resolution when applied to complex traits.
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.