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Comprehensive spatial multiomic profiling of high-grade meningiomas identifies intratumor and primary–recurrence subclonal heterogeneity. Cell line models recapitulating intratumor heterogeneity show differential sensitivity in drug screens.
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.
Integrating human pluripotent stem cell models with population genetics and cellular genomics can help elucidate functional mechanisms underlying complex disease risk loci and uncover relationships between common genetic variation and pharmacotherapeutic phenotypes.
An approach to generate unreduced, clonal gametes in hybrid tomato genotypes enables polyploid genome design through controlled combination of four predefined genome haplotypes, thereby establishing a framework for exploiting progressive heterosis in crops.
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.
By integrating spatially resolved single-cell RNA sequencing (scRNA-seq) and Stereo-seq data, two studies in this issue characterize molecular signatures of liver cell types and their interactions in homeostasis, damage, repair and regeneration.
Two low-input tagmentation-based long-read sequencing methods, single-molecule real-time sequencing by tagmentation (SMRT-Tag), which identifies genetic variation and CpG methylation, and single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which detects chromatin accessibility, are presented. Application of SAMOSA-Tag to prostate cancer patient-derived xenograft samples identifies metastasis-associated epigenomic alterations.
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.
Genomic and epigenomic techniques identify a new variation type causing Mendelian disease by altering the non-coding regulatory network in thyroid cells — solving a hidden cause linked for 20 years.
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.