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Systematic deletions of individual imitation switch (ISWI) subunits in mouse embryonic stem cell lines highlight the role of BPTF in regulating chromatin accessibility at most CTCF sites and binding at a subset, with a modest effect on its insulating function.
Cross-ancestry genome-wide association studies of 3,414 brain imaging phenotypes in Chinese Han and white British participants identify autosomal and X-chromosomal associations in more diverse populations.
Functional characterization of the regulatory landscape of the adjacent costimulatory genes CD28, CTLA4 and ICOS in primary human T cell subsets identifies context-dependent programs controlling this locus critical for immune homeostasis.
This study finds that CRISPR-knockout phenotypes from genome-wide screens systematically show increased similarity to knockouts of unrelated genomically proximal genes located on the same chromosome arm. Multiple lines of evidence suggest that this proximity bias is caused by telomeric truncations of chromosome arms and is consistent across cell types, labs and Cas9 delivery methods.
This study uses Strand-seq to explore the landscape of mosaic structural variants (mSVs) in human hematopoietic stem and progenitor cells from people of different ages. The analysis highlights patterns of enrichment for mSVs in specific cell types, with associated phenotypes, and suggests that clonal expansions due to mSVs are generally restricted to older individuals.
The study identifies TaSPL6-D as a negative regulator of TaHKT1;5-D and salinity tolerance in bread wheat. An insertion variation of TaSPL6-D, mainly hidden in landraces, shows the potential for breeding salt-tolerant crops.
Condensin-depleted mitotic chromosomes compartmentalize and form contacts among regulatory elements despite lacking transcription and most chromatin-associated factors. Heterochromatin protein 1 (HP1) proteins are surprisingly dispensable for compartmentalizing constitutive heterochromatin.
Cicer super-pangenome constructed using genome assemblies of eight Cicer annual wild species and two cultivated chickpea species provides insights into the genetic diversity and agronomic trait loci for chickpea improvement.
Characterization of seminal root number variation in the root systems of >9,000 global maize accessions and its wild relatives provides insights into root trait adaptation to environments during domestication and global expansion.
Insight from the transcriptomes of 1,032 Saccharomyces cerevisiae natural isolates emphasizes the essential contribution of accessory genes to the species-level transcriptional landscape.
Systematic assessment of cofactor dependencies of nine transcription factors (TFs) and promoters finds that TFs use unique cofactor combinations to modulate distinct steps in transcription, whereas promoter elements fit into discrete groups where their rate-limiting step for activation influences cofactor compatibility.
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.
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.