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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.
Single-cell transcriptome profiling of human aneuploid blastocysts highlights global transcriptomic alteration and identifies novel dosage-sensitive genes in aneuploidy. Aneuploid embryos undergo unstable epiblast maturation caused by defects in the TGF-β and FGF pathways that impact trophectoderm progression.
Pooled and sex-specific genome-wide association analyses identify new risk loci for restless legs syndrome and candidates for drug repurposing. Machine learning models combining genetic and other information show improved risk prediction performance.
High-quality genomes and single-cell atlases of auditory cortices from microbat and megabat species identify neuronal populations related to ultrasound perception and implicate complexin-1 as a key component of ultrasound transmission in mammals.
GSA-MiXeR models gene heritability and variant linkage disequilibrium for improved gene set enrichment testing. GSA-MiXeR implicates relevant sets of fewer than ten genes in schizophrenia, providing more nuanced insights into trait biology.
Random barcoded transposon sequencing screens of generalist and typhoidal Salmonella determine the fitness effects of genes in a range of stress conditions and during macrophage infection, characterizing unknown genes and identifying typhoidal-specific vulnerabilities.
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.