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Analyses of 2,083 globally distributed group A Streptococcus (GAS) genomes enable the development of a compendium of all GAS vaccine antigen sequences, providing a platform for population-genomics-informed vaccine design.
Swapping the Xist/Tsix transcriptional units and placing their promoters in each other’s topologically associating domain shows that the topological partitioning of the X-inactivation center is critical to ensure proper X inactivation during development.
Application of a deep-learning-based framework shows that individuals with autism spectrum disorder (ASD) harbor regulation-disrupting mutations of higher functional impact than those in unaffected siblings and identifies a convergent genetic landscape of coding and noncoding de novo mutations in ASD.
The folate pathway enzyme MTHFD1 is recruited to chromatin by BRD4. Inhibition of BRD4 or MTHFD1 similarly changes nuclear metabolite composition and gene expression, and dual inhibition synergistically impairs cancer cell viability.
CRISPR screens identify JNK–JUN family genes as repressors of definitive endoderm differentiation in human pluripotent stem cells. JUN co-occupies stem cell enhancers with OCT4, NANOG, SMAD2 and SMAD3 and inhibits the exit from pluripotency.
The authors present a new genomic prediction method for maize germplasm evaluation under genotype × environment interaction, in which genotype × environment interaction of grain yield components is modeled as genotypic sensitivity to environmental drivers.
Release of paused Pol II at specific intronic loci or chromatin domains favors the formation of abnormal DNA recombination, leading to cancer-associated chromosomal translocations.
A tomato pan-genome constructed from genome sequences of 725 tomato accessions captures 4,873 genes absent from the reference genome and identifies a rare allele of TomLoxC regulating fruit flavor.
Genome-wide analysis identifies 30 loci associated with bipolar disorder, allowing for comparisons of shared genes and pathways with other psychiatric disorders, including schizophrenia and depression.
Targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat identifies regions showing the signals of wild emmer introgression, thus suggesting that historic wild-relative gene flow shaped modern bread wheat's adaptive diversity.
High-quality genome sequence of cultivated peanut comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut.
The genome sequence of segmental allotetraploid peanut suggests that diversity generated by genetic deletions and homeologous recombination helped to favor the domestication of Arachis hypogaea over its diploid relatives.
An expanded GWAS of birth weight and subsequent analysis using structural equation modeling and Mendelian randomization decomposes maternal and fetal genetic contributions and causal links between birth weight, blood pressure and glycemic traits.
A multi-tissue transcriptome-wide association study based on genetic predictors of expression level and alternative splicing in relevant tissues identifies 25 candidate genes associated with high-grade serous ovarian cancer.
Exome sequencing of a worldwide panel of 487 wheat genotypes, including landraces, cultivars and modern varieties, sheds light on wheat genomic diversity and the evolution of modern bread wheat.
Maternal SETD2 deficiency leads to loss of H3K36me3, aberrant DNA methylation and ectopic H3K4me3 and H3K27me3 in mouse oocytes. Maternal depletion of SETD2 causes oocyte defects and subsequent zygotic arrest.
The authors use three-dimensional live-cell imaging of colorectal carcinoma organoids to show that chromosomal instability is widespread. Single-cell sequencing identifies heterogeneity of copy number alterations and shows clonal evolution.
The authors performed whole-genome resequencing of 429 chickpea lines sampled from 45 countries. They identified 122 candidate regions (204 genes) under selection during chickpea breeding.
The authors identify the formation of dynamic topologically associating domain (TAD) cliques during differentiation and reprogramming. Their analysis indicates that TAD cliques stabilize heterochromatin at the nuclear periphery.