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Previous genome-wide association studies of coronary artery disease (CAD) have discovered multiple susceptibility loci but have largely failed to uncover causal genes. A new study identifies hundreds of likely causal genes underlying the genetic risk for CAD.
For plants, the decision to germinate is a gamble on their subsequent survival. Xu et al. have now discovered a mechanism that determines the choice between germination and dormancy by regulating the level of ABA.
K27M mutation of histone H3 has been identified as a driver event in diffuse midline glioma. Two studies used comprehensive multi-model single-cell genomic, epigenomic and chromatin structure analysis to characterize the cell of origin and find a distinct etiology of H3K27M between pontine and thalamic tumors, and show that pontine gliomas harbor more immature oligodendrocyte-precursor-like cells.
Few genetic alterations have been linked to metastasis, during which cancer cells acquire abnormal migratory behavior. A new study sheds light on how loss of NECTIN1 leads to melanoma dissemination after local depletion of IGF1.
The evolutionary benefits of ongoing endogenous retrovirus (ERV) mobility in animals are largely unknown. A new paradigm suggests activation of the ERV family mdg4 at the fruitfly pupal stage may bolster adult antiviral defenses.
Mutations in the sodium channel NALCN promote epithelial cell shedding and dissemination independent of oncogenic transformation. This observation suggests that metastasis may not uniformly represent the end stage of carcinogenesis but can occur before oncogenic transformation.
A new study identifies prolyl hydroxylation of histone H3 as a signal for the recruitment of KDM5A, altering H3K4me3 and gene expression. H3P16oh is independent of the HIF hypoxia-sensing pathway and provides a further layer of complexity to oxygen-sensitive chromatin modifications.
Genetic risk factors for autism include both rare and common variants. A study shows that rare copy number variants and common variants across 16p that contribute to autism risk functionally converge to downregulate the expression of a large group of neuronally expressed genes in the 16p subtelomeric region.
KCNK3 mutations identified in sleep apnea probands affect TASK-1 X-gate function. These changes lead to an increase in potassium current and open probability, as well as impaired sensitivity to G-protein-coupled receptor inhibitors.
Clonal expansion of DNMT3A-mutant hematopoietic stem cells is a risk factor for myeloid malignancies and other morbidities. A new study uses multi-modal single-cell genomics to characterize the myeloid differentiation bias of DNMT3A-mutated clones, and finds preferential hypomethylation of binding motifs for key transcriptional regulators.
In this issue, Deng and colleagues show that the RNA m6A modification reader FXR1 recruits DNA 5-methylcytosine dioxygenase TET1 to genomic regions in order to demethylate DNA, which highlights a crosstalk between RNA methylation and DNA methylation in chromatin.
A new study uses single-cell and spatial transcriptomics to provide a systematic characterization of the recurrent gene-expression programs that control neoplastic cell states in diverse cancers.
The impact of endogenous retrovirus silencing during mammalian development is poorly understood. A new study shows that their abnormal reactivation in pluripotent cells dismantles key gene regulatory networks by perturbing transcriptional condensates linked to super-enhancer function.
A machine-learning model produces summarized sequence representations of genomic regulatory activity, and provides a functional view of regulatory DNA variation in the human genome, with the aim of better understanding the role of sequence variation in health and disease.
The boundaries of chromatin domains have an important role in genome organization and regulation. A comprehensive genetic dissection of a domain boundary in vivo provides insights into how boundary elements function and cooperate to mediate insulation between chromatin domains.
A large-scale collaborative effort now provides a comprehensive annotation of functional non-coding elements in the zebrafish genome. This work serves as an essential foundation for future studies to understand how gene regulatory circuits control embryonic development.
The use of association studies to identify candidate genes for complex biological traits in plants has been challenging due to a reliance on single reference genomes, leading to missing heritability. Graphical pangenomes and the identification of causal variants help overcome this and provide an important advance for crop breeding.
A new study employs CRISPR–Cas9-based base editing for simultaneous mutagenesis of all copies of histone H3 genes in mammals, highlighting the functional importance of H3K27me3 for Polycomb-mediated gene silencing and the dispensability of H3K27ac in transcriptional activation.
A new study highlights a strategy to link SNPs implicated in human complex traits and diseases with probable causal genes. This method prioritizes genes for functional characterization and helps address questions about the architecture of human phenotypes.
A new study demonstrates that the disordered N-terminal domain of DNMT3A1 binds PRC1-catalyzed H2AK119ub, targeting DNA methylation to bivalent promoters in mouse brain cortical cells. Methylation around bivalent genes is critical for mouse postnatal development, and could be equally important in other cell types and in disease.
