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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.
Migration can increase regional differences in both DNA variants and environmental factors that are associated with socio-economic status. Without controlling for geography, associations between genes and complex traits will therefore include effects of environmental differences between high-income and low-income regions.
The genetic landscape of human induced pluripotent stem cells (iPSCs) is strongly influenced by the somatic cells of origin, and mutational signatures directly reflect pre-reprogramming and post-reprogramming mutagenic processes. BCOR mutations are recurrent and have functional consequences for the differentiation capacity of iPSCs.
In our study of 83 tissue samples from 31 patients with pancreatic cancer receiving different treatment regimens, we directly identified normal cells transitioning to a tumor state. Single-cell technologies enabled us to observe how the tumor and the surrounding environment work together to create a treatment-resistant niche.
We comprehensively define the genomic landscape of pediatric acute lymphoblastic leukemia (ALL) in the largest cohort assembled to date, and identify new driver genes and biological pathways that are targeted by genetic alteration. These findings serve as a road map to improve our understanding of disease development and identify therapeutic targets in pediatric ALL.
We generated a cattle genotype–tissue expression atlas (CattleGTEx) as part of the farm animal GTEx project. Analysis of 7,180 public RNA-sequencing samples revealed genetic variants that regulate the transcriptome across 23 distinct bovine tissues. Integrating these data with GWAS advances our understanding of the fundamental molecular mechanisms that underpin complex traits in cattle.
Across >150,000 individuals, we identified hundreds of genes associated with autism spectrum disorder (ASD) and atypical neurodevelopment. Most ASD-related genes were also associated with developmental delay. However, increased mutation rates in ASD and shared genetic risk with schizophrenia was observed for some genes, many of which are enriched in developing neurons.
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.
In the zebrafish heart, several transient fibroblast types appear after injury. High-throughput lineage tracing revealed that injury-responsive fibroblasts are derived from two distinct lineage origins: the epicardium and the endocardium. Targeted cell-type-specific depletion showed that at least one fibroblast type has a critical role in heart regeneration.
Assemblies of hexaploid cultivated oat, and of close relatives of its diploid and tetraploid progenitors, have revealed its polyploid formation and subgenome evolution. These high-quality oat reference genomes will facilitate the discovery of candidate genes that underlie beneficial traits such as hulless grain and disease resistance.
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.
Genetic and phenotypic analyses of data from over 400,000 participants in the UK Biobank identified 10 new loci associated with the development of clonal hematopoiesis and implicated DNA damage, oncogene signaling, telomere maintenance and blood cell homing in its pathogenesis. These findings can help to decipher the pathogenesis of clonal hematopoiesis and develop therapeutic approaches.
Systematic CRISPR screens in primary human T cells uncovered the upstream regulators of crucial immune genes — IL2RA, IL2 and CTLA4. Then, using RNA-seq and ATAC-seq in knockout T cells, we mapped the downstream target genes and non-coding cis-regulatory elements of key regulators, thereby revealing a regulatory network enriched for immune disease-associated genes.
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.
In celebration of the 200th anniversary of Gregor Mendel’s birth, this Perspective discusses the historical context of Mendel’s discoveries and the importance of these insights in shaping the field of genetics.
By integrating single-cell and bulk transcriptomic analyses, we found that malignant cells belong to two major intrinsic epithelial subtypes. We propose a refined, three-tiered classification of colorectal cancer subtypes based on intrinsic epithelial subtypes, microsatellite instability status and the presence of fibrosis.
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.
