N Nature Genetics · Dec 03, 2025 ADAR1 editing is necessary for only a small subset of cytosolic dsRNAs to evade MDA5-mediated autoimmunity Endogenous long double-stranded RNAs (dsRNAs), which are not edited by the RNA editing enzyme ADAR1, may activate the antiviral dsRNA receptor MDA5 to trigger interferon-mediated immune responses. Among the large number of endogenous long dsRNAs, the key substrates that activate MDA5—termed as immunogenic dsRNAs—remain largely unidentified. Here we reveal that human immunogenic dsRNAs constitute a surprisingly small fraction of all cellular dsRNAs. We found that these immunogenic dsRNAs were highly enriched in mRNAs and depleted of introns, consistent with their role as cytosolic MDA5 substrates. We validated the MDA5-dependent immunogenicity of these dsRNAs, which was dampened following ADAR1-mediated RNA editing. Notably, immunogenic dsRNAs were enriched at genetic susceptibility loci associated with common inflammatory diseases, implying their functional importance. We anticipate that a focused analysis of immunogenic dsRNAs will enhance our understanding and treatment of cancer and inflammatory diseases, where the roles of dsRNA editing and sensing are increasingly recognized. Immunogenetics Transcriptomics biology
N Nature Genetics · Nov 27, 2025 Passenger mutations link cellular origin and transcriptional identity in human lung adenocarcinomas DNA damage is preferentially repaired in expressed genes; thus, genome-wide correlations between somatic mutation patterns and normal cell transcription may reflect tumor cell origins. Accordingly, we found that aggregate lung adenocarcinoma (LUAD) and squamous cancer (LUSC) somatic mutation density associated most strongly with distal (alveolar) and proximal (basal) lung cell-type-specific gene expression, respectively, consistent with presumed LUAD and LUSC cell origins. Analyzing individual genomes, 21% of LUADs bore mutational footprints of proximal airway origins, with 38% classified as ambiguous. Distal origin LUADs, enriched forKRASandSTK11drivers, occurred mainly in smokers; proximal origin LUADs, enriched forEGFRdrivers, were more common in never-smokers. Ambiguous origin LUADs showed APOBEC signatures andSMARCA4alterations.TP53mutant LUADs with non-distal cell origins preferentially exhibited non-distal transcriptional identity. Our study reveals a complex interplay between lineage and identity in LUAD evolution and offers a scalable strategy to infer tumor origins in human cancers. Genomics Non-small-cell lung cancer Transcriptomics biology
N Nature Genetics · Oct 27, 2025 Maternal factor OTX2 regulates human embryonic genome activation and early development Transcription factors (TFs) are instrumental in kickstarting embryonic genome activation (EGA) in many species, yet their regulatory roles in human embryos remain poorly understood. Here, we show that OTX2, a maternally provided PRD-like homeobox TF, is required for proper human EGA and early development. At the four-cell stage, OTX2 promotes activation of key EGA genes, includingTPRX1andTPRX2, and the EGA-associated repeat HERVL-int and MLT2A1. At EGA targets, OTX2 directly binds promoters and putative enhancers, many of which overlap with Alu and MaLR repetitive elements containing the OTX2 motif, and promotes chromatin accessibility. The transcriptome and developmental defects uponOTX2knockdown are partially rescued by overexpression ofTPRX1andTPRX2. Finally, joint knockdown ofOTX2andTPRXL, encoding another maternal PRD-like homeobox TF, exacerbates chromatin opening and EGA defects at the 8C stage. These findings establish OTX2 as a crucial maternal TF that awakes the genome at the beginning of human life. DNA sequencing Embryogenesis Gene regulation Transcriptomics biology
N Nature Genetics · Oct 03, 2025 Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq Reprogramming often yields heterogeneous cell fates, yet the underlying mechanisms remain poorly understood. To address this, we developed single-cell transcription factor sequencing (scTF-seq), a single-cell technique that induces barcoded, doxycycline-inducible TF overexpression and quantifies TF dose-dependent transcriptomic changes. Applied to mouse embryonic multipotent stromal cells, scTF-seq generated a gain-of-function atlas for 384 mouse TFs, identifying key regulators of lineage specification, cell cycle control and their interplay. Leveraging single-cell resolution, we uncovered how TF dose shapes reprogramming heterogeneity, revealing both dose-dependent and stochastic cell state transitions. We classified TFs into low-capacity and high-capacity groups, with the latter further subdivided by dose sensitivity. Combinatorial scTF-seq demonstrated that TF interactions can shift from synergistic to antagonistic depending on the relative dose. Altogether, scTF-seq enables the dissection of TF function, dose and cell fate control, providing a high-resolution framework to understand and predict reprogramming outcomes, advancing gene regulation research and the design of cell engineering strategies. This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells. Bioinformatics High-throughput screening RNA sequencing Stem cells Transcriptomics Single-cell Mouse Cell Biology Genomics Developmental Biology
N Nature Genetics · Sep 05, 2025 A multi-tissue single-cell expression atlas in cattle Systematic characterization of the molecular states of cells in livestock tissues is essential for understanding the cellular and genetic mechanisms underlying economically and ecologically important physiological traits. Here, as part of the Farm Animal Genotype-Tissue Expression (FarmGTEx) project, we describe a comprehensive reference map including 1,793,854 cells from 59 bovine tissues in calves and adult cattle, spanning both sexes, which reveals intra-tissue and inter-tissue cellular heterogeneity in gene expression, transcription factor regulation and intercellular communication. Integrative analysis with genetic variants that underpin bovine monogenic and complex traits uncovers cell types of relevance, such as spermatocytes, responsible for sperm motility and excitatory neurons for milk fat yield. Comparative analysis reveals similarities in gene expression between cattle and humans, allowing for the detection of relevant cell types to study human complex phenotypes. This Cattle Cell Atlas will serve as a key resource for cattle genetics and genomics, selective breeding and comparative biology. Data processing Transcriptomics Genomics Single-cell Human Genetics
N Nature Genetics · Sep 05, 2025 Genetic variants affecting RNA stability influence complex traits and disease risk Gene expression is modulated jointly by transcriptional regulation and messenger RNA stability, yet the latter is often overlooked in studies on genetic variants. Here, leveraging metabolic labeling data (Bru/BruChase-seq) and a new computational pipeline, RNAtracker, we categorize genes as allele-specific RNA stability (asRS) or allele-specific RNA transcription events. We identify more than 5,000 asRS variants among 665 genes across a panel of 11 human cell lines. These variants directly overlap conserved microRNA target regions and allele-specific RNA-binding protein sites, illuminating mechanisms through which stability is mediated. Furthermore, we identified causal asRS variants using a massively parallel screen (MapUTR) for variants that affect post-transcriptional mRNA abundance, as well as through CRISPR prime editing approaches. Notably, asRS genes were enriched significantly among a multitude of immune-related pathways and contribute to the risk of several immune system diseases. This work highlights RNA stability as a critical, yet understudied mechanism linking genetic variation and disease. Gene expression Transcriptomics Genetics Human CRISPR Immunology Genomics
N Nature Genetics · Aug 20, 2025 Super-pangenome analyses across 35 accessions of 23Avenaspecies highlight their complex evolutionary history and extensive genomic diversity Common oat, belonging to the genusAvenawith 30 recognized species, is a nutritionally important cereal crop and high-quality forage worldwide. Here, we construct a genus-level super-pangenome ofAvenacomprising 35 high-quality genomes from 14 cultivated oat accessions and 21 wild species. The fully resolved phylogenomic analysis unveils the origin and evolutionary scenario ofAvenaspecies, and the super-pangenome analysis identifies 26.62% and 59.93% specific genes and haplotypes in wild species. We delineate the landscape of structural variations (SVs) and the transcriptome profile based 1,401 RNA-sequencing (RNA-seq) samples from diverse abiotic stress treatments in oat. We highlight the crucial role of SVs in modulating gene expression and shaping adaptation to diverse stresses. Further combining SV-based genome-wide association studies (GWASs), we characterize 13 candidate genes associated with drought resistance such asAsARF7, validated by transgenic oat lines. Our study provides unprecedented genomic resources to facilitate genomic, evolution and molecular breeding research in oat. Gene expression Genomics Plant breeding Transcriptomics Genomics Genetics Machine Learning
