Transposable elements (TEs) comprise nearly half of mammalian genomes and have shaped genome architecture, chromatin organization, and transcriptional landscapes. Thanks to recent advances in long-read sequencing and functional (epi)genomics, the focus has shifted from TE families to individual TE loci, revealing widespread, locus-specific regulatory roles. While most TEs have lost the capacity to mobilize, they still retain a DNA form and, when transcribed, an RNA form, both of which can affect genome regulation. TEs can serve as alternative promoters, exons, splicing regulators, and 3' end modulators. They can also act as enhancers, drive three-dimensional (3D) genome organization, and give rise to long non-coding RNAs (lncRNAs) that serve as platforms for transcriptional and chromatin regulators. Mechanistically, TE repression involves DNA methylation, histone modification, phase-separated condensates, RNA modifications, RNA degradation, and nuclear compartmentalization, yet this repression can be selectively lifted during development or stress to expand regulatory potential. TEs therefore contribute to cell-type identity, developmental transitions, and responses to environmental stimuli, while their dysregulation is linked to human disorders including neurodegeneration, cancer, and autoimmune disease. TEs also hold translational promise as biomarkers and tools for gene and cell engineering. In summary, the pervasive integration of TEs as mini-genes, structural scaffolds, and regulatory elements redefines our view of the genome: rather than a gene-centric landscape dotted with repetitive "junk," mammalian DNA is a TE-rich ecosystem in which TEs drive gene regulatory networks and evolution.

RNA velocity can predict the direction of cell-state change, but the regulatory programs shaping these changes remain difficult to identify. In this issue of Cell, Wang et al. introduce RegVelo, a framework that integrates gene regulatory networks into RNA velocity analysis to nominate candidate regulators that may bias cell fate.

In this issue of Cell, Chen et al. analyze angiosperm genomes to map whole-genome duplication events, revealing non-random waves of polyploidy linked to climatic shifts and periods of low diversity. They suggest polyploids may have preferentially established during periods of environmental stress, shaping plant evolutionary history across multiple global events.

T cells live or die by their metabolism, yet one nutrient can serve very different ends. In this issue of Cell, Kelly et al. show that cysteine's sulfur is partitioned between glutathione and iron-sulfur cluster synthesis. This routing drives CD8+ T cell proliferation, effector function, and anti-tumor immunity.

Cellular senescence comprises diverse cell states emerging across human tissues during aging and disease. Integrating single-cell and spatial multi-omics with AI-driven analyses enables systematic mapping of senescent cell heterogeneity ("senotypes"), revealing tissue-specific programs and microenvironmental interactions. These advances provide frameworks for biomarker discovery and development of targeted senotherapeutic strategies.

Leveraging endogenous adenosine deaminase (ADAR) enzymes through engineered ADAR-recruiting RNAs (arRNAs) offers a safe, programmable strategy for RNA editing without exogenous enzyme delivery. Yet an incomplete understanding of ADAR's mechanistic basis has hindered the rational design of arRNAs with improved efficiency and precision. Here, we present LEAPER 3.0 (leveraging endogenous ADAR for programmable editing of RNA), a next-generation RNA-editing platform that integrates AlphaFold 3 structural predictions with systematic biochemical and cellular assays to define the molecular interface between ADAR1 or ADAR2 and double-stranded RNA. These insights enabled the rational optimization of arRNAs to expand the editable sequence range to previously refractory sites, suppress bystander editing within duplex regions, and achieve single-nucleotide discrimination among adjacent adenosines. This work elucidates the structural and mechanistic principles underlying arRNA-mediated editing and establishes a framework for the rational design of highly efficient and precise A-to-I RNA-editing tools.

Platinum agents are cornerstone therapies for many cancers but often cause neurotoxicity in post-mitotic tissues, for which effective interventions are lacking. This limitation reflects an incomplete understanding of neuronal responses to DNA damage. We show that nucleotide excision repair (NER) mediates cisplatin lesion removal in neurons; however, unlike its protective role in dividing cells, NER promotes neuronal death in response to cisplatin. This vulnerability arises because neurons possess low deoxynucleoside triphosphate (dNTP) pools. dNTPs are initially consumed during transcription-coupled NER to resolve transcription-blocking lesions. As dNTP levels become depleted, repair fails to complete, leading to accumulation of double-strand breaks, particularly during global-genome NER. Supplementation with deoxynucleosides or genetic upregulation of dNTP synthesis restores nucleotide pools, protects neurons from cell death, and reduces cisplatin-induced neuropathic pain. These findings identify limited dNTP availability as a key vulnerability in post-mitotic cells and suggest nucleoside supplementation as a potential strategy to mitigate chemotherapy-induced neurotoxicity.

Embryo-like structures, or embryoids, are powerful models to investigate early embryonic development. Yet, previous models cover only partial developmental stages, restricting their applications. Here, we successfully generate primate organogenetic embryoids from cynomolgus totipotent blastomere-like stem cells (cTBLCs). cTBLCs, reprogrammed from pluripotent stem cells and stably maintained, can display key totipotent-like molecular and functional features resembling zygotes/2-4-cell blastomeres. cTBLCs spontaneously generate well-organized blastoids that further progress through gastrulation to early organogenesis, thus exhibiting neural-tube-like structures and cardiac-like beating activity. Using single-cell RNA sequencing (scRNA-seq), we visualized stepwise cell-state transitions from cTBLCs to organogenetic lineages and identified an intermediate 8-cell/morula-like state. Interestingly, we uncovered a dynamic cascade of regulatory networks originating from cTBLCs, which represented an intrinsic developmental initiation program occurring independently of classical fertilization-associated events. Together, the cTBLC platform provides a unified in vitro framework to investigate developmental initiation, early lineage specification, and organogenesis.

Duchenne muscular dystrophy (DMD) is a fatal neuromuscular disorder caused by mutations in the DMD gene, leading to progressive muscle degeneration, loss of mobility, and premature death. Here, we applied leverage endogenous adenosine deaminase acting on RNA (ADAR) for programmable editing of RNA (LEAPER) 2.0, an RNA editing platform, to achieve exon skipping by harnessing endogenous ADAR through circular ADAR-recruiting RNAs (circ-arRNAs). By engaging key splicing elements, circ-arRNAs bypass out-of-frame DMD mutations and restore dystrophin expression through ADAR-dependent and ADAR-independent mechanisms. In DMD nonhuman primates (NHPs) carrying hotspot mutations, a single administration achieved durable dystrophin restoration and sustained motor improvement for at least 1.5 years without eliciting anti-dystrophin immune responses. In a first-in-human study, a single dose of adeno-associated virus (AAV)-delivered circ-arRNA produced safe, dose-dependent exon skipping in three patients, accompanied by measurable gains in motor and cardiopulmonary function. Together, consistent dystrophin restoration across DMD NHP models, patient-derived cardiomyocytes, and treated patients highlights the translational potential of circ-arRNA-mediated exon skipping as a therapeutic strategy for DMD.

Establishment of the blood-brain barrier (BBB) and blood-cerebrospinal fluid (CSF) barrier requires precise coordination between diverse cell types to protect and nourish the brain. Here, we identify developmentally programmed p21+ senescent cells that exhibit divergent senescence-associated features across these two brain interfaces in mice. In the choroid plexus (ChP), epithelial cells adopt a lifelong, non-inflammatory senescent state associated with CSF production and blood-CSF barrier integrity. In contrast, vascular endothelial cells and brain-resident macrophages transiently exhibit pro-inflammatory senescence profiles during brain vascularization, with reciprocal signaling linked to angiogenic patterning and extracellular matrix assembly. The ablation of p21+ cells during mid-gestation disrupts brain vascular patterning and ChP integrity, which results in hemorrhage, impaired CSF production, and ventricular collapse. These findings indicate that embryonic senescent cells adopt divergent transient and long-lived states that support brain-barrier formation and homeostasis, thus reframing the prevailing view of persistent senescence beyond solely a pathological state.

Mutations supply the raw material for evolution, yet because most are neutral or deleterious, elevated mutation rates are typically transient. Nonetheless, modeling predicts that a mechanism for heritable but reversible "mutagenesis switches" would be advantageous in some selective contexts. Here, we report that frequent prion-based switching of DNA repair and recombination proteins alters mutagenesis in Saccharomyces cerevisiae populations from diverse ecological niches, including the laboratory and clinic, providing adaptive benefits in short-term evolution under strong selective pressure. Self-templating protein assembly alters the activities and interactions of multiple DNA-fidelity factors, reshaping adaptive outcomes while maintaining resilience to genotoxic stress. In the WHO priority pathogen Candida albicans, which diverged from S. cerevisiae ∼300 million years ago, a key regulator of prion inheritance accelerates the rapid emergence of fluconazole resistance. These findings suggest that protein self-assembly can generate epigenetic memory that tunes genome diversification over multiple generations, enabling rapid adaptation in challenging environments.

More than 2,700 human mRNA 3' UTRs have hundreds of highly conserved nucleotides, but their biological roles are unclear. These mRNAs encode proteins strongly enriched for long intrinsically disordered regions (IDRs) with hydrophobic amino acid clusters. For MYC, UTX, and JMJD3, we show that their mRNA 3' UTRs control protein activity. Rather than affecting protein abundance or localization, we find that the KDM6B 3' UTR co-translationally changes the folding of JMJD3 protein. It promotes IDR-IDR interactions and suppresses folding between domains, suggesting that RNA has IDR chaperone activity that prevents interference between hydrophobic clusters in the IDR with folding of the structured domain. 3' UTRs with chaperone activity are multivalent and mesh-like condensate-enriched, indicating the presence of localized folding environments for IDR-containing proteins. We show here that the protein sequence is insufficient for the biogenesis of fully active IDR-containing transcriptional regulators in cells, suggesting that mRNA 3' UTRs control their activity by preventing co-translational misfolding.

Organ shortage remains a major challenge in transplantation medicine. Interspecies blastocyst complementation offers a promising strategy to generate human organs in livestock. However, efficient xenogeneic donor cell engraftment remains challenging. Here, we identify an innate immune barrier wherein host macrophages selectively eliminate viable xenogeneic donor cells, a process we term xenophagocytosis. Mechanistically, xenogeneic cells display elevated phosphatidylserine, an "eat-me" signal recognized by host macrophages through phagocytic receptor Axl. We demonstrate three orthogonal strategies for xenophagocytosis blockade: genetic ablation of macrophages or the Axl receptor in the host embryo or overexpression of the "don't-eat-me" signal CD47 or the phosphatidylserine-regulating flippase ATP11C in donor cells. Xenophagocytosis blockade enhances rat and human donor chimerism in mouse embryos and improves interspecies pancreas complementation efficiency. These findings reveal a previously unrecognized innate immune barrier that safeguards species integrity during early embryogenesis and provide mechanistic insights to enhance xenogeneic chimerism for generating human organs in livestock.

Darwinian evolution of immunoglobulin genes within germinal centers (GCs) underlies the progressive increase in antibody affinity following antigen exposure. Whereas the cellular mechanics of how competition between B cells increases affinity are well established, the evolutionary dynamics of this process are less clear. We developed an experimental evolution model in which we "replay" over one hundred monoclonal GC reactions, assigning affinities to each cell using deep mutational scanning. Our data reveal how GCs achieve predictable outcomes by means of noisy but persistent selection on an affinity landscape whose exploration is heavily constrained by somatic hypermutation biases. We infer a fitness landscape that quantitatively recapitulates the affinity maturation trajectory of our clone and find that apparent features of GC selection, such as permissiveness to low-affinity lineages and rapid plateauing of affinity, are likely artifacts of survivorship biases that distort our view of how B cell affinity progresses over time.

The deep-sea supergiant isopod is renowned for surviving over 5 years without food, which is a crucial adaptive trait for megafauna inhabiting extreme environments. Here, morphological, physiological, and genomic comparisons of deep-sea isopods reveal a dual adaptive strategy underlying this trait: a distended, food-retentive stomach that enables episodic hyperphagia and a markedly reduced basal metabolic rate (BMR). Notably, central to this adaptation is the ancient horizontal acquisition of the microbial energy metabolism-related gene ND1, which thereafter achieved significant dosage enhancement via post-transfer duplication and ultra-high expression that is specifically regulated by histone acetylation at its promoter. Functional assays in transgenic zebrafish, nematodes, and cell lines demonstrate that ND1 reduces BMR by downregulating endogenous energy-production genes and thus extends starvation survival under cold-induced metabolic suppression. These findings uncover an exceptional evolutionary strategy whereby deep-sea megafauna co-opts and epigenetically optimizes exogenous microbial genes to reconcile the metabolic conflict between energy-demanding gigantism and extreme energy limitation.

Gene expression is controlled by transcription factors (TFs), whose genome binding is shaped by chromatin accessibility and histone modifications, yet mapping these interactions, particularly those with weak affinity or a transient nature, in single cells remains technically challenging. To address this gap, we developed docking and deamination followed by sequencing (D&D-seq), a single-cell immuno-tethering technology for profiling DNA-protein interactions. D&D-seq couples an antibody-binding nanobody to a cytosine base editor, a combination that enables detection of weak or transient factor binding through targeted cytosine-to-uracil editing at protein-bound genomic sites. This approach is compatible with standard single-cell multi-omic workflows and therefore allows integrated analyses of gene regulation. Using assay for transposase-accessible chromatin using sequencing (ATAC-seq) and single-cell ATAC-seq (scATAC-seq), we assessed chromatin accessibility as a functional readout of TF activity, and by coupling D&D-seq with whole-genome sequencing, we captured CTCF binding in both active and inactive chromatin compartments.

Biomolecular condensates compartmentalize the interior of cells to organize complex functions, yet linking molecular interactions within condensates to their mesoscale organization remains a major challenge. To bridge this gap, we developed a neural-network-based framework-Deep-Phase (deep learning of phase-separated condensates)-that uses microscopy images to directly measure condensate morphology changes resulting from pharmacological alterations in associated biochemical processes. We use Deep-Phase to precisely quantify time- and concentration-dependent structural perturbations to the multiphase nucleolus and show that they are tightly coupled to potencies of drugs inhibiting ribosomal RNA (rRNA) transcription and processing. Applying Deep-Phase in a chemical screen, we identify a unique nucleolar morphology and discover a role for a DNA topoisomerase in rRNA processing. Mechanistic studies of this morphology provide insights into how the interfaces between nucleolar sub-compartments are maintained. We demonstrate Deep-Phase's adaptability to diverse cell lines, labeling techniques, and condensates, offering a powerful platform for connecting molecular pathways to cellular mesoscale organization.

Predicting lung cancer risk would enhance prevention trials. Although the Canakinumab Anti-inflammatory Thrombosis Outcome Study (CANTOS) trial demonstrated reduced lung cancer incidence with interleukin (IL)-1β inhibition, the high number needed to treat (NNT) to prevent lung cancer limits its use in unselected populations. Using machine learning, we identified a 14-protein plasma signature predicting lung cancer more than 5 years before diagnosis. The signature, validated across eight cohorts, was elevated in current smokers and individuals exposed to particulate matter (PM) and linked to lung myeloid and alveolar cells. In epidermal growth factor receptor (EGFR)-driven lung adenocarcinoma, diverse epithelial lineages converged on a keratin8+/claudin4+ alveolar transitional state (KAC), whose transcriptional programs correlated with signature emergence. Components of the signature were induced by PM, oncogenic EGFR, or IL-1β, whereas IL-1β inhibition restrained PM-driven KAC expansion and early tumorigenesis. In CANTOS, the signature identified individuals who seemed to benefit more from anti-IL-1β therapy, lowering the NNT threshold and nominating circulating signals of tumor promotion for prevention.

The Eurasian cave lion was abundant across the Northern Hemisphere before the Late Pleistocene megafaunal extinctions. However, the extent of the distinction between cave and modern lions and their adaptive differences have remained unclear. Using 12 cave lion genomes spanning more than 100,000 years, we show that modern and cave lions were distinct evolutionary lineages with separate demographic histories and unique non-synonymous variants. We also identify evidence of ancient gene flow between them, with the best modern lion proxy for this ancestry being an extinct Southwest Asian population. This admixture correlates with global ice extent, with 3.2%-4.4% modern lion ancestry detected in a ∼20,000-year-old cave lion from Central East Asia. These findings provide insight into the evolutionary history of the cave lion, once one of the Northern Hemisphere's most ecologically impactful megafaunal species.

The outer cell surface of an organism is the frontline for detecting and responding to environmental stimuli. In plants, this interface consists of the plasma membrane that lies beneath the cell wall and remains associated with it through attachment sites. These wall-membrane attachments become evident upon hyperosmotic shock, when severe water loss causes the membrane to retract from the wall. Despite their long-standing observation, the molecular identity and function of these attachments remain poorly understood. Here, we identified two mechanisms governing wall-membrane attachments: one dependent on the cellulose synthase complex (CSC), whose density at the plasma membrane positively correlates with resistance to hyperosmotic stress, and the other on remorin (REM), which acts antagonistically to the CSC mechanism. Using proximity-labeling proteomics, we identified SHOU4/4L as REM-associated proteins that mediate this antagonism. Together, our findings reveal how wall-membrane attachments are patterned to mediate plant cell resilience under water stress.