Epithelial-to-mesenchymal transition (EMT) is a pivotal developmental program that is frequently co-opted to drive cancer aggressiveness and metastasis. While the dynamic remodelling of histone H3 lysine 27 acetylation (H3K27ac) landscapes is a hallmark of EMT, the specific chromatin readers decoding these epigenetic signals remain largely unknown. Here, we identify ATAD2B as a novel H3K27ac reader essential for cell migration in both cancer metastasis and brain development. Multi-omics profiling revealed that, at EMT onset, ATAD2B targets H3K27ac at active epithelial identity genes via its bromodomain and recruits HDAC1 to epigenetically silence them, enforcing a mesenchymal state. ATAD2B loss impairs migration and invasion in breast cancer lines and Patient-Derived organoids, whereas its overexpression accelerates in vivo lung metastasis and correlates with poor patient survival. Furthermore, ATAD2B promotes the migration of newborn neurons in the developing brain. Our findings establish ATAD2B as a versatile chromatin reader orchestrating cell motility across development and disease.

The human nigrostriatal pathway, comprising dopaminergic neurons in the ventral midbrain that project to the dorsolateral striatum, is essential for motor control and selectively vulnerable in Parkinson's disease. How this circuit assembles during human development remains poorly understood, and in vitro models capturing its long-range connectivity and spatial organization have been lacking. Here, we establish a compartmentalized, human stem cell-based model of the nigrostriatal pathway by integrating ventral midbrain and striatal organoids within a custom-engineered microfluidic device that confines cell bodies while guiding axonal growth to recapitulate key aspects of in vivo topography. Functional connectivity was confirmed by retrograde rabies tracing, and optogenetic and pharmacological stimulation. Single-nucleus transcriptomic analysis reveals that axonal target engagement with spatially separated striatal neurons promotes maturation of human dopaminergic neurons and activates transcriptional programs associated with neurotransmitter secretion. Our study establishes a biologically relevant in vitro system for investigating how long-range connectivity regulates neuronal assembly in the nigrostriatal circuit and for modelling key pathological features of Parkinson's disease.

Transposable elements (TEs) comprise about half of the human and mouse genomes and contribute to gene regulation during immune responses. However, how TEs acquire cis-regulatory functions during immune cell development remains poorly understood. Here, we analyzed hundreds of datasets profiling chromatin accessibility, gene expression, transcription factor occupancy and DNA-DNA contact across diverse mouse and human immune cell types. We identified two rodent-specific TE subfamilies, ORR1E and ORR1D2 (collectively, ODE) that have diversified after genomic insertion into cell type-specific enhancers across the mouse immune system. Post-insertion mutations in ODE loci generated differential binding sites for lineage-specifying transcription factors. ODEs showed evidence of evolutionary sequence constraint and contacted promoters of hundreds of genes in immune cells. Predicted ODE target genes were enriched for cell type-specific functions and showed increased expression in mouse compared to human cell types lacking ODEs. Together, these findings show how a single TE family can diversify after genomic spread to generate cell type-specific enhancers that reinforce lineage-specific gene programs.

Drought is a major consequence of climate change and significantly limits crop productivity. Plant growth-promoting bacteria offer a promising solution to mitigate drought stress. The root endophyte Pseudomonas argentinensis SA190 has been shown to enhance plant performance under drought stress conditions, but the mechanistic basis of SA190's beneficial effects remained unclear. Given the pivotal role of sulfur-containing compounds in abiotic stress responses, we investigated multiple sulfur-related Arabidopsis mutants under PEG-induced drought stress. We found that SA190 enhances sulfate uptake and promotes glutathione (GSH) accumulation in shoots under stress conditions. SA190 treatment increased the GSH/GSSG ratio, providing an enhanced redox resilience under PEG stress. Inhibition of GSH biosynthesis in Arabidopsis with buthionine sulfoximine (BSO) provided evidence that SA190 contributes to elevated GSH levels under PEG-induced drought stress. Using bacterial mutants defective in GSH biosynthesis, we further show that SA190 contributes to Arabidopsis growth under PEG-induced stress, potentially through a mechanism involving bacterial GSH itself or its precursor, γ -glutamylcysteine (γ-EC). In summary, SA190 enhances tolerance to PEG-induced drought stress by modulating host sulfur metabolism and improving cellular redox homeostasis.

Innate immune systems must detect infection rapidly and reliably, yet pathogens can often evade direct recognition by host pattern-recognition receptors. An alternative and increasingly appreciated strategy is damage-driven immune surveillance, whereby hosts detect pathogen-induced perturbations to essential cellular and tissue functions rather than microbial molecules themselves. This mode of detection is particularly prominent in Caenorhabditis elegans, which lacks professional immune cells and most canonical innate immune receptors, and therefore relies extensively on monitoring disruptions to core homeostatic pathways. Perturbations to protein translation, proteostasis, mitochondrial function, genome and nucleolar integrity, lysosomal homeostasis, and Golgi function can all trigger immune responses. Recent studies have further uncovered roles for inter-organelle communication, effector-triggered surveillance of lysosome-related organelles, and physiological signals such as intestinal distension in regulating immune activation. Here, we integrate these advances into an organelle- and tissue-centric framework and explore parallels with other organisms to identify emerging and potentially conserved principles of damage sensing in innate immunity. These findings highlight the surveillance of cellular homeostasis as a central strategy for immunity that operates beyond canonical pattern-recognition mechanisms.

Spindle assembly checkpoint (SAC) components have been proposed to act as both a surveillance mechanism monitoring mitotic fidelity and as a timer that ensures sufficient time for chromosome alignment to occur. To evaluate these roles, we utilized an SAC-deficient cell line generated by eliminating the full-length Cdc20 translational isoform (Cdc20 ∆FL), and defined genetic interactions using CRISPR/Cas9-based screening. Cdc20 ∆FL cells display synthetic-lethal relationships with genes required for chromosome segregation, highlighting the role of the SAC in error surveillance. Interestingly, we found that the SAC component Mad2, which has been proposed to act as an essential "timer" to control anaphase onset by preventing premature APC/C activation, becomes dispensable for viability in Cdc20 ∆FL cells. Our targeted analysis indicates that regulation of mitotic timing involves a combination of Mad2 inhibition of APC/C-Cdc20, Cdk1-mediated Cdc20 phosphorylation preventing premature APC/C-Cdc20 activation, and total Cdc20 protein levels. Simultaneously perturbing these pathways results in premature mitotic exit and catastrophic chromosome mis-segregation.

Multiple lines of evidence suggest that RNase H1-sensitive RNA:DNA hybrids could disrupt the stability and restart of stalled replication forks. The prolonged over-expression of RNase H1 is the most popular method to manipulate RNA:DNA hybrids in situ but it cannot discriminate between direct and indirect effects resulting from their loss. To overcome this limitation, we developed iCoRD (in Cellulo RNase H Delivery) to rapidly deliver comparable amounts of either Escherichia coli RNase H1 (RnhA) or control proteins in live cells, with a negligible impact on the transcriptome. iCoRD-delivered RnhA recognises RNA:DNA hybrids in situ, is enriched in the vicinity of active replication forks and rescues replication fork progression in different stress conditions. While iCoRD-delivered RnhA had a clear impact on stress-induced, fork-proximal RNA:DNA hybrids and R-ChIP signals, it had no effect on DRIP or S9.6 Cut&Tag signals, even when these were induced by stress. Our results strongly suggest the existence of distinct populations of RNA:DNA hybrids that are best mapped by different methods and are differently sensitive to RNase H1 activity in situ.

Aurora A kinase is a conserved regulator of mitotic spindle assembly whose activity must be precisely balanced to ensure genome stability. Its activation at centrosomes and spindle microtubules is promoted by CEP192, TACC3 and TPX2, and counteracted by protein phosphatase 6 (PP6), which dephosphorylates the Aurora A T-loop. PP6 forms three holoenzymes defined by regulatory subunits PPP6R1-R3, yet how these confer substrate recognition and regulation is poorly understood. Here, we identify a phenylalanine-rich motif (A-box), present in PPP6R2 and PPP6R3 but absent from PPP6R1, that binds a surface on Aurora A overlapping those used by CEP192, TPX2 and TACC3. Mutation of A-box phenylalanine residues disrupts Aurora A binding and T-loop dephosphorylation, elevating spindle-associated Aurora A activity, and enlarging mitotic spindles. PPP6R2 additionally contains a unique PLK1-docking site downstream of its A-box, explaining how PLK1 competes with Aurora A for PPP6R2 and thereby suppresses PP6 activity towards Aurora A. Together, these findings show that PP6 regulatory subunits mimic Aurora A activators to direct dephosphorylation, and reveal how competing interactions regulate PP6 in mitosis.

Synaptic plasticity requires the coordinated regulation of membrane remodelling, energy production, and protein turnover. However, how these processes are integrated at the molecular level remains unclear. Here, we propose that activity-dependent lipid flux represents a central mechanism linking these processes. Saturated free fatty acids (sFFAs) released from membrane phospholipids, triglycerides, or from extracellular uptake can be activated to acyl-CoA and directed to mitochondrial β-oxidation and synaptic protein lipidation. These represent two emerging pathways adding to the complexity of roles played by sFFAs, including membrane fluidity and receptor activation. Recent work identifies DDHD2 as a mechanistic entry point into this broader synaptic lipid network. We position DDHD2-dependent lipid mobilisation in the wider context of glia-neuron lipid transfer and ApoE/sortilin-dependent fatty acid uptake. Key unresolved questions include the source and fate of fatty acids, the relative contribution of β-oxidation versus glycolysis to ATP production, and whether these pathways are altered in neurodegenerative disease.

RNA-binding E3 ubiquitin ligases have the ability to link RNA regulation to the protein ubiquitination machinery, thereby influencing diverse biological processes. Here, we identify the RNA-binding E3 ubiquitin ligase DZIP3 as an innate immune sensor that couples viral RNA recognition to downstream immune signaling. Upon viral infection, binding of viral RNA to the DZIP3 RNA-binding motif induces conformational changes that promote K63-linked auto-ubiquitination, oligomerization, and stabilization of DZIP3. Activated DZIP3 associates with RIG-I and MAVS at the mitochondrial membrane, promoting K63-linked ubiquitination of RIG-I and robust activation of the type-I interferon response. Consequently, DZIP3 depletion impairs host antiviral defense, whereas DZIP3 restricts infection by a broad range of RNA viruses. Our findings establish DZIP3 as an innate immune co-sensor that integrates viral RNA detection with ubiquitin-mediated signaling, revealing a regulatory mechanism of RIG-I-MAVS-mediated antiviral immunity.

Nuclear speckles (NS) enhance the expression of NS-associated genes, possibly by elevating local levels of factors involved in multiple steps of gene expression. While dozens of large NS are distributed throughout interchromatin regions, the extent to which NS components dynamically redistribute between NS to adjust to local physiological demands remains unknown. Here, we used live-cell imaging of endogenous NS proteins to identify an interchromatin network of connections that functionally link NS throughout the nucleus. Over timescales ranging from tens of seconds to minutes, NS material is transferred through these curvilinear connections, rather than through isotropic exchange across the NS/nucleoplasm interface followed by diffusion in all directions throughout the nucleoplasm as predicted by current models. Multiphase NS-connecting structures form through the dynamic juxtapositions of multiple NS component phases. Each phase exhibits distinct yet recurrent dynamic patterns, but together, they integrate into a more stable, multiphase, NS-connecting structure in an ATP- and transcription-dependent manner. Our findings reveal the existence of a cellular mechanism that facilitates coordinated inter-NS protein trafficking through multiphase connections.

Selective autophagy of the Golgi apparatus (Golgiphagy) is essential for Golgi quality control, yet its regulation and physiological functions remain poorly understood. Here, we identify the deubiquitinase USP28 as an upstream regulator of the Golgiphagy receptor TM9SF3. USP28 removes degradative K48-linked ubiquitin chains from TM9SF3, preventing its proteasomal degradation and sustaining Golgiphagy under nutrient and Golgi stresses. CRM1-dependent nuclear export enables the stress-induced translocation of USP28 to the Golgi, where it stabilizes TM9SF3, promoting Golgi fragmentation and autophagic clearance. Loss of USP28 or TM9SF3 impairs Golgiphagy, disrupts glycosylation fidelity, and inhibits breast cancer cell proliferation. Proteomic and functional analyses identify the glycosyltransferase MGAT5 as a selective TM9SF3-dependent Golgiphagy cargo, revealing how this pathway maintains glycosylation homeostasis. In syngeneic tumor models, USP28 knockout or pharmacological inhibition reduces TM9SF3 abundance, compromises Golgiphagy, perturbs glycosylation, and markedly suppresses tumor growth-effects restored by wild-type but not LC3-binding-deficient TM9SF3. Together, these findings reveal a USP28-TM9SF3-Golgiphagy axis that couples ubiquitin signaling to Golgi glycosylation control and represents a therapeutically targetable pathway for breast cancer.

Azole resistance in Candida species is often caused by the overexpression of Cdr1. Despite its clinical relevance, the structural basis for its ATP-driven efflux pump function remains elusive. We present four high-resolution cryo-EM structures of Candida glabrata Cdr1 obtained in the absence and presence of ATP-Mg[2+], itraconazole, and vanadate, capturing distinct nucleotide- and substrate-occupancy states. Additional low-population cryo-EM conformers were unveiled by 3D variability analysis, offering a detailed view of structural transitions linked with ATP-hydrolysis. The motion shows a 4 Å piston-like retraction of the C-helix from the γ-phosphate/vanadate of the hydrolyzed ATP. This causes the nearby transmembrane helix-1 (TMH-1) to open the drug-binding site via lateral displacement and unwinding of the inner-leaflet region of TMH-2. A reverse 'squeeze-and-push' motion of TMH-2 possibly drives substrate extrusion. High-resolution structures also reveal how itraconazole adapts its shape to fit into the drug-binding site. Our findings provide a dynamic structural framework for Cdr1-mediated azole resistance and the conserved chemo-mechanical cycle of ABC proteins, including non-membranous members.