Transcription initiation in eukaryotes is a major regulatory checkpoint for ensuring that genes are precisely activated. Although the basic components of the transcription machinery were identified decades ago, recent breakthroughs in high-resolution cryo-electron microscopy have transformed our understanding of how these massive complexes function as dynamic assemblies rather than as static entities. In this Review, we focus on transcription by RNA polymerase II (Pol II) and discuss the integrated roles of the universal promoter scaffold factor TFIID, the transcription co-activator Mediator and the epigenetic status of the +1 nucleosome. We first discuss the structural basis of TFIID-mediated recognition of the core promoter and the modular assembly of the pre-initiation complex and pre-initiation complex-Mediator, which involves phosphorylation of the Pol II C-terminal domain. We then discuss how the chromatin environment regulates selection of the transcription start site and transcription directionality, before turning to the progression from transcription initiation to elongation, including promoter opening and promoter escape. Finally, we discuss transcription initiation as a programmed process, in which inhibitory factors are released and regulatory factors are progressively exchanged through competition for binding surfaces.
Methods to study cellular omics, morphology and spatial context evolved independently, yet evidence shows their integration outperforms single-methodology analyses. In this Comment, we propose that use of next-generation 3D-oids that combine molecular, morphological and spatial information will promote tissue analyses and bring us closer to engineering functional organs. Combined analyses of cellular omics, morphology and spatial context in 3D-oids would advance tissue studies and organ engineering.
During mitosis, the m6A methyltransferase METTL3 regulates transcription through functional interplay with the positive transcription elongation factor P-TEFb.
A 2010 paper identified PRDM9 as the sequence-specific regulator of meiotic recombination hotspots, showing it co-evolves with its rapidly changing binding motifs.
Mitochondria are essential metabolic and signalling hubs exposed to stress, and mitochondrial damage is highly detrimental to the cell. Mitophagy - the autophagy of mitochondria - is a key mechanism that maintains both mitochondrial integrity and metabolic flexibility. Mitophagy occurs via multiple pathways that either involve activation of PTEN-induced kinase 1 (PINK1) and the E3 ubiquitin-protein ligase Parkin, or are independent of PINK1 and Parkin. Recessive mutations in PINK1 and PKRN (the gene that encodes Parkin) cause early-onset Parkinson's disease and have provided key mechanistic insights into mitophagy. However, emerging findings indicate that mitophagy is also executed by other molecular routes. Despite these molecular advances in mitophagy characterization, the physiological roles of these pathways in mammals and the specific contexts or conditions in which they operate remain poorly defined. This Review summarizes current understanding of PINK1-Parkin-dependent and independent mitophagy pathways, highlighting mechanistic distinctions and coordinated regulation. We also examine physiological and pathological triggers of mitophagy, as well as the expanding therapeutic potential of targeting mitophagy in disease.
In this Tools of the Trade article, Xu and Zhang (Yang lab) discuss the invention of Spatial-EV-seq, which allows researchers to spatially map extracellular vesicles in tissue slices.
This Journal Club highlights the landmark study that provided the first evidence of regeneration in mammals, demonstrating that neonatal mice can regenerate damaged hearts and influencing regenerative medicine until today.
Synthetic cell research is an artificial intelligence (AI)-driven global endeavour that is outpacing conventional regulatory frameworks. Here, I argue for anticipatory governance that integrates ethics review, trustworthy AI policies and cross-border cooperation. There is an opportunity for the USA and China to co-lead international collaboration for responsible SynCell innovation. Li Du advocates for stronger legal frameworks and an interdisciplinary, international approach to governing synthetic cell research.
Mirroring bacterial persisters, cancer cells reprogram their iron homeostasis to acquire a drug-tolerant cell state that paradoxically confers vulnerability to ferroptosis. We propose a conserved principle, positioning iron as a driver of cell adaptations across mammalian malignant and microbial persistence. Bacterial persisters and drug-tolerant persister cells in cancer both show reprogrammed iron homeostasis and a vulnerability to ferroptosis. Agostinis and Rodriguez propose that this iron logic is a conserved principle with implications for therapeutics development.
Transcription termination by RNA polymerase II (Pol II) defines transcriptional boundaries of protein-coding and noncoding transcription units throughout the genome. Rather than being a passive endpoint of elongation, termination is a tightly regulated and context-dependent process that shapes gene expression, RNA surveillance pathways and chromatin environments. This Review summarizes mechanistic and conceptual aspects of Pol II termination, focusing primarily on studies in metazoans and incorporating insights from yeast where relevant. We discuss the major termination pathways operating across different genomic contexts, including canonical cleavage and polyadenylation-dependent termination at 3' ends of genes, promoter-proximal termination mediated by the Integrator-PP2A complex (INTAC), Pol II turnover via the E3 ligase CRL3ARMC5 and cap-dependent RNA surveillance. We further examine how termination restrains pervasive transcription and how its dysregulation compromises genome stability, particularly through the accumulation of R-loops. Finally, we discuss how termination interfaces with RNA processing, export and nuclear decay pathways to guide RNA fate decisions.
Accurate chromosome segregation in eukaryotic cells ensures that each daughter cell receives the same chromosome complement during cell division. Key to this process is the kinetochore, a macromolecular complex that connects spindle microtubules to the chromosome. The kinetochore is composed of a diverse array of proteins that can be broadly separated into an inner and outer kinetochore. Each chromosome also contains a distinct site that specifies the location of kinetochore formation, the centromere, which in many species is epigenetically defined by the specialized histone H3 variant centromere protein A (CENP-A). In this Review, we discuss recent advances in determining the complete structure and function of the inner kinetochore, as well as the sequence and 2D and 3D organization of centromeric chromatin. We discuss the implications of these recent advances for our understanding of the assembly and function of the inner kinetochore. We refer readers to a complementary review published in the same issue for a discussion on the structure and function of the outer kinetochore. Finally, we outline key questions persisting in the field driving future studies of the kinetochore and centromere.
The kinetochore is the complex molecular machine that controls chromosome segregation. The kinetochore comprises two regions: the inner kinetochore, which assembles on the specialized chromatin structure of the centromere, and the outer kinetochore, the site of microtubule binding and feedback control of mitotic progression. The core of the outer kinetochore is the Knl1-Mis12-Ndc80 (KMN) complex. The KMN binds directly to microtubules, controls the recruitment of additional microtubule binders and modulators, and is the primary switch for the spindle assembly checkpoint, a feedback control mechanism that coordinates mitotic exit with completion of chromosome biorientation. Live-cell imaging analyses of chromosome alignment in mitosis, combined with sophisticated biochemical reconstitutions and high resolution structural analyses, are finally shedding light on the dynamic integration of these activities. In this Review, we focus on how the handful of KMN complexes present at each microtubule-binding site achieves this complex regulation with high accuracy. We refer readers to a complementary Review published in the same issue for a discussion on the structure and function of the inner kinetochore.
The biogenesis, modifications and function of mitochondrial transfer RNAs (mt-tRNAs) reflect the symbiotic relationship and coordinated evolution between the domesticated organelle and the outer cell. Through evolution, mt-tRNA structures have been severely degenerated, and mt-tRNA-associated proteomes have acquired additional domains and interfaces, leveraging post-transcriptional modifications to maintain functional affinity and specificity. Considerable progress has been made in the past decade in elucidating mt-tRNA structure, biogenesis, modifications and functions. In this Review, we outline how mt-tRNAs are excised from polycistronic transcripts and mature through coordinated actions of mitochondrial processing enzymes. We then examine how mitochondrial aminoacyl-tRNA synthetases and mitoribosomes have coevolved to recognize degenerated mt-tRNAs and support a streamlined genetic code. The roles of post-transcriptional modifications in mt-tRNA structure stabilization, mt-tRNA decoding and the coupling of metabolism to translation are also discussed. Moreover, we review mt-tRNA-associated pathologies and emerging therapeutic strategies, highlighting unifying principles that inform efforts to restore coherence of mitochondrial translation.
Necroptosis is a programmed lytic cell death pathway executed through mixed lineage kinase domain-like protein (MLKL)-driven plasma membrane disruption and has pivotal roles in both health and disease. Recent advances have led us to propose the classification of mammalian necroptosis into two subtypes: extrinsic and intrinsic necroptosis, which differ in their mechanisms of trigger sensing and signal integration. Extrinsic necroptosis is initiated by membrane-bound receptors, including cell-surface receptors such as tumour necrosis factor receptor 1 (TNFR1) and Toll-like receptor 4 (TLR4), as well as endosomal receptors such as TLR3, whereas intrinsic necroptosis is initiated intracellularly through sensors such as Z-DNA-binding protein 1 (ZBP1) detecting cytosolic Z-nucleic acids. In this Review, we provide an overview of the molecular mechanisms of necroptosis, highlighting the latest insights into their complex regulatory networks, execution pathways, and the growing clinical relevance and therapeutic potential of targeting necroptosis in human diseases.
The blood-brain barrier (BBB) is a unique specialization of central nervous system (CNS) capillary endothelial cells that controls molecular traffic between the blood and the brain. In doing so, the BBB maintains a safe and homeostatic environment for proper neuronal function. The BBB restricts drug delivery to the CNS, while BBB defects contribute to neurodevelopmental and neurodegenerative disorders. In this Review, we discuss the distinct features of CNS capillary endothelial cells that form the BBB. Meanwhile, interactions between capillary endothelial cells and surrounding pericytes, astrocytes and with the extracellular matrix of the basement membrane, are crucial for BBB formation and maintenance. We examine how molecular regulators of capillary endothelial cells and signalling pathways that control cell-cell interactions render the BBB a dynamic and selective interface. We highlight emerging areas of BBB research, including heterogeneity of brain vascular permeability and technology development. Finally, we discuss how insights from BBB biology are shaping therapeutic strategies targeting the BBB.
Already thirty years ago, DNA replication, transcription and repair machineries were proposed to form and function in nuclear ‘factories’, later also dubbed hubs and condensates.
A demonstration that phase separation of biomolecules is promoted by multivalent interactions, which form dynamic polymer networks with cellular functions.
Aminoacyl-tRNA synthetases (ARSs) are best known for their central role in translation, where they attach specific amino acids to their matching tRNAs to ensure accurate protein synthesis. However, in humans, these enzymes have evolved far beyond this textbook function. Emerging research reveals that ARSs have versatile roles in cells, acting as sensors, signalling hubs and regulators of cellular and systemic homeostasis. The structural adaptability of ARSs enables them to connect metabolic cues with gene expression, protein networks and stress responses. Disruptions in ARS functions are increasingly linked to a wide range of diseases, from cancer to neurodegeneration. In this Review, we examine how ARSs operate at the intersection of translation and signalling networks: we discuss their catalytic regulation functions, structural diversification, non-canonical functions such as in transcription and translation regulation, protein degradation and signal transduction and their disease relevance. By bringing these insights together, we offer a unified view of ARSs as multifaceted proteins and open new avenues for discoveries in molecular biology, pathophysiology and drug design.
