Cellular function is frequently interpreted in terms of gene presence, protein abundance, and dose-response relationships. Yet interacting proteins operate within binding and assembly regimes in which relative abundance can alter which molecular complexes predominate. We propose a protein-ratio rheostat framework in which functional output depends jointly on component ratios, absolute concentrations relative to binding affinities, interaction stoichiometry, and in multivalent systems, valency and cooperativity. The same protein ratio can therefore generate different molecular and functional states under different concentration or affinity regimes. We develop testable predictions of this framework, illustrate its application to competitive protein interactions and biomolecular condensates, and outline experimental strategies for identifying composition-sensitive behavior within defined abundance and affinity regimes.

The regulation of replication fork (RF) speed is essential for faithful genome duplication and the maintenance of genome stability, and its dysregulation contributes to carcinogenesis and developmental disorders. Although many anticancer therapies perturb DNA replication, the molecular mechanisms by which RF speed is controlled remain incompletely understood. A major limitation has been the frequent omission of direct measurements of cellular deoxynucleotide triphosphate (dNTP) pools, despite their strong and immediate influence on DNA polymerase kinetics. In this review, we first summarize how dNTP availability constrains RF progression under physiological and stress conditions. We then discuss how anticancer agents targeting DNA replication modulate RF speed through phosphorylation-dependent signaling pathways. Finally, we examine emerging roles of PARylation and UFMylation as rapid, replisome-centered regulatory mechanisms that fine-tune fork progression and stability, and we highlight their clinical implications, including a mechanistic link between aberrant replisome regulation and microcephalic primordial dwarfism.

A complex network of protein interactions promotes the cooperative assembly of biomolecular condensates that control the formation of meiotic DNA double-strand breaks (DSBs). In many species, programmed DSBs made by SPO11 are required for the faithful pairing and segregation of homologous chromosomes during meiosis I. DSBs must be tightly regulated to support their intended function but also to minimize the risk of genomic damage from mutation or defective DSB repair. Multiple chromosome axis-associated proteins are important for the control of meiotic DSB formation and recombination, but the underlying mechanisms of those proteins remain poorly understood. Here, we present a current view of how these proteins work together in mice, based on recent advances in the characterization of their function and structure.

Telomerase-free cancer cells use a recombination-based alternative lengthening of telomeres (ALT) pathway to maintain telomere length. ALT cancer cells exhibit extreme heterogeneity in telomere length, which requires the formation of a specialized nuclear condensate, the ALT telomere-associated PML bodies (APBs). Recent findings on APB assembly reveal that APBs form through two mechanistically and kinetically distinct pathways. These pathways modulate the strength of ALT activity. In this essay, I discuss how APB formation dynamics may contribute to telomere-length variability in ALT cells and consider the broader implications of these findings for other chromatin-associated nuclear condensates.

Advanced vertebrates (gnathostomes) differ from the rest of the animal tree of life by their use of an elaborate endoskeleton and the deployment of the catecholamine neurotransmitters epinephrine and norepinephrine. Here we propose that the coordinated origins of these seemingly unrelated signature traits are explained by the varied propensities of different catecholamines to oxidize and polymerize into the light absorbent and structurally stable biopolymer melanin. Compared to dopamine and its precursor DOPA (L-3,4-dihydroxyphenylalanine), norepinephrine and epinephrine are much less susceptible to polymerization. The latter were therefore likely adaptively favored for peripheral signaling in vertebrates. In addition to the chemical evidence, we explore how peripheral nervous system development correlated with changes in gene family content, immune response organization, and internal support structure elaboration during early vertebrate evolution.

Recent human genetic studies revealed that Alzheimer's disease risk loci are enriched in genes expressed in myeloid cells, including microglia, the brain's resident immune cells. Notably, several risk-associated genes, such as SPI1 and MEF2C, encode transcription factors (TFs) that control critical microglial functions, including phagocytosis, inflammatory responses, and neurotrophic support. The objective of this article is to review the recent progress in understanding these TFs and evaluate them as therapeutic targets rather than as markers of microglial state. We examine the genetic evidence implicating PU.1, MEF2C, IRF8, and BHLHE40/41, the in vivo evidence from animal models, the transcriptional network these factors regulate, and the barriers to clinical translation. Because these TFs orchestrate broad gene expression networks by regulating multiple disease-relevant downstream partners, targeting their expression level or activity could achieve greater therapeutic efficacy than targeting single genes, provided that the dose and disease stage of modulation are carefully considered.

The rapid, unprecedented rate of worldwide pressures organisms are currently exposed to, from climate instability to pollution, urges to expand research focus toward stress resilience. Here, our main goal is to call for an integrative effort to understand conserved processes underlying whole-organism stress resilience with a specific focus on the following questions: (i) How can stress resilience be defined? (ii) What are its main underlying metrics at the whole-organism level (focus on glucocorticoid hormones, oxidative stress, neural and behavioral metrics)? (iii) What is the role of stress inoculation- and hormetic-like effects to build resilience throughout an organism´s lifespan? By building up on emerging knowledge spanning from behavioral biology and ecophysiology to biomedicine, we explore conserved mechanisms of stress resilience that are relevant for both environmental and human health. Finally, we encourage for more research on wildlife study systems, which experience natural and cumulative stressors across ecologically relevant settings, and can thus help uncover functional mechanisms of stress resilience across vertebrates, including humans.

Transcription and three-dimensional (3D) genome organization are closely coupled, but their precise relationship remains unresolved. Evidence from perturbation, imaging, and modeling studies suggests that transcription is not strictly required for the establishment of large-scale genome features such as compartments and topologically associating domains (TADs). Instead, transcription seems to exert more prominent effects at finer spatial scales, where it influences enhancer-promoter interactions, local chromatin loops, and microcompartments. RNA molecules, polymerase-driven supercoiling, and R-loop formation may further modulate chromatin organization at the gene level. At the same time, many architectural proteins and transcriptional regulators operate with functional overlap, complicating efforts to disentangle cause and consequence. Together, these observations suggest that genome architecture provides a relatively stable framework for regulated gene expression, while transcription and associated factors refine chromatin organization in a context-dependent manner. Understanding how these processes are integrated will require systematic, multi-scale perturbations across different biological and biochemical systems.

Tetracycline destructases (TDases) pose an emerging global threat by enzymatically inactivating all generations of tetracycline (Tet) antibiotics, including last-resort agents such as tigecycline. Despite their recent identification, TDases have rapidly disseminated worldwide, largely driven by mobile genetic elements and environmental reservoirs. This review synthesizes current knowledge on TDase genomics, structural and catalytic mechanisms, ecological niches, and clinical impacts. We detail the mechanistic distinctions between type 1 and type 2 TDases, emphasizing their divergent structural configurations and substrate specificity profiles. Additionally, we examine strategies for therapeutic intervention, highlighting progress in structure-guided inhibitor development. Key gaps remain in understanding ancestral reservoirs, evolutionary trajectories, and effective surveillance strategies. Addressing these areas through integrative evolutionary, biochemical, and ecological studies is critical for mitigating the clinical spread and therapeutic impact of TDases globally.

Neural progenitor cells (NPCs) must preserve lineage identity while remaining responsive to developmental cues. Here, we discuss the hypothesis that ATRX condensates help organize enhancer-centered nuclear microenvironments in NPCs. ATRX has long been studied in heterochromatin maintenance, histone variant deposition, and chromatin remodeling; earlier work has also shown that ATRX can occupy euchromatic and active regulatory regions and contribute to transcriptional regulation. Recent evidence in human NPCs indicates that ATRX forms nuclear puncta with condensate-like properties, associates with neurogenic enhancer-rich regions, and incorporates regulatory factors such as CHD7 and p300. Perturbation of ATRX condensate formation is associated with changes in enhancer-associated ATRX occupancy, neural gene-expression programs, and neuroepithelial organization, suggesting a regulatory mode that may complement canonical heterochromatin-associated functions. We propose a dual-mode model in which folded domains contribute to chromatin anchoring at repressive regions, whereas intrinsically disordered regions support condensate-associated organization at active developmental enhancers. We emphasize that whether ATRX condensates activate enhancers de novo, stabilize pre-existing enhancer states, buffer transcriptional variability, or primarily organize cofactor localization remains unresolved. We also discuss limitations of the current evidence and outline acute, locus-specific experiments needed to test the model.

The cyclin-dependent kinase subunit (CKS) remains the least well-understood component of the tripartite cyclin-dependent kinase (CDK) complexes that specify the proper sequence of events required to duplicate and segregate genomes during eukaryotic cell division. Our recent investigation of CKS requirements during Caenorhabditis elegans oocyte meiosis I and II documents an essential role for CKS in the execution of anaphase B and expands the known range of CKS influence on cell cycle regulation to a third class of E3 ligases. Our findings also further document how C. elegans oocytes use very different mechanisms to progress through these two sequential cell divisions that ultimately produce a haploid oocyte. In this Think Again article, we discuss our findings as they relate to previous studies of CKS in different model systems.

The efficient repair of chromosome breaks by homologous recombination depends on the ability of the ends of a double-strand break (DSB) to locate homologous sequences to serve as templates to repair the lesion. These repair mechanisms are conserved across eukaryotic evolution. Repair depends on 5' to 3' resection of the broken ends, allowing the assembly of a Rad51 filament. In yeast, fruit flies, and mammals, broken chromosome ends display increased mobility, allowing the ends to explore a larger volume. The Arp2/3 actin nucleator complex plays a key role in increased local chromatin mobility near a DSB. In budding yeast, Arp2/3, LAS17WASP, and myosins are required both to initiate and to maintain long-range end resection, affecting both DNA repair and the maintenance of the DNA damage checkpoint. At least in budding yeast, the connection between controlling long-range resection and increased mobility is direct, as inhibiting resection prevents damage-induced chromatin mobility. Moreover, although the search for homology by Rad51-coated broken DNA ends would seem to be improved by greater exploration of the nuclear volume, increased local mobility through Arp2/3 per se does not affect the efficiency of ectopic recombination in yeast. Here, we review the recently defined roles of nuclear actin in DNA damage repair, with a focus on new observations in budding yeast.

Lactate is among the most frequently measured metabolites in physiology and medicine, yet it remains one of the most persistently misunderstood. Long regarded as a metabolic waste product, a marker of anaerobic metabolism, or a direct cause of acidosis and fatigue, lactate remains burdened by misconceptions that obscure its true biological roles. Recent advances in metabolic flux analysis, isotope tracing, hyperpolarized magnetic resonance spectroscopy, and cellular imaging have revised this view and established lactate as a central intermediary in energy metabolism, redox homeostasis, and interorgan metabolic communication. Here, we re-examine common myths surrounding lactate biology and clarify the distinction between correlation and causation in its interpretation. By reframing lactate as a dynamic indicator and, in some contexts, a regulator, of metabolic state rather than a toxic by-product, this review improves experimental reasoning and clinical interpretation across diverse physiological and pathological contexts.

Faithful chromosome segregation requires the kinetochore, a macromolecular protein complex that assembles on centromeric chromatin. In vertebrates, centromere identity is epigenetically defined by the histone H3 variant CENP-A, whose nucleosomes are replenished during early G1 phase through a cell cycle-regulated deposition mechanism. The CENP-A chaperone HJURP is recruited to centromeres via the Mis18 complex to enable CENP-A incorporation (Mis18C pathway). Recent genetic analyses in chicken cells, however, revealed an additional, independent recruitment route via direct HJURP-CENP-C interaction (CENP-C pathway). Structural studies show that CENP-C and the Mis18C subunit KNL2/M18BP1 engage pre-existing CENP-A nucleosomes at different surfaces of the Constitutive Centromere-Associated Network (CCAN), constraining the spatial coordinates where new CENP-A is incorporated. This review summarizes current understanding of HJURP recruitment mechanisms for vertebrate CENP-A deposition and proposes that this structure-defined deposition geometry underlies epigenetic self-propagation of centromere positional information by maintaining proper CCAN spacing across cell divisions.