Ribosome collisions during aberrant translation activate ribosome-associated quality control (RQC) to resolve stalled ribosome complexes and triage incomplete nascent chains. How this co-translational surveillance is coordinated with other ribosome-associated activities remains unclear. Here, we identify the ribosome-associated Hsp40 chaperone DNAJC2 that restrains translational flux and limits RQC engagement during collision-prone translation. Genetic epistasis analysis revealed that DNAJC2 titrates the flux of aberrant translation intermediates through the canonical RQC pathway, from the collision-sensing RQC factor ZNF598 to the downstream NEMF-LTN1 E3 ligase complex for proteasomal degradation. DNAJC2 depletion further sensitized cells to collision-induced ribotoxic stress response (RSR), indicating increased vulnerability to global translation stress. Mechanistically, loss of DNAJC2 accelerated translation elongation, thereby promoting ribosome collisions and ZNF598-dependent ribosome disassembly. Accordingly, reducing translational flux with the translation inhibitor homoharringtonine or a huntingtin upstream ORF rescued DNAJC2-depletion phenotypes during RQC-sensitive poly(A)-mediated translational stalling. Together, we propose that DNAJC2 acts as a translational rheostat to buffer ribosome collisions, prevent RQC overload, and set the threshold for RSR activation.

Polyglutamine (polyQ) diseases are fatal neurodegenerative disorders caused by pathological CAG repeat expansions in disease-associated genes. They are characterized by progressive motor dysfunction and typically late onset. Although multiple mechanisms have been proposed, accumulating evidence indicates that lipid dysregulation contributes to neuronal dysfunction and degeneration. Lipids are essential for brain development and homeostasis, and disrupted lipid metabolism is implicated across neurodegenerative conditions. Within the polyQ spectrum, Huntington's disease is the best studied and shows strong links between altered lipid pathways and neuronal pathology, whereas the role of lipid dysregulation in other polyQ disorders remains less well defined. In this review, we summarize key lipid functions in the central nervous system, synthesize reported lipid alterations across polyQ diseases, and evaluate the therapeutic potential of targeting lipid metabolism.

Alternative lengthening of telomeres (ALT) is a telomerase-independent, recombination-based pathway utilized by some cancers. Previously, we established two distinct types of ALT survivors derived from mouse embryonic stem cells (mESCs), characterized by either a unique non-telomeric insertion (type I) or canonical telomeric repeats (type II). In this study, we used telomere-specific proteomics to elucidate the divergent telomere maintenance strategies of these ALT types. We identified distinct proteomic profiles enriched in type I versus type II ALT telomeres. ICE1 is a component of the Little Elongation Complex, which is specifically recruited to type I ALT telomeres, where it supports the transcription of telomeric repeat-containing RNA (TERRA) and telomere maintenance. In contrast, the serine/threonine kinase VRK2 is highly enriched in type II ALT telomeres, where it regulates telomere-nuclear envelope interactions. Depletion of ICE1 or VRK2 impairs telomere stability in type I and type II ALT mESCs, respectively. Our results indicate that cells with a common mESC origin can adopt distinct molecular mechanisms to maintain telomere integrity, highlighting the mechanistic heterogeneity of ALT telomere maintenance.

The RNA of all living organisms and most viruses exhibits pervasive suppression of uracil-adenine (UpA) dinucleotides, yet the underlying molecular mechanisms remain poorly understood. Here, we use RNA affinity purification coupled with mass spectrometry to identify diverse host factors that preferentially bind UpA-high RNA sequences. The identified proteins include the canonical antiviral proteins IFIT1 and OAS1, as well as multiple components of the U1 and U2 small nuclear ribonucleoproteins (snRNPs), core elements of the splicing machinery. These splicing factors display increased affinity for artificially UpA-enriched RNA and the West Nile virus (WNV) 3' UTR, which naturally contains higher frequencies of UpA dinucleotides. The functional relevance of splicing factor interactions was demonstrated by pharmacological inhibition of early splicing events, which partially restored the replicative fitness of synonymously recoded and otherwise attenuated UpA-high mutants of Zika virus and WNV. Together, these findings reveal a novel antiviral role for splicing factors, linking their preferential association with UpA-rich RNA to the restriction of UpA-high viruses. Given the evolutionary conservation of the splicing machinery, our results suggest that splicing factor-mediated recognition may contribute to maintain the universal suppression of UpA dinucleotides in host and viral RNA.

The retina serves as a uniquely accessible entry point to the central nervous system, enabling both cell type-specific manipulation and circuit-level interrogation of visual pathways. Viral vectors have emerged as indispensable tools in this context, facilitating precise gene delivery, functional perturbation, and connectivity mapping across retinal and brain circuits. Among retinal neurons, retinal ganglion cells (RGCs) represent a major focus due to their role as the sole output neurons conveying visual information to central targets. Accordingly, recent advances in viral engineering including capsid design, transcriptional targeting, and synthetic regulatory elements have significantly improved the efficiency and specificity of RGC-directed gene delivery, while also enabling targeting of diverse retinal cell populations. Beyond retinal targeting, viral tools have transformed the study of RGC connectivity with downstream brain nuclei. In particular, transsynaptic and projection-specific viral strategies now enable mapping of RGC inputs and outputs across visual pathways with increasing precision. Approaches using retrograde AAVs, monosynaptic rabies systems, and anterograde tracers have revealed complex, cell type-dependent wiring patterns linking the retina to thalamic, midbrain, and cortical circuits. In this review, we highlight current viral technologies for targeting RGCs and other retinal cell types and subsequently discuss viral approaches for dissecting retinal-brain connectivity. Together, these complementary strategies provide a powerful framework for linking molecular identity, circuit architecture, and visual function, thereby advancing both basic neuroscience and translational efforts in vision research.

RNA sequencing (RNA-seq) and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) are widely used for RNA quantification. RNA species with distinct structural and biogenetic features require specific computational and experimental approaches. Here, we provide an updated MiniResource that extends our previous guides to RNA-seq analysis and RT-qPCR-based RNA quantification. We introduce available tools and key considerations for analyzing circular RNAs, double-stranded RNAs, ribosomal RNAs, and transfer RNAs. This guide will help researchers choose appropriate methods for RNA species-specific quantification.

Liver cancer treatment with epigenetic drugs remains challenging because demethylating agents such as 5-azacytidine (5-AZA) induce genome-wide toxicity and may activate oncogenes. We hypothesized that a low, nontoxic dose of 5-AZA could prime liver cancer cells by partially relaxing chromatin at selected loci to restore silenced cell-death regulators. HepG2 cells treated with 2 μM 5-AZA underwent ATAC-seq and RNA-seq to identify genes with promoter opening and increased expression. Among ten candidates, BFL-1 and SQOR were prioritized for roles in cell death and redox control. Forced expression of either gene increased sensitivity to TNF-α/cycloheximide (CHX) and sorafenib, both of which elevated mitochondrial reactive oxygen species. To establish causality in a physiological context, we used CRISPR-dCas9-TET1 to demethylate CpG-rich promoter regions of BFL-1 or SQOR. Locus-specific editing sensitized cells to TNF-α/CHX more rapidly than conventional overexpression and reproduced the heightened death response elicited by low-dose 5-AZA without baseline toxicity. Analysis of the cancer cell line encyclopedia and The Cancer Genome Atlas datasets showed consistent BFL-1 downregulation in liver cancer, variable SQOR expression across cancers, and positive correlations of both genes with tumor-suppression markers and immune-cell infiltration. These results indicate that targeted reactivation of BFL-1 and SQOR increases cell-death susceptibility in liver cancer cells. Integrating low-dose pharmacologic priming with precise epigenetic editing may preserve genome-wide methylation while restoring cell-death competence, providing proof-of-concept for locus-specific epigenetic therapy in liver cancer.

Plant photoreceptors are well known for their roles in light-dependent developmental processes such as photomorphogenesis, shade avoidance, and circadian regulation. These canonical functions involve light perception through specific receptors, including phytochromes and cryptochromes, and downstream transcriptional reprogramming mainly in the context of early seedling growth. Beyond their classical roles, recent studies have revealed that photoreceptors also act as integrators of diverse environmental signals, contributing to abiotic stress adaptation, root development, and vascular differentiation. Notably, these non-canonical functions involve direct protein-protein interactions, post-translational modifications, and hormonal crosstalk, enabling photoreceptors to respond to environmental cues beyond light. Moreover, photoreceptor activity has been detected in tissues with limited or no light exposure, such as roots and adult vascular tissues, where they contribute to developmental and stress-responsive processes. In selected cases, particularly for phyB, non-light stress-related signals have been reported to modulate photoreceptor stability or subnuclear organization, suggesting that the functional repertoire of photoreceptors may extend beyond traditional photoperception. This review summarizes emerging insights into the non-canonical functions of photoreceptors in abiotic stress adaptation and root and vascular development, with particular focus on light-independent signaling, root-local photoreceptor activity, and non-cell autonomous light signaling. By integrating recent findings, we aim to provide a broader perspective on how photoreceptors serve as central regulators of plant plasticity in response to both light and non-light environmental factors, spanning from early to adult developmental programs.

Nuclear lamins provide structural integrity to the nuclear envelope through coiled-coil dimer meshworks. Lamin A contains a C-terminal immunoglobulin (Ig)-like domain and a cysteine-rich unstructured tail, whereas lamin C lacks the latter, retaining only 1 cysteine within the Ig-like domain. Mutations R435C and R471C in the Ig-like domain are linked to progeroid syndromes, fatal disorders characterized by premature aging. Here, we elucidate a pathogenic mechanism driven by aberrant disulfide cross-linking. We found that the R435C mutation, but not R471C, facilitates successive disulfide bond formation between Ig-like domains in vitro using purified recombinant proteins, causing nuclear deformation in lamin C-overexpressing cells. In lamin A-overexpressing cells, both R435C and R471C mutations induce additional intermolecular disulfide bonds involving the lamin A-specific cysteine residues in the C-terminal tail. Importantly, we demonstrate that glutathione and its precursor, N-acetyl cysteine, can disrupt these aberrant bonds. Using Caenorhabditis elegans as an in vivo model, we show that the orthologous cysteine mutation causes progeria phenotypes, which are suppressed by antioxidant treatment. These findings identify aberrant disulfide cross-linking as a key driver of progeria and suggest antioxidant therapies as a potential treatment strategy. Our study offers broader implications for vertebrate aging, suggesting that oxidative stress-mediated changes in lamin architecture are a conserved mechanism contributing to the loss of nuclear structural integrity and age-dependent nuclear aberration.

De novo variants in the ubiquitin-proteasome pathway are linked to autism spectrum disorder (ASD), yet their functional impact on neurodevelopment remains poorly understood. We investigated USP15, a deubiquitinating enzyme with rare damaging variants identified in individuals with ASD, using isogenic human iPSC-derived brain organoids and single-cell transcriptomics. USP15 mutant organoids showed genotype-dependent, progenitor-centered alterations during corticogenesis. Heterozygous organoids modeling haploinsufficiency displayed a shift toward later pseudotime states together with altered maturation and synaptic organization of deep-layer neurons. In contrast, homozygous organoids showed broader phenotypes, including mitotic suppression, aberrant HOX gene expression, and stress-response activation. Regulon analysis showed reduced activity of progenitor-associated regulons, including SOX2, NR2F1, and NR2F2, in heterozygous organoids, whereas homozygous organoids exhibited broader changes in transcriptional regulatory networks. Furthermore, USP15 mutant-associated gene expression patterns were significantly enriched for established ASD risk genes. Comparison with the mouse brain perturbation atlas showed that the transcriptional signature of the USP15 mutant showed notable overlap with those of Fezf2 and Foxp1 mutants, key regulators of deep-layer projection neuron identity. These findings characterize genotype-dependent neurodevelopmental phenotypes associated with reduced USP15 dosage and provide a human neural framework for investigating ASD-relevant developmental mechanisms in the context of a rare ubiquitin-pathway variant.

In vivo reprogramming using the Yamanaka factors (OCT4, SOX2, KLF4, and c-MYC; OSKM) enables tissue regeneration but raises major safety concerns when factor expression is sustained. Here, using a doxycycline-inducible OSKM mouse model, we show that prolonged systemic OSKM induction causes early lethality associated with hepatocyte dedifferentiation and oxidative stress in the absence of tumor formation. Single-nucleus RNA sequencing revealed activation of reactive oxygen species (ROS), oxidative stress, and NRF2 signaling pathways in hepatocytes. Increased ROS production in hepatocytes, together with the higher resistance of female mice and sex-dependent differences in antioxidant response programs, implicates oxidative stress as a primary driver of mortality during sustained OSKM expression. Importantly, antioxidant treatment with N-acetylcysteine (NAC) alleviated oxidative stress and significantly improved survival without impairing reprogramming-associated cellular plasticity. These findings establish oxidative stress as a key driver of liver failure during sustained in vivo reprogramming and provide a mechanistic rationale for cyclic induction strategies.

A member of the secretory calcium-binding phosphoprotein (SCPP) family, scpp5 is specifically expressed in zebrafish tooth germ. Although preliminary data indicates that scpp5 deficiency impairs tooth mineralization, its molecular mechanism and role in tooth repair remain unclear. In this study, we generated scpp5[-/-] knockout and Tg(hsp70l:scpp5-GFP; cryaa:venus) overexpression zebrafish lines. Tooth germ cells were labeled using Tg(dlx2b:Dendra2-NTR), and a tooth injury model was established via the nitroreductase (NTR)/metronidazole (MTZ) system. Loss-of-function studies showed that scpp5 knockout inhibited tooth mineralization and tooth germ cell development during normal development, attenuated Wnt/β-catenin signaling, downregulated calcium efflux channel gene expression, and suppressed both enameloid and dentin matrix-related genes. Rescue of Wnt pathway activity restored calcium efflux channel and dentin matrix gene expression, but not enameloid matrix gene expression. Gain-of-function studies revealed that scpp5 overexpression did not affect normal tooth development, but during repair after injury, it accelerated mineralization and cell regeneration. Mechanistically, scpp5 overexpression during repair activated Wnt/β-catenin signaling, specifically enhancing calcium channel and dentin matrix gene expression, without affecting enameloid matrix gene expression. Collectively, these findings demonstrate that scpp5 promotes tooth mineralization during normal development via Wnt/β-catenin-dependent regulation of both enameloid and dentin matrix genes, whereas during injury repair, scpp5 facilitates regeneration by selectively activating Wnt/β-catenin to drive dentin matrix and calcium channel gene expression, independent of enameloid matrix genes.

Organismal survival depends on coordinated responses to oxidative stress and DNA damage. Using Caenorhabditis elegans, we investigate mul-1, a robust transcriptional target of ionizing radiation and reactive oxygen species. Although annotated as a mucin, MUcin-Like 1 protein (MUL-1) is a small Stichodactyla helianthus K[+] channel toxin (ShKT) domain-containing protein belonging to an invertebrate expanded family of cysteine-rich proteins. mul-1 is selectively induced by oxidative stress, including ionizing radiation, hydrogen peroxide, Pseudomonas aeruginosa infection, or loss of the peroxiredoxin PeRoxireDoXin-2 (PRDX-2), via the p38 Mitogen-Activated Protein Kinase-cAMP-dependent Transcription Factor (MAPK-ATF-7) pathway in intestinal cells. Loss of mul-1 and its paralogs increases reactive oxygen species accumulation, oxidative stress sensitivity, and C. Elegans P53-like protein (CEP-1)/p53-dependent germ cell apoptosis. Combined deletion of mul-1 paralogs causes constitutive apoptosis, reduced fecundity, and compensatory activation of abnormal DAuer Formation (DAF)-16/FoxO and SKiNhead-1 (SKN-1)/Nuclear factor erythroid 2-related factor 2 (Nrf2) stress response pathways. Together with genetic analysis of SYstemic Stress signaling Mediator 1 (SYSM-1), these findings suggest MUL-1-like ShKT proteins buffer oxidative stress.

Voltage dependent anion channels (VDACs 1, 2 and 3) in the outer mitochondrial membrane control the flux of anions and oxidizable substrates that sustain mitochondrial metabolism. Nicotinamide adenine dinucleotide (NADH) closes VDAC by binding to a pocket, conserved in all isoforms, located in the inner wall of the channel. Previously, we identified the small molecule SC18 that targets the NADH-binding pocket of VDAC1 employing computational analysis. Here, we explored the interaction between SC18 and VDAC1 using high-resolution nuclear magnetic resonance spectroscopy and molecular dynamics simulations. Atomically resolved data precisely confirmed the computational results, showing that SC18 binds to a site on VDAC1 that partially overlaps with the NADH binding pocket. SC18, in the presence of NADH blocked the conductance of VDAC1 reconstituted in lipid bilayers. To determine the metabolic effect of SC18, we combined readouts of mitochondrial metabolism and glycolysis with functional metabolomics and proteomics. Short-term treatment with SC18 inhibited mitochondrial metabolism and adenosine triphosphate production. Treatment over 24 h and 48 h further reduced mitochondrial uptake of pyruvate and glutamine, utilization of tricarboxylic acid cycle intermediates, as well as lipid, DNA and amino acid synthesis. Concomitant with the inhibition of mitochondrial metabolism, cellular uptake of glucose and glutamine increased in parallel with augmented lactate release. These results indicate that compensatory enhanced glycolysis sustains adenosine triphosphate production after impaired mitochondrial function induced by SC18 blockage of VDAC1. Our work sets a mechanistic foundation for VDAC1 inhibition as a novel strategy to target and reprogram cancer metabolism through modulation of the biosynthetic ability of mitochondria.