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.
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, 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.
Melanoma metastasis involves dynamic cellular reprogramming that enables tumor cells to survive detachment and disseminate to distant organs. We investigated the role of adherent-to-suspension transition (AST) in melanoma metastasis, examining its dynamics during metastatic dissemination and its relationship with epithelial-to-mesenchymal-like transition (EMT-like transition). Our findings reveal that AST genes, IKZF1, IRF8, and NFE2, critically modulate anchorage dependence through the regulation of cell adhesion and survival pathways. AST gene expression exhibits dynamic plasticity throughout the metastatic cascade, peaking in circulating tumor cells and reverting in established metastases. Clonal phylogenetic reconstruction reveals that AST-high circulating tumor cell clones possess enhanced metastatic capacity and dominate distant lesions. Notably, AST enhances metastatic capabilities and invasiveness in melanoma independently of EMT-like transition. Spatial analysis further indicated that AST-positive tumor cells preferentially localize near blood vessels, suggesting a facilitating role in blood-borne metastasis. These findings provide new insights into the mechanisms driving melanoma metastasis and highlight AST as a key factor contributing to tumor cell plasticity and dissemination.
Despite growing understanding of the various roles mitochondria play in neurons, how they contribute to higher brain functions such as learning and memory remains underexplored. Here, using the nematode Caenorhabditis elegans, we found that the mitochondrial calcium uniporter (MCU) pore-forming unit MCU-1 is required for aversive learning of specific odors sensed by the AWC sensory neuron. MCU-1 expression was required in the sensory neuron at the time of odor conditioning for proper behavioral response to 60 min of prolonged odor exposure. We discovered that calcium entry into the mitochondria in AWC responds to the length of odor stimulus: calcium is elevated after 60 minutes of odor but not after 30 minutes, suggesting a gating mechanism that can discriminate the duration of sensory stimuli. Through genetic and pharmacological manipulation, we show that calcium influx through the MCU causes mtROS production, leading to NLP-1 secretion from the AWC neuron and odor learning. Overall, our results demonstrate that, by regulating mitochondrial calcium entry, mitochondria can respond to the length of a sensory stimulus to modulate the synaptic response, resulting in context-appropriate learning and behavior.
The pharmaceutical industry is currently engaged in an intense competition to maximize weight reduction percentages. The evolution from standard glucagon-like peptide-1 (GLP-1) receptor agonists to dual and triple agonists and even more complex combinations has fundamentally shifted clinical benchmarks and investor expectations. We are now witnessing targets of 30% to 40% of body mass, a range that could be achieved only through bariatric surgery previously. However, this numerical obsession is starting to decouple the metric of weight loss from the real objective of metabolic health. By focusing purely on total mass reduction, the industry risks sacrificing metabolic integrity and vital physiological components like muscle mass in the pursuit of higher percentages (Figure 1).
Serine metabolism is pivotal in regulating immune cell function and molding the host microenvironment during infection, yet its impact on antimycobacterial immunity remains elusive. Here, we probe the role of serine metabolism in Mycobacterium tuberculosis (Mtb)-infected macrophages. We reveal that Mtb infection induces enzymes associated with the serine synthesis pathway (SSP) and serine transporters. Moreover, inhibition of the key SSP enzyme or restriction of exogenous serine boosts antimycobacterial immunity in both in vitro and in vivo. Depletion of serine reduces reactive oxygen species (ROS) levels by diminishing the levels of reduced nicotinamide adenine dinucleotide. This ROS reduction destabilizes hypoxia-inducible factor 1 alpha, impairing glucose uptake and adenosine triphosphate (ATP) production. Consequently, reduced ATP production activates adenosine monophosphate-activated protein kinase, which inhibits mTOR and induces autophagy, thereby exerting an antimycobacterial effect. These findings underscore serine's role as a crucial immune metabolite during Mtb infection and propose that manipulating serine metabolism holds therapeutic promise against mycobacterial infections.
Elucidating molecular interactions such as protein-DNA (PDIs) and protein-protein (PPIs) has traditionally relied on yeast-based 1-hybrid (1H) and 2-hybrid (2H) systems. To provide an alternative platform that better reflects the native cellular environment of plants, we optimized the tRUBY reporter system for 1H and 2H assays in Nicotiana benthamiana, enabling direct in planta analysis of PDIs and PPIs. Specifically, the 2A peptide sequence used for co-expressing the 3 betalain biosynthetic genes-responsible for the visible RUBY coloration-was replaced with T2A from the Thosea asigna virus in place of P2A or F2A from mammalian-pathogenic Picornaviridae viruses, improving biosafety for agricultural applications. The resulting tRUBY-1H and tRUBY-2H systems operate under near-physiological conditions with physiologically relevant expression levels, enabling quantitative, multiplexed, and directly compatible protein-level analyses, thereby offering high sensitivity and flexibility for advanced molecular studies. Ultimately, these systems demonstrate that the streamlined, cost-effective, and visually scorable in planta platform provided by RUBY is well-suited for intuitive, non-destructive monitoring of molecular interactions in plant tissues.
The 2025 volume of Molecules and Cells connects molecular and cellular pathways to physiology and disease, emphasizing genome and RNA maintenance, cell-level regulation, stress resistance, cancer, and immunity. This Editorial introduces the Molecules and Cells papers published in 2025 from a molecule-to-organism perspective.
The precise assembly of neural circuits is a marvel of cellular engineering, requiring the seamless coordination of long-range axon navigation and short-range synapse formation. Traditionally, these 2 processes were thought to be governed by distinct sets of molecular cues. However, emerging evidence challenges this dichotomy, revealing that proteins canonically associated with mature synaptic transmission are "repurposed" early in development to instruct selective neuronal pairing, including axon guidance and target recognition. In this mini-review, we discuss the molecular versatility of key synaptic proteins, including latrophilins, N-methyl-D-aspartate receptors, cerebellins, neurexins, and other complementary adhesion systems. We highlight how these molecules utilize non-canonical mechanisms, such as ion flux-independent signaling and trans-neuronal adhesion, to couple initial wiring decisions with later synaptic specialization. This functional duality suggests a "molecular continuum" in brain development, offering broader insights into how cells maximize their proteomic toolkit to build complex biological systems.
Drosophila melanogaster is a powerful genetic model organism due to its short life cycle, simple husbandry, and versatile genetic toolkit. Reliable experimental outcomes, however, depend on standardized husbandry and stock maintenance practices that are often underemphasized in research protocols. Here, we provide a concise, practical guide covering essential procedures for Drosophila culture conditions, anesthetization, phenotypic sorting, genetic crosses, developmental synchronization, and use of stock center resources. By documenting the standard methodologies and practices, this guide aims to help researchers, particularly trainees and newcomers, establish and maintain healthy fly stocks and minimize common pitfalls. These standardized practices will improve reproducibility and enable more effective use of the extensive genetic resources available in Drosophila research, thereby enhancing its utility across diverse fields of biology.
Calcium/calmodulin-dependent serine protein kinase (CASK) is an X-linked multidomain scaffolding protein originally identified as an intracellular binding partner for Neurexins, a family of presynaptic cell-adhesion molecules. Loss-of-function mutations in CASK cause microcephaly with pontine and cerebellar hypoplasia (MICPCH), a severe neurodevelopmental disorder predominantly affecting females. Although CASK has been implicated in synaptic organization and transcriptional regulation, the mechanisms underlying the cerebellar hypoplasia have remained unsolved. Recent studies using genetically engineered mouse models and cerebellar granule cell cultures suggest that CASK is essential for neuronal survival rather than for initial patterning in the cerebellum. These works further reveal that X-chromosome inactivation-driven mosaicism influences the pathology of this disorder and that CASK deficiency activates c-Jun N-terminal kinase (JNK) signaling. In this review, we integrate these findings with the synaptic cell-adhesion biology, in relevance to Neurexin-CASK interaction and role of CASK in cerebellar neuron survival and discuss emerging therapeutic implications for CASK-related disorders.
Virus-induced genome editing (VIGE) is expanding plant functional genomics by enabling precise and heritable genome modification across diverse species. While classical model systems such as Arabidopsis thaliana have provided foundational genetic insights, many ecologically, agriculturally, and chemically important traits reside in species that remain difficult to manipulate genetically. By coupling CRISPR-Cas systems with plant viral vectors, VIGE bypasses key limitations of conventional transformation and enables rapid mutagenesis without repeated tissue culture and plant regeneration. This approach enables researchers to examine gene function in species selected for biological relevance rather than technical convenience. Here, we review the conceptual framework, technical considerations, and applications of VIGE, and discuss its current limitations and future prospects in ecological, evolutionary, and crop research.
