Biology subjects

Saito, H.

Publications and source records attributed to Saito, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Alignment-free discovery of conserved RNA structures in the human genome

Many functional RNAs were first found as conserved RNA structures, and their roles in gene regulation were identified later. In humans and other vertebrates, imperfect genome alignments have hindered the discovery of such structures. Here we present RLMHelix, which selects candidate conserved RNA structures from single sequences before any alignment by scoring helices supported by language-model dependencies and thermodynamics. Through distillation, RLMHelix rapidly scans the transcribed human genome and ranks known RNAs higher than conventional thermodynamic scanning. Two-thirds of 15,821 candidates are new to four earlier genome-wide screens, yet agree with in-cell probing, and over half retain structural signal in homologues. In eCLIP data and in exploratory pull-downs, higher RLMHelix scores were associated with more binding by double-stranded RNA-binding proteins. By linking candidates to their binding proteins, RLMHelix yields testable functional hypotheses and illuminates a path from unrecognized human RNA structures to RNA biology and therapeutic targets.

bioinformatics↗

bioRxiv2026

Mycothiazole enables structural characterization of entire ubiquinone-accessing tunnel in mitochondrial respiratory complex I

Mitochondrial NADH-ubiquinone (UQ) oxidoreductase (respiratory complex I) reduces UQ within its long tunnel-like cavity, which is coupled to triggering proton translocation at the membrane domain. Although mammalian complex I adopts distinct "open" and "closed" conformations, the architecture of the UQ-accessing tunnel in the open conformation remains poorly defined owing to partial disorder of the UQ catalytic region near Fe-S cluster N2 in the tunnel. Here, we applied cryo-electron microscopy (EM) single particle analysis to determine the structures of complex I in bovine heart submitochondrial particles in the presence or absence of a mycothiazole-type inhibitor. Preceding photoaffinity labeling experiments using a synthetic photoreactive derivative ([125I]pMT) revealed that mycothiazole specifically labels the 49-kDa and ND1 subunits, both of which form a part of the UQ-accessing tunnel. Cryo-EM analysis demonstrated that bound mycothiazole reorganizes and stabilizes the UQ catalytic region in both open and closed conformations, enabling the first complete structural modeling of the entire UQ-accessing tunnel in the open conformation. Unexpectedly, in the presence of bound mycothiazole, loops of the PSST subunit forming the catalytic region in the tunnel adopted closed conformation-like features, whereas open conformation-like features were determined for the transmembrane helices of ND1 and ND6 subunits. The present study revealed that bound mycothiazole can reorganize the UQ catalytic region in the UQ-accessing tunnel and lead to a hybrid conformational state beyond the canonical open-versus-closed conformational model.

biochemistry↗

bioRxiv2026

Comprehensive functional mapping of accessory chromosomes identifies a dominant virulence-regulator paralog in tomato wilt pathogen

Accessory chromosomes (ACs) serve as flexible genomic compartments that facilitate rapid adaptive evolution in eukaryotic microbes. In the tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici, ACs are essential for virulence and host specificity; however, their structural complexity and functional redundancy have hindered a systematic characterization of their distinct roles. Here, we established a CRISPR/Cas9-based chromosomal dissection platform to generate a comprehensive functional map of pathogenicity determinants within ACs. Using this platform, we successfully generated a library of 36 large deletion mutants across the approximately 10 Mb putative AC region, enabling a chromosome-scale functional characterization of these compartments. A systematic screen of this library identified seven discrete AC segments that are indispensable for full virulence toward tomato. High-resolution chromosomal dissection of one virulence-associated segment through iterative subdivision and targeted gene disruption revealed that FTF1a-1, a single member of the Fusarium transcription factor 1 (FTF1) family that originated from the duplication of core-chromosomal virulence gene FTF2 into the AC region, functions as a dominant regulator of virulence. Given that the FTF1a-3 paralog contributes only marginally to virulence and the deletion of other paralogs does not markedly affect disease development, our findings demonstrate a functional hierarchy within the duplicated FTF1 gene family. These results imply that neofunctionalization of virulence genes within plastic fungal genomes promotes hyper-virulence and drives host-specific adaptation in F. oxysporum.

microbiology↗

bioRxiv2026

A cuffed CRISPR guide RNA for microRNA activity-dependent genome editing

Cells in multicellular eukaryotic systems are diverse biological units, with characteristics and functions determined by their molecular profiles. CRISPR-Cas9 genome editing has been widely used across biology to modulate gene expression and study gene function. However, there is currently no versatile and scalable method for editing a cells genome in response to endogenous cellular signals. Here, we report the engineering of a CRISPR guide RNA that efficiently confers genome editing in response to the catalytic activity of a target microRNA (miRNA) within a cell. miRNAs are short non-coding RNAs that are widely conserved across eukaryotes and can cleave their target RNA through almost perfect base pairing. In mammals, miRNAs are largely involved in development and homeostasis as well as disease progression and developmental disorders. To leverage these properties for genome editing, we developed a cuffed guide RNA (cgRNA) which is composed of a permutated order of sequence domains from the commonly used single guide RNA (sgRNA). These permutated domains were then concatenated with a miRNA target sequence, yielding a warped guide RNA that is inactive until cleaved by a complementary miRNA. We demonstrated that cgRNA enabled efficient miRNA activity-dependent genome editing in human and mouse cell lines. Biochemical and structural analyses revealed three stages of inhibition of the CRISPR genome-editing pathway for unprocessed cgRNA. Utilizing a lentiviral library of cgRNAs containing miRNA targets covering mouse genome-wide miRNAs, we identified miRNA cleavage activities and their sequence specificities in mouse embryonic stem cells and during smooth muscle cell differentiation. Furthermore, we showed that endogenous mRNA expression could be irreversibly recorded into a DNA sequence using a cgRNA targeted by a synthetic miRNA repeat. cgRNA is a simple, robust, miRNA activity-gated genome editing system that could facilitate the development of cell state-specific genome editing, the mapping of miRNA activity and gene expression landscapes, and the recording of molecularly determined cell states during the long-term progression of multicellular systems.

bioengineering↗

bioRxiv2026

Historical rice samples from the 1950s reveal pre-modern-breeding population structure in indica landraces of mainland Southeast Asia

Understanding crop population history requires genetic material that predates modern breeding. Here, we analyzed historical seeds of rice landraces assembled in Southeast Asia from 1957 to 1958. Target capture resequencing of coding regions yielded high-quality genomic data from 66 historical accessions (seven from North Vietnam, 30 from South Vietnam, 13 from Cambodia, two from Laos, and 14 from Thailand). When integrated with published rice panels, all historical accessions were assigned to indica, and the previously described major regional structure was recovered. Within the historical collection, South Vietnamese, Cambodian, and Thai accessions formed a largely continuous group, whereas North Vietnamese accessions were clearly distinct and comprised two differentiated groups corresponding to the traditional growth seasons (fifth- and tenth-month rice). Notably, the fifth-month rice accessions were assigned to the recently reported Vietnam-I5 cluster. Admixture graph, f-statistics, and qpAdm analyses further indicated that Vietnam-I5 is closely related to a China-associated lineage; however, this relationship was not fully explained by sampled indica, japonica, or aus proxies. Together, these results show that major components of the present-day indica regional structure were already present before modern cultivar replacement, and highlight northern Vietnam as a historical zone of lineage differentiation between Chinese and mainland Southeast Asian rice. HighlightGenomic analyses of historical indica rice seeds reveal that a distinctive northern Vietnamese lineage and a genetic continuum across southern Vietnam, Cambodia, and Thailand predated modern cultivar replacement.

plant biology↗

bioRxiv2026

Targeting integrin αvβ3 by chimeric antigen receptor neural stem cell (CAR-NSC) therapy for stroke

Stroke remains a leading cause of adult disability due to the brains limited regenerative capacity. Although stem cell therapies show favorable safety and feasibility profiles in early clinical trials, poor spatial retention and limited engagement with peri-infarct salvageable tissue constrain efficacy. Here, we engineered human induced pluripotent stem cell-derived neural stem cells (NSC) with a chimeric antigen receptor (CAR)-like architecture to enable targeted recognition of injury-associated cues. Specifically, cells were modified to express a membrane-anchored single chain variable fragment (scFv) targeting integrin v{beta}3, a receptor selectively upregulated in peri-infarct vasculature after stroke. Engineered CAR-NSC retained progenitor identity and selectively bound recombinant integrin v{beta}3 in vitro. Following focal transplantation into a photothrombotic stroke mouse model, CAR-NSC displayed broader dispersion within peri-infarct tissue and covered a greater proportion of the ischemic lesion compared to non-binding control-CAR-NSC. CAR-NSC grafts extended longer neurites that aligned more closely with the lesion border. In addition, CAR-NSC transplantation reduced microglial activation and was associated with increased vascular density and blood-brain barrier integrity in the peri-infarct zone. Together, these findings establish a CAR-like NSC strategy for stroke to direct the spatial distribution and tissue engagement of transplanted cells. Molecular targeting of injury-associated cues may improve the precision and regenerative efficacy of cell-based therapies for stroke and related neurological disorders.

neuroscience↗

bioRxiv2025

Transient let-7/miR-98 reprograms primed pluripotency to induce naivehuman PSCs

Naive human pluripotent stem cells (hPSCs) are valuable for modeling early development and enabling regenerative applications, yet resetting from the primed state remains inefficient and mechanistically unclear. We identify an unexpected role for miR-98-5p, a let-7 family microRNA (miRNA) typically linked to differentiation, in promoting naive induction. Using a synthetic mRNA screen containing diverse miRNA-responsive elements, we uncovered miR-98-5p as a potent enhancer of resetting. Single-cell RNA sequencing and targeted perturbations show that miR-98-5p directly represses NR6A1 while transiently activating BMP2/4 signaling, triggering network transitions. These changes destabilize the primed gene-regulatory network and enable acquisition of a naive state. Leveraging this mechanism, we establish a feeder-free, miRNA-based, editing-free protocol that boosts resetting efficiency from <10% to [~]80%. To our knowledge, this is the first demonstration that a let-7 miRNA can drive naive induction by coupling direct target repression with activation of pro-naive signaling, suggesting a generalizable reprogramming principle of transient network destabilization.

developmental biology↗

bioRxiv2025

Developmental Reorganization of Whole-Body Muscle Synergies During Overarm Throwing in Children

Overarm throwing is a uniquely human skill that requires precise whole-body coordination. Although throwing behavior emerges early in childhood, the neuromuscular mechanisms that support its development remain poorly characterized. Here, we provide novel evidence for the developmental reorganization of whole-body muscle synergies during maximum-effort throwing in preschool-aged (PS) and school-aged (SA) children. Electromyography was recorded from 16 muscles, and non-negative matrix factorization was applied to extract low-dimensional coordination modules (muscle synergies). We compared ball speed, number of synergies, synergy structure, and temporal consistency between groups. Ball speed was significantly higher in SA than PS (33.6 {+/-} 10.2 vs. 21.4 {+/-} 6.2 km/h, p < 0.05), reflecting improved performance. Yet, the number of synergies did not differ (PS: 6.0 {+/-} 1.1; SA: 6.4 {+/-} 1.3, p > 0.05), suggesting that the dimensionality of coordination is largely established by the preschool years. Instead, developmental improvements were driven by structural and temporal reorganization: trunk- and upper-limb synergies merged into a single module in SA, reflecting improved postural integration, while a bilateral soleus-dominant synergy fractionated into lateralized modules, reflecting increased lower-limb specialization. Moreover, the temporal variability of synergy activation was reduced in SA (p < 0.01), indicating that movement sequences became more precise and stable with development. These findings reveal that early gains in throwing arise not from expanding synergy number but from reorganizing their structure and sharpening temporal coordination, offering mechanistic insight into how complex whole-body skills are refined during childhood. Significance StatementThrowing is a hallmark of human motor behavior, requiring precise sequencing of whole-body muscle activity. Yet how children develop this ability has remained unclear. By applying muscle synergy analysis to electromyographic recordings of preschool and school-aged children performing maximum-effort throws, we found that improvements in performance were not due to an increase in synergy number but rather to structural reorganization and greater temporal precision. Specifically, trunk and upper-limb modules merged, lower-limb modules fractionated, and activation timing became more consistent. These results identify merging and fractionation as complementary mechanisms supporting developmental refinement of motor skills. More broadly, they provide a mechanistic framework for understanding how complex whole-body actions are acquired and offer markers for pediatric training and rehabilitation strategies.

neuroscience↗

bioRxiv2025

Natural variation in IBF1 disrupts its interaction with CHS1 and affects metabolism of hulls in rice

Secondary metabolites in plants have various physiological functions, including antioxidant and antibacterial activities. Previous studies have suggested genes and associated molecular mechanisms involved in the production of diverse secondary metabolites. However, much less is known about the genetic bases underlying within-species diversity in metabolite accumulation patterns, particularly in less focused tissues such as rice hulls. In this study, we aimed to identify the causal variant that affects flavonoid accumulation in rice hulls. We identified an F-box containing protein IBF1 is causal for genotypic differences in hull color through positional cloning. The variety IR64, with straw-white hulls, harbors functional IBF1 proteins that interact with a chalcone synthase, CHS1. Conversely, frame-shift mutations of IBF1 in the variety DJ123, which has pigmented hull color, resulted in a lack of a Kelch domain essential for the IBF1-CHS1 interaction. As a result, the DJ123 variant of IBF1 (IBF1DJ123) no longer interacted with CHS1, which was further supported by deep learning-based protein structural modeling. Further metabolome and transcriptome analyses using IR64 and an IR64-based chromosomal segment substitution line (CSSL) carrying IBF1DJ123 revealed an increase in the content of multiple flavonoids (such as naringenin and luteolin), while suppressing the expression of CAD involved in lignin synthesis. Metabolites in the CSSL carrying IBF1DJ123 suppressed the growth and siderophore generation activity of Pantoea species, which can act as beneficial or pathogenic endophytes. This study highlights the impact of a single gene on diverse metabolite accumulation patterns and suggests that this change may provide defense against pathogens.

plant biology↗

bioRxiv2025

Contrasting ecological communities in rice paddy fields under conventional and no-fertilizer farming practices

Global crop production is essential for providing energy and nutrients to humans, but agricultural systems contribute substantially to environmental issues, making it crucial to find sustainable methods for crop production. In this study, we conducted extensive field monitoring of two rice paddy fields in Kyoto Prefecture, Japan, where a rice variety, Hinohikari, was cultivated to investigate how ecological communities influence rice growth and yields under two contrasting farming practices: conventional farming and no-fertilizer farming. We had three objectives: (1) to monitor rice growth and ecological dynamics to create a comprehensive ecological time series using quantitative environmental DNA metabarcoding and complementary monitoring methods, (2) to identify ecological variables that causally affect rice performance using nonlinear time series analysis, and (3) to examine the effects of the two farming practices on ecological variables and rice performance. As expected, the no-fertilizer paddy field showed lower rice growth and yields but still produced 40-50% of the yields of the conventional field. Ecological monitoring revealed contrasting ecological communities between the two fields, particularly among plant species on the paddy ridges and microbial taxa. Twenty-five taxa had statistically clear causal influences on rice performance. While the per-abundance influences of the causal taxa were largely similar in both paddy fields, their abundances were different, contributing to the differences in the overall effects of these taxa on the rice performance. These findings suggest that the abundance of causal taxa, along with nutrient conditions, may have driven differences in rice growth between the two paddy fields.

ecology↗

bioRxiv2025

The common neural representation in the primary motor area between motor execution and kinesthetic motor imagery

Although motor imagery activates higher-order motor-related areas, the role of the primary motor area (M1) in motor imagery remains unclear. This study aimed to investigate whether motor imagery recruits a neural representation of fingers similar to that of motor execution in the hand M1. Ten healthy right-handed adults executed and kinesthetically imagined tapping using one of four fingers. Using functional magnetic resonance imaging with multi-voxel pattern analysis, we trained the decoder to classify which finger the participants were moving using brain activation during motor execution and tested whether it could predict which finger the participants were imaging to move during motor imagery (cross-classification). We also performed the classification in the reverse direction. The average accuracy of these cross-classifications was significantly higher than chance in the left hemisphere hand M1 (hand-M1). Analysis of the representational geometry showed that the distance of neural representations for the same fingers was statistically shorter than that for different fingers between motor execution and imagery. Furthermore, we conducted a replication study with 14 participants and found results similar to those of the original study. Our results suggest that the neural representation of kinesthetic motor imagery is partially similar to that of motor execution in the contralateral hand M1.

neuroscience↗

bioRxiv2025

Identification of an early-heading mutant in Indonesian native rice cultivar: 'Gemdjah Beton'

Rice is one of the worlds most widely cultivated field crops and a short-day adapted plant. It possesses a complex genetic regulatory mechanism for heading date determination. Gemdjah Beton (GB) is an Indonesian rice cultivar that takes approximately 17 weeks to flower after being transplanted into a rice field in Japan. We isolated early-heading mutant line GB-10 (flowers around two to three weeks early in the field). Under long-day (LD) conditions, GB-10 flowered approximately two weeks earlier than GB. Under short-day conditions, the heading date between GB-10 and GB plants shows no apparent difference. In agreement with the heading date, Hd3a and RFT1 expressions show around a 10-time relative transcript quantity difference under LD conditions in GB-10 compared to GB. Interestingly, Ghd7 expression was significantly reduced in GB-10, which may trigger the Hd3a and RFT1 activation. A bulk segregation analysis indicated that a single nucleotide variant on chromosome 7 was genetically linked to the early heading phenotype of GB-10 lines. Taken together, we reported the successful isolation of GB-10 as an early-heading mutant.

plant biology↗

bioRxiv2024

IL-13/IL-13Rα2 axis promotes proliferation of angiosarcoma cells

Angiosarcoma is a rare and aggressive soft tissue sarcoma with a poor prognosis and limited treatment options. The role of interleukin-13 (IL-13) and its receptors in angiosarcoma pathogenesis has been largely unknown. We detected high IL-13 receptor 2 (IL-13R2) expression in angiosarcoma cell lines and patient samples compared to other cell types and benign vascular tumors. Moreover, histological analysis showed the presence of IL-13 in the angiosarcoma microenvironment. Functional studies using angiosarcoma cell lines, MO-LAS-B cells, revealed the promoting effect of IL-13 on cell proliferation. The effect was inhibited by siRNA-mediated knockdown of IL13RA2 or neutralizing antibodies against IL-13, suggesting the direct impact of IL-13/IL-13R2 axis in the angiosarcoma proliferation. In addition, IL-13 stimulation increased mRNA levels of IL13RA2 and VEGFA, suggesting an underlying positive feedback mechanism, which was attenuated by a STAT6 inhibitor. These findings highlight the importance of the IL-13/IL-13R2 axis in angiosarcoma progression and its potential as a novel therapeutic target for this challenging malignancy.

cancer biology↗

bioRxiv2024

Split RNA switch: Programmable and precise control of gene expression by ensemble of pre- and post-translational regulation

Regulating gene expression in response to biomolecules is a powerful strategy for monitoring intracellular environments and controlling cellular programs. RNA switch is a synthetic mRNA-based technology that controls gene expression at the translational level in response to cellular RNA and protein molecules, thus enabling cell type-specific gene regulation and showing promise for gene therapy, regenerative medicine, and cell therapy. However, single RNA switches often lack the specificity required for practical applications due to low ON/OFF ratios and difficulty in finding distinct and single biomolecule targets. To address these issues, we developed "split RNA switches" that integrate outputs from multiple RNA switches by exploiting protein splicing, a post-translational modification mechanism. We demonstrated that split RNA switches significantly improve the ON/OFF ratio of microRNA (miRNA)-responsive ON switch systems by canceling undesirable leaky OFF level. We achieved efficient and robust target cell purification based on endogenous miRNA profiles, which was impossible with an ON switch alone. Additionally, we constructed multi-output and multi-input RNA-based synthetic circuits using split RNA switches to enable the detection of multiple miRNAs for precise gene control with logical operations. Split RNA switches illustrate a novel application of protein splicing and demonstrate the potential of post-translational processing as a comprehensive solution for advancing translational control technologies toward widespread mRNA therapies.

synthetic biology↗

bioRxiv2023

Low blood concentration of alcohol enhances activity related to stopping failure in the right inferior frontal cortex

This study investigated the effects of low doses of alcohol, which are acceptable for driving a car, on inhibitory control and neural processing using the stop-signal task (SST) in 17 healthy right-handed social drinkers. The study employed simultaneous functional magnetic resonance imaging and electromyography (EMG) recordings to assess behavioural and neural responses under conditions of low-dose alcohol (breath-alcohol concentration of 0.15 mg/L) and placebo. The results demonstrated that even a small amount of alcohol consumption prolonged Go reaction times in the SST and modified stopping behaviour, as evidenced by a decrease in the frequency and magnitude of partial response EMG that did not result in button pressing during successful inhibitory control. Furthermore, alcohol intake enhanced neural activity during failed inhibitory responses in the right inferior frontal cortex, suggesting its potential role in behavioural adaptation following stop-signal failure. These findings suggest that even low levels of alcohol consumption within legal driving limits can greatly impact both the cognitive performance and brain activity involved in inhibiting responses. This research provides important evidence on the neurobehavioural effects of low-dose alcohol consumption, with implications for understanding the biological basis of impaired motor control and decision-making and potentially informing legal guidelines on alcohol consumption.

neuroscience↗

bioRxiv2023

Tgif1-deficiency impairs cytoskeletal architecture in osteoblasts by suppressing PAK3 signaling

Osteoblast adherence to bone surfaces is important for remodeling of the bone tissue. This study demonstrates that deficiency of TG-interacting factor 1 (Tgif1) in osteoblasts results in altered cell morphology, reduced adherence to collagen type I-coated surfaces, and impaired migration capacity. Tgif1 is essential for osteoblasts to adapt a regular cell morphology and to efficiently adhere and migrate on collagen type I-rich matrices in vitro. Furthermore, Tgif1 acts as transcriptional repressor of p21-activated kinase 3 (PAK3), an important regulator of focal adhesion formation and osteoblast spreading. Absence of Tgif1 leads to increased PAK3 expression, which impairs osteoblast spreading. Additionally, Tgif1 is implicated in osteoblast recruitment and activation of bone surfaces in the context of bone regeneration and in response to parathyroid hormone 1-34 (PTH 1-34) treatment in vivo. These findings provide important novel insights in the regulation of the cytoskeletal architecture of osteoblasts.

cell biology↗

bioRxiv2023

SERF2, an RNA G-quadruplex Binding Protein, promotes stress granule formation

Liquid-liquid phase transitions govern a wide range of protein-protein and protein-RNA interactions. Although the importance of multivalency and protein disorder in driving these transitions is clear, there is limited knowledge concerning the structural basis of phase transitions or the conformational changes that accompany this process. In this work, we found that a small human protein, SERF2, is important for the formation of stress granules. We determined the solution NMR structure ensemble of SERF2. We show that SERF2 specifically interacts with non-canonical tetrahelical RNA structures called G-quadruplexes, structures linked to stress granule formation. The biophysical amenability of both SERF2 and RNA G4 quadruplexes have allowed us to characterize the multivalent protein-RNA interactions involved in liquid-liquid phase transitions, the role that protein disorder plays in these transitions, identify the specific contacts involved, and describe how these interactions impact the structural dynamics of the components enabling a detailed understanding of the structural transitions involved in early stages of ribonucleoprotein condensate formation.

cell biology↗

bioRxiv2023

Pateamine A mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs

Small-molecule compounds that elicit mRNA-selective translation repression have attracted interest due to their potential for expansion of druggable space. However, only limited examples have been reported to date. Here, we show that pateamine A (PatA) represses translation in an mRNA-selective manner by clamping eIF4A, a DEAD-box RNA-binding protein, on GNG motifs. Through a systematic comparison of multiple eIF4A inhibitors by ribosome profiling, we found that PatA has unique mRNA selectivity in translation repression. Unbiased Bind-n-Seq revealed that PatA-targeted eIF4A exhibits a sequence preference for GNG motifs in an ATP-independent manner. This unusual RNA binding sterically hinders scanning by 40S ribosomes. In silico simulation, combination of classical molecular dynamics simulation and quantum chemical calculation, and the subsequent development of an inactive PatA derivative revealed that the positive charge of the tertiary amine on the trienyl arm induces G selectivity. Moreover, we identified DDX3, another DEAD-box protein, as an alternative target of PatA, showing the same effect as on eIF4A. Our results provide an example of the sequence-selective anchoring of RNA-binding proteins and mRNA-selective inhibition of protein synthesis by small-molecule compounds.

molecular biology↗