Biology subjects

Matsushima, T.

Publications and source records attributed to Matsushima, T..

9 recordsLinked to original sources

bioRxiv2026

NAT10 supports CAG repeat-associated mRNA stabilization and is associated with hepatic metabolic reprogramming during spaceflight

The regulatory factors underlying posttranscriptional adaptation to spaceflight are incompletely understood. We identified NAT10, an RNA acetyltransferase, among RNA modification enzymes significantly upregulated in spaceflight-exposed mouse liver. Transcriptome-wide correlation analysis linked NAT10 expression to an RNA-metabolism module enriched for CAG repeat density in coding sequences. Actinomycin D chase assays showed that NAT10 knockdown destabilized CAG repeat-containing transcripts, with DDX17 serving as the primary validated target; DCP1A showed a directionally consistent pattern. Wild-type NAT10 re-expression fully rescued DDX17 mRNA stability, the acetyltransferase-dead G641E mutant rescued mRNA stability to a comparable extent, and the K290A helicase-domain mutant failed to rescue, consistent with a requirement for helicase domain integrity, whereas acetyltransferase activity was not strictly required under these experimental conditions. RNA immunoprecipitation further supported preferential NAT10 association with CAG repeat-containing mRNAs, with reduced association after single-site CAGCAG deletion in DDX17 and DCP1A reporters. Gene set enrichment analysis associated NAT10 upregulation in spaceflight liver with suppressed fatty acid beta-oxidation and induced cholesterol biosynthesis; NAT10 depletion in hepatocellular carcinoma cells selectively opposed the cholesterol-associated, but not the broader metabolic, component of this signature. These findings support a model linking NAT10 to CAG repeat-associated mRNA stabilization in the context of hepatic metabolic and posttranscriptional adaptation to spaceflight.

molecular biology↗

bioRxiv2026

One-step generation of mice by Transposon-Enhanced Multi-Plex Orchestration Editing(TEMPO-Editing)

Genome-edited mice are widely used to elucidate molecular mechanisms in vivo and are an indispensable tool, particularly for studies aimed at clarifying gene function at the organismal level. Currently, there is an increasing demand for mice in which multiple genes are simultaneously modified in order to investigate interactions among multiple genes. Notably, generating conditional multiple-gene knockout mice with temporal and spatial specificity requires extensive crossing between multiple Cre-driver mice and floxed mice, resulting in a prolonged time frame for line establishment. To address this limitation, we developed Transposon-Enhanced Multi-Plex Orchestration Editing (TEMPO-editing), a single-step strategy for generating multiple-gene-edited mice. TEMPO-editing enables simultaneous modification of multiple genes through the integration of transposon, Cre-loxP, and CRISPR/Cas9 systems. Using the DNA transposon piggyBac, we constructed a single cassette harboring gRNAs targeting genes of interest together with a conditionally expressed Cas9 (lsl-Cas9). By injecting this cassette into fertilized eggs of Cre mice, we enabled the generation of temporally and spatially specific genome edited mice in the F0 generation. In this study, we generated double-gene-edited mice targeting Hoxa13 and Hoxd13, which are key regulators of embryonic body patterning and are essential for autopod development. The phenotype observed in these mice was consistent with the incomplete autopod phenotype previously reported in mice generated by crossing Hoxa13 knockout and Hoxd13 knockout mice. These results demonstrate the utility of TEMPO-editing for the generation of multiple-gene-edited mice in the F0 generation. Notably, this study establishes a simplified strategy for producing conditional multi-gene-edited mice, a process that has traditionally required substantial time and labor using conventional methods.

developmental biology↗

bioRxiv2024

Single-nucleus transcriptional and chromatin accessibility analyses of maturing mouse Achilles tendon uncover the molecular landscape of tendon stem/progenitor cells

Tendons and ligaments are crucial connective tissues linking bones and muscles, yet achieving full functional recovery after injury remains challenging. We investigated the characteristics of tendon stem/progenitor cells (TSPCs) by focusing on the declining tendon repair capacity with growth. Using single-cell RNA sequencing on Achilles tendon cells from 2-and 6-week-old mice, we identified Cd55 and Cd248 as novel surface antigen markers for TSPCs. Combining single-cell RNA sequencing with single-nucleus RNA and ATAC sequencing analyses revealed that Cd55 and Cd248 positive fractions in tendon tissue represent TSPCs, as confirmed by their expression of established TSPC markers, with this population decreasing at 6 weeks. We also identified candidate upstream transcription factors regulating these fractions. Functional analyses of isolated CD55/CD248 positive cells demonstrated high clonogenic potential and tendon differentiation capacity, forming functional tendon-like tissue in vitro. This study establishes CD55 and CD248 as novel TSPC surface antigens, potentially advancing tendon regenerative medicine and contributing to the development of new treatment strategies for tendon and ligament injuries.

developmental biology↗

bioRxiv2024

Embryonic exposure to valproic acid and neonicotinoid deteriorates the developmental GABA switch and impairs long-term potentiation in the local circuit of intermediate medial mesopallium of chick telencephalon

Embryonic exposure to valproic acid (VPA) and imidacloprid (IMI, a neonicotinoid insecticide) impairs filial imprinting in hatchlings, and the deteriorating effects of VPA are mitigated by post-hatch injection of bumetanide, a blocker of the chloride intruder NKCC1. Here, we report that these exposures depolarized the reversal potential of local GABAergic transmission in the neurons of the intermediate medial mesopallium (IMM), the pallial region critical for imprinting. Furthermore, exposure increased field excitatory post-synaptic potentials in pre-tetanus recordings (fEPSPs) and impaired long-term potentiation by low-frequency tetanic stimulation (LTP). Bath-applied bumetanide rescued the impaired LTP in the VPA slices, whereas VU0463271, a blocker of the chloride extruder KCC2, suppressed LTP in the control slices, suggesting that hyperpolarizing GABA action is necessary for the potentiation of excitatory synaptic transmission. However, the transcriptional profiles of IMM slices did not support the expected increase in the NKCC1/KCC2 ratio, suggesting a potential modification of post-transcriptional processes. Instead, exposure to both VPA and IMI downregulated several transcriptional regulators (FOS, NR4A1, and NR4A2) and upregulated the RNA component of signal recognition particles (RN7SL1). As a limited set of response genes were shared, VPA and IMI could cause common neuronal malfunctions via distinct molecular cascades.

neuroscience↗

bioRxiv2023

Leveraging Machine Learning to Uncover the Hidden Links between Trusting Behavior and Biological Markers

Understanding the decision-making mechanisms underlying trust is essential, particularly for patients with mental disorders who experience difficulties in developing trust. We aimed to explore biomarkers associated with trust-based decision-making by quantitative analysis. However, quantification of decision-making properties is difficult because it cannot be directly observed. Here, we developed a machine learning method based on Bayesian hierarchical model to quantitatively decode the decision-making properties from behavioral data of a trust game. By applying the method to data of patients with MDD and healthy controls, we estimated model parameters regulating trusting decision-making. The estimated model was able to predict behaviors of each participant. Although there is no difference of the estimated parameters between MDD and healthy controls, several biomarkers were associated with the decision-making properties in trusting behavior. Our findings provide valuable insights into the trusting decision-making, offering a basis for developing targeted interventions to improve their social functioning and overall well-being.

bioinformatics↗

bioRxiv2022

Impaired Epigenesis of Imprinting Predispositions Causes Autism-like Behavioral Phenotypes in Domestic Chicks

Several environmental chemicals are suspected as risk factors for autism spectrum disorder (ASD), including valproic acid (VPA) and pesticides acting on nicotinic acetylcholine receptor (nAChR) if exposed during pregnancy. However, their target processes in fetal neuro-development are unspecified. We report that fetal injection of VPA impaired the imprinting of an artifact object in hatchlings, while the predisposed preference to biological motion (BM) remained intact. Blockade of nAChR acted oppositely, namely, spared imprinting and impaired BM in chicks. Beside ketamine and tubocurarine, significant effects of imidacloprid (a neonicotinoid insecticide) appeared at dose [≤]1ppm. Despite the distinct processes, both VPA and nAChR blockade similarly impaired imprinting of biological image composed of point-light animation. Furthermore, both impairments were rescued by post-natal bumetanide treatment, suggesting common pathology underlying the social attachment malformation. Ambient neonicotinoid could hinder adaptive socialization through impaired development of visual perception in early neonates.

animal behavior and cognition↗

bioRxiv2020

Resurgence of a perinatal attraction for animate objects via thyroid hormone T3

For inexperienced brains, some stimuli are more attractive than others. Human neonates and newly-hatched chicks preferentially orient towards face-like stimuli, biological motion, and objects changing speed. In chicks, this enhances exposure to social partners, and subsequent attachment trough filial imprinting. Early preferences are not steady. The preference for stimuli changing speed fades away after three days in chicks. To understand the physiological mechanisms underlying these transient responses, we tested whether the early preferences for objects changing speed can be promoted by thyroid hormone 3,5,3-triiodothyronine (T3). This hormone determines the start of imprintings sensitive period. We found that the preference for objects changing speed can be re-established in female chicks treated with T3. Moreover, day-one chicks treated with an inhibitor of endogenous T3 did not show any preference. These results suggest that the time windows of early predispositions and of high plasticity are controlled by the same molecular mechanisms.

animal behavior and cognition↗

bioRxiv2020

Transcriptome analysis of sevoflurane exposure effects at the different brain regions

BackgroundsSevoflurane is a most frequently used volatile anaesthetics, but its molecular mechanisms of action remain unclear. We hypothesized that specific genes play regulatory roles in whole brain exposed to sevoflurane. Thus, we aimed to evaluate the effects of sevoflurane inhalation and identify potential regulatory genes by RNA-seq analysis. MethodsEight-week old mice were exposed to sevoflurane. RNA from four medial prefrontal cortex, striatum, hypothalamus, and hippocampus were analysed using RNA-seq. Differently expressed genes were extracted. Their gene ontology terms and the transcriptome array data of the cerebral cortex of sleeping mice were analysed using Metascape, and the gene expression patterns were compared. Finally, the activities of transcription factors were evaluated using a weighted parametric gene set analysis (wPGSA). JASPAR was used to confirm the existence of binding motifs in the upstream sequences of the differently expressed genes. ResultsThe gene ontology term enrichment analysis result suggests that sevoflurane inhalation upregulated angiogenesis and downregulated neural differentiation in the whole brain. The comparison with the brains of sleeping mice showed that the gene expression changes were specific to anaesthetized mice. Sevoflurane induced Klf4 upregulation in the whole brain. The transcriptional analysis result suggests that KLF4 is a potential transcriptional regulator of angiogenesis and neural development. ConclusionsKlf4 was upregulated by sevoflurane inhalation in whole brain. KLF4 might promote angiogenesis and cause the appearance of undifferentiated neural cells by transcriptional regulation. The roles of KLF4 might be key to elucidating the mechanisms of sevoflurane induced functional modification in the brain.

genetics↗

bioRxiv2020

The tRNA pseudouridine synthase TruB1 regulates the maturation and function of let-7 miRNA

Let-7 is an evolutionary conserved microRNA that mediates post-transcriptional gene silencing to regulate a wide range of biological processes, including development, differentiation, and tumor suppression. Let-7 biogenesis is tightly regulated by several RNA-binding proteins, including Lin28A/B, which represses let-7 maturation. To identify new regulators of let-7, we devised a cell-based functional screen of RNA-binding proteins using a let-7 sensor luciferase reporter, and identified the tRNA pseudouridine synthase, TruB1. TruB1 enhanced maturation specifically of let-7 family members. Rather than inducing pseudouridylation of the miRNAs, HITS-CLIP (High throughput sequencing crosslinking immunoprecipitation) and biochemical analyses revealed direct binding between endogenous TruB1 and the stem-loop structure of pri-let-7, which also binds Lin28A/B. TruB1 selectively enhanced the interaction between pri-let-7 and the microprocessor DGCR-8, which mediates miRNA maturation. Finally, TruB1 suppressed cell proliferation, which was mediated in part by let-7. Altogether, we reveal an unexpected function for TruB1 in promoting let-7 maturation and function.

molecular biology↗