Biology subjects

Gotoh, Y.

Publications and source records attributed to Gotoh, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Polycomb establishes TAD-scale H3K27me3 mega-domains to safeguard neuronal identity

During development, pluripotent stem cells generate diverse cell types through gene regulatory networks orchestrated by combinations of transcription factors (TFs). Following terminal differentiation, however, cellular identities become remarkably stable and resistant to TF-mediated perturbation, yet the mechanisms underlying this stability remain poorly understood. Here, we identify Polycomb repressive complexes (PRCs) as key regulators of neuronal identity maintenance. Although PRCs are well known for repressing the promoters of developmental genes during early cell fate specification, we unexpectedly find that PRC-mediated H3K27me3 expands into megabase-scale domains during neuronal maturation that align with topologically associating domains (TADs). These H3K27me3 "mega-domains" selectively encompass genes associated with alternative neural and non-neural lineages. While depletion of H3K27me3 in mature neurons has only modest effects on basal gene expression, it significantly increases neuronal activity-dependent c-FOS binding and induction of lineage-inappropriate genes within these mega-domains. Our findings reveal a previously unrecognized role for PRCs in establishing TAD-scale repressive chromatin domains during neuronal maturation, thereby safeguarding neuronal identity from external stimuli through broad silencing of alternative cell fate programs.

developmental biology↗

bioRxiv2026

Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians

Subcuticular bacteria (SCB) are widespread symbionts of echinoderms and often dominate the body-wall microbiome, suggesting important roles in host physiology. However, their diversity, metabolic properties, and host associations remain poorly characterized. Here, we report a novel dominant SCB lineage associated with deep-sea holothurians, Scotoplanes spp. collected from the Northwest Pacific. We recovered two high-quality genomes, including a 649-kb complete circular genome, and propose a new genus and species, "Candidatus Abyssoplasma scotoplanesicola", within Mycoplasmatota. The two genomes showed a highly reduced metabolic repertoire, lacking central pathways including glycolysis. In contrast, acidic cell-surface-associated proteins, including large proteins exceeding 5,000 amino acids, accounted for 27.6% of the complete genome and clustered near defense islands. Localized genome plasticity in these regions, revealed by comparison between the two closely related genomes, suggests a possible mechanism for diversification of cell-surface proteins at the host-symbiont interface. "Candidatus Abyssoplasma scotoplanesicola" occupied 76.4-98.9% of the body-wall microbiome of the Scotoplanes specimens. Fluorescence in situ hybridization analysis confirmed that these bacteria formed aggregates on the epidermal side of the body wall. Overall, this study provides genome-and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.

microbiology↗

bioRxiv2026

Type I IFN dynamics define an early checkpoint for survival and orchestrate systemic neutrophil heterogeneity in lethal viral infection

The early host response is critical for protection against viral infections, yet the systemic events that dictate individual differences in outcomes remain poorly defined. Here, we leveraged variability in survival following intranasal vesicular stomatitis virus (VSV) challenge in genetically identical mice to retrospectively profile systemic immune responses associated with survival or lethality. Survival was strongly associated with a robust systemic type I interferon (IFN) surge within 24 hours of infection, and blockade of type I IFN signaling during this narrow early window markedly reduced survival, establishing early IFN induction as a key determinant of outcome. This protective IFN surge rapidly remodeled the systemic immune landscape. Single-cell profiling revealed a transcriptionally and functionally distinct ICAM1 neutrophil subset as the strongest early correlate of survival, primed within the bone marrow. ICAM1 neutrophils exhibited a pro-inflammatory signature and enhanced phagocytic activity compared with ICAM1- neutrophils, which predominated in lethal outcomes. Together, these findings define a type I IFN-driven early checkpoint that governs survival in lethal viral infection and identify ICAM1 neutrophils as a blood-accessible biomarker of protective immunity, highlighting the critical role of early innate immune dynamics in shaping disease trajectories and providing a framework for early prognostic markers and host-directed therapies.

immunology↗

bioRxiv2025

Candidatus Rickettsia mendelii has the smallest and most ancestral-like genome in the genus Rickettsia

Rickettsia species, which constitute obligate intracellular bacteria adapted to a host-dependent lifestyle, have traditionally been classified into four phylogenetic groups. However, the available genomes are biased toward the Typhus and Spotted Fever groups, with early-diverging Ancestral group (AG) lineages being underrepresented. Here, we isolated six Candidatus Rickettsia mendelii strains from Ixodes turdus ticks in Japan. We obtained their whole-genome sequences, including one closed genome, and found that they form a distinct lineage in the AG and have the smallest genome among the known rickettsial species. Gene tree-aware reconstruction of evolutionary events using amalgamated likelihood estimation revealed that the last common ancestor of Rickettsia had a smaller gene family size than modern species do, and Ca. R. mendelii retains the most similar genomic content to this ancestral state. Various patterns of gene gain and loss among Rickettsia lineages were also suggested, highlighting their divergent evolutionary trajectories. These findings increase our understanding of Rickettsia genome evolution.

microbiology↗

bioRxiv2025

Local niche-derived immunosuppressive CXCR2+ cells impair antiviral immunity

Symptom severity after viral infection varies among individuals, yet its mechanism remains poorly understood. We categorized mice into recovering and non-recovering groups based on body weight after infection of the same titer of vesicular stomatitis virus (VSV). We revealed that in the olfactory bulb (OB) where VSV initially expands, non-recovering mice exhibited an anti-inflammatory environment, suggesting its detrimental effect. Importantly, CXCR2+ cells resembling immunosuppressive myeloid-derived suppressor cells (MDSCs) were more abundant in the OB of non-recovering mice than in that of recovering mice after VSV infection. Depleting CXCR2+ MDSC-like cells from the brain increased inflammatory responses and the animals survival after infection. Furthermore, site-specific labeling indicated that a significant fraction of these cells in the OB originate from the skull-bone marrow (skull-BM) as well as circulation. This study reveals the lethal effects of CXCR2+ MDSC-like cells on local immune responses to viral infection, highlighting their therapeutic potential for antiviral defense.

immunology↗

bioRxiv2025

Age-associated microglia populations identified from several single cell transcriptome data

Microglial senescence contributes to inflammation and various neurodegenerative diseases. Recent single-cell transcriptome data have revealed age-associated microglial substates (AAMs) and their potential roles in the development of neurodegenerative diseases. However, the characteristics identified in each study are not necessarily consistent. Here, we perform an integrative analysis of seven previously reported single-cell RNA-seq and four single-nucleus RNA-seq datasets of microglia from young and aged mouse brains. We identify four common AAMs across all datasets and two dataset-specific AAMs. Each AAM exhibits distinct transcriptomic patterns, including alterations in ribosomal genes, Apoe, cytokine genes, interferon-responsive genes, and phagocytosis-related genes. Time-series and pseudotime analyses indicate that the production of AAMs is initiated by the upregulation of ribosomal genes. Predictions based on single-cell transcriptomic data of age-associated manipulations reveal an increase in specific AAMs in a stimulation-type-dependent manner. We also identify similar AAMs in human brains. Altogether, our large-scale integrative analysis highlights promising age-associated microglial populations, which may serve as novel therapeutic targets for age-related neurodegenerative diseases.

neuroscience↗

bioRxiv2024

Concentration-dependent formation of intersegment interactions in viral droplets of influenza A virus infected cells

The influenza A virus genome consists of eight RNA segments, each incorporated into a virion. It has been proposed that intersegment interactions bundle these segments, and viral inclusions, which contain viral ribonucleoproteins (vRNPs) and Rab11, facilitate this process. However, the locations and mechanisms of intersegment interaction formation remain unclear. To investigate this, we identified comprehensive intersegment interactions in infected cells using customized LIGR-seq. Our results revealed that intersegment interactions in infected cells overlapped with those in the virion and were partially formed through direct RNA-RNA interactions. Additionally, we found that the formation of these interactions was delayed in cells expressing a Rab11 dominant-negative. Furthermore, artificially increasing vRNP concentrations in the nucleus, where intersegment interactions typically do not occur, triggered the formation of these interactions, which again overlapped with those in the virion. These results suggest that intersegment interactions are formed in viral inclusions where progeny vRNPs accumulate.

microbiology↗

bioRxiv2024

Age-associated transcriptomic and epigenetic alterations in mouse hippocampus

Aging represents a major risk for human neurodegenerative disorders, such as dementia and Alzheimers disease, and is associated with a functional decline in neurons and impaired synaptic plasticity, leading to a gradual decline in memory. Previous research has identified molecular and functional changes associated with aging through transcriptomic studies and neuronal excitability measurements, while the role of chromatin-level regulation in vulnerability to aging-related diseases is not well understood. Moreover, the causal relationship between molecular alterations and aging-associated decline in functions of different cell types remains poorly understood. Here, we systematically characterized gene regulatory networks in a cell type-specific manner in the aging mouse hippocampus, a central brain region involved in learning and memory formation, by simultaneously profiling gene expression and chromatin accessibility at a single nuclei level. The analysis of multiome (RNA and ATAC) sequencing recapitulated the diversity of glial and neuronal cell types in the hippocampus, and allowed revealing transcriptomic and chromatin accessibility level changes in different cell types, among which oligodendrocytes and dentate gyrus (DG) neurons exhibited the most drastic changes. We found that aging-dependent chromatin-level changes were more pronounced than transcriptomic changes for genes related to synaptic plasticity among neurons. Our data suggest that BACH2, a candidate transcription factor in the aging- mediated functional decline of DG neurons, potentially regulates genes associated with synaptic plasticity, cell death, and inflammation during aging.

neuroscience↗

bioRxiv2024

In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex

During the differentiation process of neurons, their gene transcription pattern changes according to both intrinsic and extrinsic stimuli-induced programs. Chromatin regulation at regulatory elements is involved in this precise control of gene expression. However, developmental changes in chromatin accessibility of the cortical neurons in vivo are less understood, partly because there is no convenient method to genetically label neurons of a specific lineage. Here, we establish a method for labeling the differentiating neurons of specific birthdates. Using this method, we traced the four-day differentiation process of in vivo deep-layer excitatory neurons in mouse embryonic cortex and examined the changes in the genome-wide transcription pattern and chromatin accessibility with RNA-seq and DNase-seq, respectively. The genomic regions of genes associated with mature neuron functions, such as deep layer-specific genes and genes responsive to external stimuli, became open even in the embryonic stage. Moreover, genes with bivalent marks in neural precursor/stem cells (NPCs) became open. Together, our data demonstrate the importance of chromatin regulation in vivo differentiating neurons during the embryonic stage to follow activation of neuronal genes in their maturation process.

developmental biology↗

bioRxiv2024

Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity

Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics in these viruses remain largely unknown. In this study, we investigated population and intra-population dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed near-automatic computational pipeline generated 1,065 high-quality metagenome-assembled genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community at the study site and distinct dynamics of different viral populations classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. Notably, year-round recovery patterns were observed at the intra-population genetic diversity level for viruses classified as persistent or seasonal. Our results further indicated that the viral genome dynamics were associated with intra-population diversity; specifically, giant viruses with broader niche breadth tended to exhibit greater levels of microdiversity. We argue that greater microdiversity in viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.

microbiology↗

bioRxiv2024

Embryonic diversification of adult neural stem cells and ependymal cells

Both adult neural stem (type B) cells and ependymal (type E) cells in the mouse ventricular-subventricular zone (V-SVZ) are derived from slowly dividing (or quiescent) embryonic neural stem-progenitor cells (NPCs) that are set aside during development. However, it has remained unclear whether fate diversification between adult type B and type E cells actually occurs during embryogenesis. Here we performed single-cell transcriptomic analysis of slowly dividing embryonic NPCs and identified cell subpopulations transcriptionally similar to adult type B or type E cells. The type B- like embryonic cells appeared to emerge before embryonic day (E) 13.5, whereas the type E-like cells became evident between E13.5 and E16.5. Genes differentially expressed in B-like embryonic cells (versus E-like cells) included Tmem100, Cadm2, and bone morphogenetic protein (BMP)-induced genes. Forced expression of an active form of BMP receptor (ALK2QD), TMEM100, or CADM2 in embryonic NPCs resulted in preferential generation of adult type B cells relative to type E cells in the postnatal brain. Moreover, knockdown of TMEM100 resulted in relative enrichment of type E cells over type B cells. Our results indicate that the embryonic origin of adult type B cells and that of type E cells have already diverged molecularly during embryogenesis, and they have identified key molecular players in this fate bifurcation.

developmental biology↗

bioRxiv2024

Arachidonic acid incorporation into phosphatidylinositol by LPLAT11/MBOAT7 ensures radial glial cell integrity in developing neocortex

Arachidonic acid, a vital polyunsaturated fatty acid in brain development, is enriched in phosphatidylinositol (PI). The arachidonic acyl chain in PI is introduced by lysophospholipid acyltransferase 11 (LPLAT11)/membrane-bound O-acyltransferase 7 (MBOAT7), the loss of which causes cortical atrophy in humans and mice. Here, we show that LPLAT11 deficiency impaired indirect neurogenesis in the developing neocortex, resulting in fewer layer II-V neurons. LPLAT11-deficient radial glial cells had defects in differentiation into intermediate progenitor cells and increased apoptosis. Prior to these anomalies, LPLAT11 deficiency caused a fragmentation of the Golgi apparatus, accompanied by impaired apical trafficking of E-cadherin, and deregulated apical detachment. Moreover, impaired PI acyl chain remodeling led to a decreased amount of PI(4,5)P2, leading to Golgi apparatus fragmentation. Thus, these results clarify the underlying mechanism of cortical atrophy by LPLAT11 deficiency and highlight the critical role of arachidonic acid in PI in the integrity of radial glial cells.

neuroscience↗

bioRxiv2024

Effect of phage variation on Shiga toxin 2 (Stx2) production and the virulence of Stx-producing Escherichia coli

Shiga toxin (Stx)-producing Escherichia coli (STEC) causes serious gastrointestinal illness, including hemorrhagic colitis and hemolytic uremic syndrome. Although all known Stxs (Stx1 and Stx2) are encoded by bacteriophages (Stx phages), the production of Stx2 is known to be a major risk factor for severe STEC infections. The production of Stx2, but not Stx1, is tightly coupled with the induction of Stx phages, and Stx2 production levels vary between STEC strains, even within the same serotype. Here, we analyzed the genomic diversity of all Stx phages in 71 strains representing the entire O145:H28 lineage, one of the major STECs. Our analysis revealed the highly dynamic nature of the Stx phages in O145:H28, including the independent acquisition of similar Stx phages by different sublineages and the frequent changes in Stx phages in the same sublineages due to the gain and loss of Stx phages. Analyses of Stx2 production levels in O145:H28 strains and K-12 lysogens of Stx2 phages of specific groups and types, which were defined by their early region sequences and CI repressors, respectively, revealed that short-tailed Stx2a phages (S-Stx2a phages) confer significantly greater Stx2 production to host strains than long-tailed Stx2a phages (L-Stx2a phages). However, L-Stx2a phages that encode a specific type of CI repressor promoted Stx2 production, comparable to the level of production among S-Stx2a phages, as well as promoted virulence to host strains, exceeding the level among other L-Stx2a phages. We also showed a clear link between the phage induction efficiency, which was primarily determined by the early region of each phage, and the level of Stx2 production by host strains. These results provide important insights into the diversification and dynamism of Stx phages and the relationship between the variations in Stx2 phages and the amount of Stx2 production by their host strains. Author summaryShiga toxin (Stx)-producing Escherichia coli (STEC) is an important human intestinal pathogen that causes severe illnesses. These bacteria produce Stx1, Stx2 or both toxins, but the production of Stx2 is an important measure of the virulence of STEC strains. While both types of Stx are encoded by bacteriophages (Stx phages), Stx2 production is tightly coupled with phage induction, and variations in Stx2 phages have been associated with variations in Stx2 production levels by their host O157:H7 STEC strains. However, in non-O157 STEC strains, the variation in Stx phages and its association with host strain production of Stx2 have not yet been fully analyzed. This systematic study of Stx phages in O145:H28 STEC reveals not only the marked genomic diversity and dynamism of Stx phages in this STEC lineage but also that short-tailed Stx2 phages and a specific group of long-tailed Stx2 phages induce high levels of Stx2 production by host strains, and this increased production is linked to the efficient induction of phages.

microbiology↗

bioRxiv2023

Mitochondrial protein FKBP8 captures PDZD8 to form mitochondria-ER contacts

Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identified the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-Electron Microscopy (Cryo-EM) tomography, and correlative light-EM (CLEM). Single molecule tracking revealed highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and capture at MERCS. Overexpression of FKBP8 was sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrated their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.

cell biology↗

bioRxiv2023

Identification of Core Yeast Species and Microbe-Microbe Interactions Impacting Larval Growth of Drosophila in the Wild

Microbiota consisting of various fungi and bacteria have a significant impact on the physiological functions of the host. However, it is unclear which species are essential to this impact and how they affect the host. This study analyzed and isolated microbes from natural food sources of Drosophila larvae, and investigated their functions. Hanseniaspora uvarum is the predominant yeast responsible for larval growth in the earlier stage of fermentation. As fermentation progresses, Acetobacter orientalis emerges as the key bacterium responsible for larval growth, although yeasts and lactic acid bacteria must coexist along with the bacterium to stabilize this host-bacterial association. By providing nutrients to the larvae in an accessible form, the microbiota contributes to the upregulation of various genes that function in larval cell growth and metabolism. Thus, this study elucidates the key microbial species that support animal growth under microbial transition.

developmental biology↗

bioRxiv2023

Propagation of neuronal micronuclei regulates microglial states

Microglia, resident immune cells in the central nervous system, undergo morphological and functional changes in response to signals from the local environment and mature into various homeostatic states. However, niche signals underlying microglial development and maturation remain largely unknown. In this study, we show that neuronal micronuclei propagate microglia, followed by changing microglial states during the postnatal period. We discovered that neurons passing through a dense region of the developing neocortex give rise to micronuclei and release them into the extracellular space. Moreover, neuronal micronuclei were incorporated into microglia and affected morphological changes. Loss of the cGAS gene alleviates effects on micronucleus-dependent morphological changes. Notably, neuronal micronuclei-harboring microglia exhibit unique transcriptome signatures. These results demonstrate that neuronal micronuclei serve as niche signals that produce novel microglial states. Our findings provide a potential mechanism for regulating the microglial state in the early-postnatal neocortex.

neuroscience↗

bioRxiv2023

A centrifugation-based method for high-throughput biomaterial separation using magnetic microbeads

Magnetic microbeads are small iron oxide nanoparticles coated with a bioaffinity material that selectively binds to specific biomolecules of interest, enabling their capture and isolation from complex biological samples. Magnetic microbeads are widely used for purification of specific biomolecules in various experiments in molecular biology. However, current methods of manual pipetting to separate supernatants from magnetic microbeads are often inefficient- time-consuming, labor intensive and inaccurate. Furthermore, the use of pipetting robots and liquid handlers specifically designed for multi-well plates can be a cost-prohibitive approach due to the high cost of equipment and disposable supplies. Here, we developed a centrifugation-based method for high-throughput separation of supernatant from magnetic microbeads. To facilitate the centrifugal separation process, we used the 384 transfer plate (Watson, Japan) and a magnetic stand equipped with a 384-well magnetic stand, allowing easy handling of several hundred samples and rapid separation of supernatant from magnetic microbeads. The centrifugal force was used to drive the separation of target molecules from the magnetic microbeads, and sample were successfully separated with relatively high recovery rates. Thus, this technology provides a simple, rapid, and cost- and labor-effective biomolecule separation method with potential applications in various fields, including molecular biology, clinical diagnostics, and biotechnology, and is a valuable addition to the existing toolbox of biomolecule separation methods.

molecular biology↗

bioRxiv2022

Dynamic behavior of nuclear shape induced by visual stimulation in excitatory neurons of visual cortex

Neurons decline in their functionality over time, and age-related neuronal alterations are associated with phenotypes of neurodegenerative diseases. In non-neural tissues, an infolded nuclear shape has been proposed as a hallmark of aged cells and neurons with infolded nuclei have also been reported to be associated with neuronal activity. Here, we perform time-lapse imaging in the visual cortex of Nex-Cre;SUN1-GFP mice. Nuclear infolding was observed within 15 minutes of stimulation in young nuclei, while the aged nuclei were already infolded pre-stimulation and showed reduced dynamics of the morphology. In young nuclei, the depletion of the stimuli restored the nucleus to a spherical shape and reduced the dynamic behavior, suggesting that nuclear infolding is a reversible process. We also found the aged nucleus to be stiffer than the young one, further relating to the age-associated loss of nuclear shape dynamics. We reveal temporal changes in the nuclear shape upon external stimulation and observe that these morphological dynamics decrease with age.

cell biology↗