Biology subjects

Ito, M.

Publications and source records attributed to Ito, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Arabidopsis epigenetic factor AS2 attenuates nucleolar stress by camptothecin and establishes leaf polarity by repressing a CDK inhibitor

The Arabidopsis thaliana leaf, exhibiting a symmetrically extended flat morphology, consists of two distinct cellular domains: adaxial and abaxial layers. The ASYMMETRIC LEAVES2 (AS2) gene is essential for specifying the adaxial domain, and its protein forms nucleolar structures, termed AS2 bodies, at ribosomal-DNA loci. Numerous nucleolus-related genes have been reported to be cooperatively involved in leaf adaxialization together with AS2. However, the molecular relationships between AS2 and these genes remain unclear. To identify chemical modulators of AS2 function, we screened a chemical library containing natural products and identified eight molecules, including camptothecin, that induced filamentous leaves in the as2 mutant. Camptothecin is an inhibitor of topoisomerase I, which is required for transcription of ribosomal-RNA genes, and induces nucleolar stress. Treatment with 10-hydroxy-camptothecin increased KIP-RELATED-PROTEIN5/INHIBITOR-OF-CYCLIN-DEPENDENT-KINASE3 (KRP5/ICK3) transcript levels, encoding a CDK inhibitor, and caused notable changes in the number and morphology of AS2 bodies. Given its role in leaf morphogenesis, our findings suggest that AS2 is a key factor in establishing leaf adaxial-abaxial polarity by regulating cell proliferation and protecting against nucleolar stress through coordinated interactions with nucleolar proteins.

developmental biology↗

bioRxiv2025

An NLP-inherited motif confers broad DNA-binding specificity to NIN in root nodule symbiosis

Nitrogen-fixing root nodule symbiosis (RNS) occurs in some eudicots, including legumes, and is regulated by the transcription factor NODULE INCEPTION (NIN), derived from the NIN-LIKE PROTEIN (NLP) family. However, how the NIN protein acquired RNS-specific functions remains unclear. We identify a previously undescribed motif in Lotus japonicus NIN, located downstream of the RWP-RK domain, which we term the FR. This motif broadens the DNA-binding specificity of NIN by stabilizing the RWP-RK dimer interface. nin mutants lacking the FR motif show defective nodulation and impaired nitrogen fixation. Arabidopsis NLP2 carries a NIN-type FR and shares key features with NIN. Furthermore, the NIN-type FR likely originated as early as gymnosperms, suggesting that the molecular feature of NIN for RNS regulation was inherited from ancestral NLPs before RNS emerged.

plant biology↗

bioRxiv2025

The generation of viable, structurally integrated human-mouse chimaeras through enhanced hPSCs proliferation

The generation of human organs in animals through blastocyst complementation offers a promising solution to the shortage of transplantable organs. While human pluripotent stem cells (hPSCs) can contribute to interspecies chimaeric embryos when injected into preimplantation embryos of mice, pigs, or monkeys, their integration is often limited due to low chimaerism and segregation from host tissues, significantly impeding progress toward exogenic organ generation. Here, we demonstrate that co-overexpression of the anti-apoptotic gene BCL2 and the proto-oncogene MYCL, along with various cell cycle regulators significantly enhances human cell chimaerism by promoting cell proliferation. This strategy facilitates the generation of viable mouse pups containing hPSC-derived tissues without tumorigenesis. scRNA-seq analysis revealed that hPSCs already exit pluripotent by early post-implantation stage yet hPSCs with enhanced proliferation were able to integrate effectively into the cardiomyocytes and vasculature of both embryonic and extraembryonic tissues with gene expression profiles reflecting their structural integration. These findings highlight the critical role of cell cycle regulation in overcoming xenogeneic barriers. Our findings offer new insights into strategies for enhancing interspecies organogenesis and advancing the field of regenerative medicine. HighlightO_LIEnhancing hPSC proliferation increases human cell contribution in interspecies chimaeras C_LIO_LIAchieving the generation of viable human-mouse chimaeras without tumour formation C_LIO_LIhPSCs in post-implantation mouse epiblast exit pluripotency but retain the capacity to integrate into mouse embryogenesis C_LIO_LIhPSCs derivatives integrate into vasculature and cardiac tissues with lineage-matched transcriptional profiles C_LI

developmental biology↗

bioRxiv2025

Structural dynamics of mixed-subunit CaMKIIα/β heterododecamers filmed by high-speed AFM

CaMKII predominantly assembles into a 12-meric ring assembly, primarily consisting of CaMKII and CaMKII{beta} variants in the brain. Previous biochemical studies have reported varying ratios of these CaMKII variants across different brain regions and developmental stages. However, direct evidence for the formation of CaMKII/{beta} heterooligomers within a 12-meric ring assembly has been lacking at the single-molecule level. Here, we employed high-speed atomic force microscopy to visualize the conformational dynamics of forebrain-mimicked CaMKII/{beta} at a 3:1 ratio. Our findings revealed that the CaMKII and CaMKII{beta} subunits are intermixed within the 12-meric ring assembly, with more than 83% probability that CaMKII{beta} subunits adjacent to one another. Furthermore, in the activated state, CaMKII/{beta} heterooligomers form a stable kinase domain complex via interactions between adjacent CaMKII{beta} subunits, resulting in a long-lasting structure with an exposed target binding site. Collectively, our observations provide insights into the structural role of CaMKII{beta} subunits within the CaMKII/{beta} heterododecamer.

neuroscience↗

bioRxiv2025

TET3 protects the Dlk1-Dio3 Imprinted Locus from DNA hypomethylation during adult NSC Reprogramming

Genomic imprinting is an epigenetic mechanism that drives monoallelic gene expression depending on parental origin. Loss of imprinting (LOI) is associated with human imprinting disorders, fetal development, and cancer progression. Imprinted genes, organized in clusters, are regulated by methylation at imprint control regions (ICRs), differentially methylated regions (DMRs) between parental chromosomes. Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) is a valuable tool for studying pluripotency and holds promise for patient-specific therapies. Discerning whether genomic imprinting changes during reprogramming represent epigenetic abnormalities or essential adaptations linked to pluripotency is crucial. Here, we perform RNA-seq and MeDIP-seq analysis on mouse iPSCs derived from neural stem cells (NSCs). Our findings reveal that ICRs undergo DNA hypomethylation, confirming widespread LOI in pluripotent cells. However, the IG-DMR within the Dlk1-Dio3 imprinted cluster resists hypomethylation, a hallmark of successful pluripotency acquisition. We also identify a non-canonical role of TET3 in IG-DMR methylation protection through transcriptional regulation of Oct4 and Trim28. These findings highlight genomic imprinting as a key mechanism of gene dosage control in pluripotency acquisition and maintenance.

cell biology↗

bioRxiv2024

Cooperation shapes bacterial niche breadth evolution and patterns of diversification

Bacteria exhibit varying niche breadths, with generalists thriving in diverse environments and specialists confined to specific habitats. This variability reflects the adaptability of bacteria to their environment and may influence their speciation and extinction rates. We used phylogenetic causal inference and diversification analysis techniques to investigate the influence of cooperation on bacterial niche breadth evolution and patterns of diversification across 25,785 species. We found: (1) a positive correlation between the proportion of genes for cooperation and niche breadth; (2) a decreased proportion of genes for cooperation promotes niche contraction; and (3) species with a higher proportion of genes for cooperation show increased speciation and extinction rates when their niche breadths are narrower. Our study highlights the role of genes for cooperation in shaping both niche breadth and diversification of bacteria, underscoring their critical function in maintaining the ecological versatility and diversity of bacteria.

evolutionary biology↗

bioRxiv2024

How Alzheimer's Abeta propagates and triggers tau pathology in intact neurons

Alzheimers disease begins with A{beta} accumulation, progresses to tau aggregates and results in widespread neurodegeneration1-3. Simultaneous propagation of A{beta} aggregates from very limited to wide and distant brain regions is one of the outstanding events in the early stage. Here, we demonstrate that the neurovascular unit4,5 comprising capillaries and pericytes, the machinery supplying oxygen and glucose to neurons, is also the machinery for propagating effector molecules that impose Alzheimers pathologies on intact neurons. We discovered two distinct signaling cascades, one activated in capillary endothelial cells and the other in pericytes. At the origin of either cascade, we identified amylospheroid (ASPD)6,7, a highly toxic 30-mer assembly of A{beta}, and its sole target NKA38, a neuron-specific isoform of Na+,K+-ATPase9,10 but present in endothelial cells and pericytes. In endothelial cells, ASPD binding to NKA3 releases angiotensin II, which increases {beta}-secretase in intact neurons, causing a huge increase of A{beta}42and resultant accumulation. In pericytes, ASPD binding to NKA3 releases an unknown effector molecule that activates {delta}-secretase in intact neurons, further augmenting A{beta}42and producing pathogenic tau1-368 fragment. Thus, A{beta} and tau pathologies are directly linked. Stopping the signaling cascades near the origin by inhibiting ASPD-NKA3 interaction8 may provide a new therapeutic approach.

neuroscience↗

bioRxiv2024

Patho-transcriptomic analysis of invasive mucinous adenocarcinoma of the lung (IMA): comparison with lung adenocarcinoma with signet ring cell features (SRCC)

BackgroundInvasive mucinous adenocarcinoma (IMA) comprises [~]5% of lung adenocarcinoma. There is no effective therapy for IMA when surgical resection is not possible. IMA is sometimes confused with adenocarcinoma with signet ring cell features (SRCC) pathologically since both adenocarcinomas feature tumor cells with abundant intracellular mucin. The molecular mechanisms by which such mucin-producing lung adenocarcinomas develop remain unknown. MethodsUsing a Visium spatial transcriptomics approach, we analyzed IMA and compared it with SRCC patho-transcriptomically. Combining spatial transcriptomics data with in vitro studies using RNA-seq and ChIP-seq, we assessed downstream targets of transcription factors HNF4A and SPDEF that are highly expressed in IMA and/or SRCC. ResultsSpatial transcriptomics analysis indicated that there are 6 distinct cell clusters in IMA and SRCC. Notably, two clusters (C1 and C3) of mucinous tumor cells exist in both adenocarcinomas albeit at a different ratio. Importantly, a portion of genes (e.g., NKX2-1, GKN1, HNF4A and FOXA3) are distinctly expressed while some mucous-related genes (e.g., SPDEF and FOXA2) are expressed in both adenocarcinomas. We determined that HNF4A induces MUC3A/B and TM4SF4 and that BI 6015, an HNF4A antagonist, suppressed the growth of IMA cells. Using mutant SPDEF that is associated with COVID-19, we also determined that an intact DNA-binding domain of SPDEF is required for SPDEF-mediated induction of mucin genes (MUC5AC, MUC5B and AGR2). Additionally, we found that XMU-MP-1, a SPDEF inhibitor, suppressed the growth of IMA cells. ConclusionThese results revealed that IMA and SRCC contain heterogenous tumor cell types, some of which are targetable.

cancer biology↗

bioRxiv2024

Post-translational cleavage of Mei5 of Dmc1 mediator, Mei5-Sae3 complex, in yeast meiosis

Interhomolog recombination in meiosis is mediated by the Dmc1 recombinase. The Mei5-Sae3 complex of S. cerevisiae promotes Dmc1 assembly and functions with Dmc1 for homology-mediated repair of meiotic DNA double-strand breaks. How Mei5-Sae3 facilitates Dmc1 assembly remains poorly understood. In this study, we created and characterized several mei5 mutants featuring the amino acid substitutions of basic residues. We found that Arg97 of Mei5, conserved in its ortholog, SFR1(complex with SWI5), RAD51 mediator, in humans and other organisms, is critical for complex formation with Sae3 for Dmc1 assembly. Moreover, the substitution of Arg117 with Ala in Mei5 resulted in the production of a C-terminal truncated Mei5 protein during yeast meiosis. Notably, the shorter Mei5-R117A protein was observed in meiotic cells but not in mitotic cells when expressed, suggesting a unique regulation of Dmc1-mediated recombination by post-translational processing of Mei5-Sae3.

molecular biology↗

bioRxiv2024

Alterations of genomic imprinting appear during the reprogramming of adult neural stem cells

Genomic imprinting is an epigenetic mechanism that causes monoallelic expression of genes depending on their parental origin. Loss of imprinting (LOI) is associated with cancer progression and human imprinting disorders (IDs), impacting foetal development, metabolism and cognition. Imprinted genes, organized in clusters, rely on methylation at imprint control regions (ICRs), which are differentially methylated regions (DMRs) on both parental chromosomes. Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) is a valuable tool to understand the mechanisms associated with pluripotency and holds promise for generating patient-specific stem cells for therapeutical applications to treat different pathologies such as IDs. Here, we conduct genome-wide RNA-seq and MeDIP-seq analysis on mouse iPSCs derived from adult neural stem cells (NSCs). Our findings reveal a comprehensive alteration in iPSCs transcriptome profile, aligning with DNA hypomethylation. This correlation is pivotal in discerning which modifications in genomic imprinting during the reprogramming process represent undesirable epigenetic abnormalities that could compromiise the quality of iPSCs. Simultaneously, it helps identify genuine epigenetic modifications that are inherently linked to pluripotency, thus ensuring a clearer understanding of the factors influencing iPSC quality and pluripotent potential.

cell biology↗

bioRxiv2023

Characterization of carotenoid-producing Muricauda sp. strains isolated from the reef-building coral Galaxea fascicularis and subtropical seawater

Bacterial symbionts in corals and coral-associated zooxanthellae are attracting increasing attention as potential probiotics. Some members of the family Flavobacteriaceae are zooxanthellae-associated bacteria, which are known to protect zooxanthellae from stresses such as heat and light by producing carotenoids that reduce reactive oxygen species production. This study characterized two Flavobacteriaceae bacteria, Muricauda sp. strains ORYM1 (NBRC115792) and ORYM2 (NBRC115793), isolated from the reef-building coral Galaxea fascicularis and its surrounding seawater in Okinawa, Japan, respectively. The Muricauda sp. strain ORYM2 was isolated from subtropical seawater, and carotenoid production was assessed using ORYM2 as well as ORYM1, which was previously isolated from G. fascicularis. De novo genome sequencing revealed that both strains contain complete sets of zeaxanthin biosynthesis genes, similar to those found in other Muricauda spp. Thin-layer chromatography and high-performance liquid chromatography analyses demonstrated that ORYM1 and ORYM2 produce several carotenoids. The bacterial strains and carotenoids identified in this study provide insights into the biological roles of zooxanthellae-associated bacteria in protecting zooxanthellae and reef-building corals from environmental stresses. Statements and declarationsCompeting interests: The authors declare no competing interests.

microbiology↗

bioRxiv2023

Distinct and interdependent functions of three RING proteins regulate recombination during mammalian meiosis

During meiosis, each pair of homologous chromosomes becomes connected by at least one crossover, as required for accurate segregation at the first division, and adjacent crossovers are widely separated thereby limiting total numbers. In coarsening models, crossover patterning results from nascent recombination sites competing to accrue a limiting pro-crossover RING-domain protein (COR) that diffuses between synapsed chromosomes. Here we delineate the localization dynamics of three mammalian CORs in mouse and determine their interdependencies. RNF212, HEI10 and a new member RNF212B show divergent spatiotemporal dynamics along synapsed chromosomes, including profound differences in spermatocytes and oocytes, that are not easily reconciled by elementary coarsening models. Contrasting mutant phenotypes and genetic requirements indicate that RNF212B, RNF212, and HEI10 play distinct but interdependent functions in regulating meiotic recombination and coordinating the events of meiotic prophase-I by integrating signals from DNA breaks, homolog synapsis, the cell-cycle, and incipient crossover sites. SIGNIFICANCEMeiosis produces haploid gametes by precisely halving the chromosome complement. Crossing over between homologous chromosomes (homologs) is essential for their accurate segregation and defects are associated with infertility, miscarriage, and congenital disease. Factors that ensure crossing over between each pair of homologs include mammalian RING-domain proteins RNF212, HEI10, and RNF212B, alleles of which are linked to infertility and heritable variation in crossover rate. This study focuses on understanding the functions and relationships between pro-crossover RING proteins (CORs) in mouse, providing important insights into their roles in regulating recombination, the DNA repair process that gives rise to crossovers. Notably, chromosomal localization dynamics of the three CORs are distinct and show striking sexual dimorphism with important implications for models of crossover control.

genetics↗

bioRxiv2023

Convolutional neural network model detected lasting behavioral changes in mouse with kanamycin-induced unilateral inner ear dysfunction

In acute aminoglycoside ototoxicity to unilateral inner ear, physical abnormalities, such as nystagmus and postural alteration, are relieved within a few days by neural compensation. To examine exploratory behavior over an extended period, freely moving behavior of a mouse after unilateral kanamycin injection was recorded in a home-cage environment. A tail was excluded from deep learning-mediated object detection because of its delayed movement relative to the body. All detection results were confirmed by convolutional neural network classification model. In kanamycininjected mice, total distance moved in 15 minutes increased at 3 days after surgery. Moreover, the injured mouse turned frequently toward healthy side up to 17 days after surgery. Tail suspension and twist toward healthy side induced fast rotation of trunk around longitudinal axis with dorsal bending after 14 days. Our analysis strategy employing deep learning is useful to evaluate neuronal compensatory process and screen a drug candidate with therapeutic potency.

animal behavior and cognition↗

bioRxiv2023

Replication protein-A, RPA, plays a pivotal role in the maintenance of recombination checkpoint in yeast meiosis

DNA double-strand breaks (DSBs) activate DNA damage responses (DDR) in both mitotic and meiotic cells. A single-stranded DNA (ssDNA) binding protein, Replication protein-A (RPA) binds to the ssDNA formed at DSBs to activate ATR/Mec1 kinase for the response. Meiotic DSBs induce homologous recombination monitored by a meiotic DDR called the recombination checkpoint that blocks the pachytene exit in meiotic prophase I. In this study, we showed the essential role of RPA in the maintenance of the recombination checkpoint during S. cerevisiae meiosis. The depletion of an RPA subunit, Rfa1, in a recombination-defective dmc1 mutant, fully alleviates the pachytene arrest with the persistent unrepaired DSBs. RPA depletion decreases the activity of a meiosis-specific CHK2 homolog, Mek1 kinase, which in turn activates the Ndt80 transcriptional regulator for pachytene exit. These support the idea that RPA is a sensor of ssDNAs for the activation of meiotic DDR. Rfa1 depletion also accelerates the prophase I delay in the zip1 mutant defective in both chromosome synapsis and the recombination, suggesting that the accumulation of ssDNAs rather than defective synapsis triggers prophase I delay in the zip1 mutant.

genetics↗

bioRxiv2023

Characterization of an EG.5.1 clinical isolate in vitro and in vivo

EG.5.1 is a subvariant of the SARS-CoV-2 Omicron XBB variant that is rapidly increasing in prevalence worldwide. EG.5.1 has additional substitutions in its spike protein (namely, Q52H and F456L) compared with XBB.1.5. However, the pathogenicity, transmissibility, and immune evasion properties of clinical isolates of EG.5.1 are largely unknown. In this study, we used wild-type Syrian hamsters to investigate the replicative ability, pathogenicity, and transmissibility of a clinical EG.5.1 isolate. Our data show that there are no obvious differences in growth ability and pathogenicity between EG.5.1 and XBB.1.5, and both EG.5.1 and XBB.1.5 are attenuated compared to a Delta variant isolate. We also found that EG.5.1 is transmitted more efficiently between hamsters compared with XBB.1.5. In addition, unlike XBB.1.5, we detected EG.5.1 virus in the lungs of four of six exposed hamsters, suggesting that the virus tropism of EG.5.1 is different from that of XBB.1.5 after airborne transmission. Finally, we assessed the neutralizing ability of plasma from convalescent individuals and found that the neutralizing activity against EG.5.1 was slightly, but significantly, lower than that against XBB.1.5 or XBB.1.9.2. This suggests that EG.5.1 effectively evades humoral immunity and that the amino acid differences in the S protein of EG.5.1 compared with that of XBB.1.5 or XBB.1.9.2 (i.e., Q52H, R158G, and F456L) alter the antigenicity of EG.5.1. Our data suggest that the increased transmissibility and altered antigenicity of EG.5.1 may be driving its increasing prevalence over XBB.1.5 in the human population.

microbiology↗

bioRxiv2023

Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex

Genome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than twofold heritable genome size variation among the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale (C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1 segregation analysis. Six de novo assembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in the C. psl. complex, despite its possible detrimental effects.

evolutionary biology↗

bioRxiv2023

SAM68-regulated ALE selection of Pcdh15 maintains proper synapse development and function

Thousands of mammalian genes encode alternatively spliced isoforms in their 3 untranslated region (3UTR). Alternative 3UTR diversity may contribute to several neurological processes in developing and adult brains. SAM68 is the key splicing regulator for the diversity of neuronal 3UTR isoforms through alternative last exon (ALE) selection. However, the mechanisms underlying the control of splicing at the 3 end and its function in the nervous system remain unclear. Here, we show that neuronal SAM68-dependent ALE splicing is regulated depending on its target transcripts. For example, the selection of the ALE of protocadherin-15 (Pcdh15), a gene implicated in Usher syndrome and several neuropsychiatric disorders, is largely dependent on the expression of SAM68, partially regulated via the CaMK pathway, but independent of the U1 small nuclear ribonucleoprotein. We found that the aberrant ALEs of Pcdh15 caused membrane-to-soluble isoform conversion of the produced protein and disrupted its localization into excitatory and inhibitory synapses. In addition, the neuronal expression of the soluble form of PCDH15 (sPCDH15) preferentially affected the number of inhibitory synapses. sPCDH15 further reduced neuroligin-2-induced inhibitory, but not excitatory, synapses in artificial synapse formation assays. Our findings provide insights into the role of alternative 3UTR isoform selections in synapse development.

neuroscience↗

bioRxiv2023

The Effect of Evaluating Self's Emotions on Frontal Alpha Asymmetry

In this research to assess emotions from biometric signals, participants are asked to evaluate the emotions they subjectively experienced in order to confirm whether the assumed emotions were actually elicited. However, the evaluation of emotions is not routinely performed in daily life, and it is possible that this evaluation may alter biological signals. In fMRI studies, evaluation has been shown to activate the amygdala, which is said to be related to emotional expression. However, electroencephalography (EEG) studies do not take into consideration the effects of such evaluations, and it is unclear how these evaluations affect emotion-related brain activity observed in EEG. We hypothesized that emotion evaluations would amplify emotions and c alter Frontal Alpha Asymmetry (FAA), which has been shown to be related to emotional pleasantness and unpleasantness. We suspect this is because in order to evaluate ones emotions, one must pay attention to ones internal state, and this self-focused attention has been found to enhance the subjective emotional experience. We measured a 29-channel EEG when presented with unpleasant and highly arousing images from the International Affective Picture System (IAPS) from 40 healthy male and female participants. The results revealed that FAA was significantly lower in the condition in which participants rated their own emotions compared to the condition in which they did not. Similar to fMRI studies, this result indicates that emotion-related brain activity is amplified on an EEG. This paper provides a cautionary note regarding the use of such evaluations in EEG emotion estimation studies.

neuroscience↗