Biology subjects

Kadota, M.

Publications and source records attributed to Kadota, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Ductal myofibroblasts reactivate contractile program to stabilize alveolar architecture during lung regeneration

The alveolar sac architecture is essential for efficient gas exchange and must be precisely maintained throughout life; however, how this delicate structure is preserved during adult regeneration remains poorly understood. Using a mouse pneumonectomy model, we found that Lgr6+ Hhip+ ductal myofibroblasts, a poorly characterized mesenchymal population, are indispensable for maintaining alveolar integrity during lung regrowth. Comprehensive characterization using single-cell transcriptomics, mouse genetics, and pharmacological assays demonstrated that these ductal myofibroblasts secrete myogenic factors, most notably CCN4, to reactivate a myogenic program that converts them into contractile PA-DMFs, thereby preserving alveolar architecture. Lineage-tracing further revealed that these ductal myofibroblasts originate from embryonic MCAM- SMA+ distal progenitors via subepithelial TGF-{beta} signaling, serving as a lifelong guardian of alveolar structural integrity. Notably, cross-species analysis identified an analogous population of LGR6+ fibromyocytes in human respiratory bronchioles. Together, these findings indicate ductal myofibroblasts as a developmentally programmed cell population that reactivate a contractile program to structurally support the regeneration of adult lungs.

developmental biology↗

bioRxiv2026

Stressor-Selective Sympathetic Preganglionic Modules for Organ-Biased Control

The sympathetic nervous system coordinates organ function during stress, yet the spinal organization that converts autonomic commands into selective peripheral outputs remains poorly understood. Here, we combined spatial transcriptomics, immediate early gene mapping, anatomical tracing, and functional perturbation to define the cellular logic of spinal sympathetic preganglionic neurons (SPNs) in mice. SPN transcriptomic subtypes were spatially organized by spinal segment and sex and recruited in distinct combinations by physiological stressors, revealing stressor-selective sympathetic output modules. Focusing on cold-responsive neurotensin-expressing (Nts+) SPNs in the lower thoracic spinal cord, we found that they formed a distinct output channel to the lower sympathetic trunk and aorticorenal ganglia, promoted female-biased mobilization of white adipose tissue lipids, and were required for cold tolerance when food was unavailable. These findings establish a cell-type-resolved spinal architecture that links physiological demand to organ-biased sympathetic output and identifies the preganglionic layer as a key organizer of brain-body control.

neuroscience↗

bioRxiv2026

A single-nucleus and spatial transcriptomic atlas of the Syrian hamster preoptic area across hibernation states

Hibernation is an extreme physiological state in certain mammals that is characterized by a reversible reduction in metabolic and thermogenic demands. Although the preoptic area has been implicated in the regulation of hibernation, comprehensive molecular and spatial resources for this brain region in hibernating mammals remain limited. Here, we present an integrated transcriptomic resource of the preoptic area generated using single-nucleus RNA sequencing (snRNA-seq) and Xenium-based spatial transcriptomics in a mammalian hibernator, Syrian hamster. The resource includes cross-species transcriptomic annotations relative to mouse preoptic area datasets, seasonal snRNA-seq datasets obtained under non-hibernating and hibernating conditions, and spatially resolved cell-type annotations generated from Xenium profiling. Together, these datasets provide a reference framework for identifying neuronal populations, examining molecular conservation across species and conditions, and integrating transcriptomic identity with spatial organization.

neuroscience↗

bioRxiv2026

Transcriptomic Landscape of Microglia in Mouse Models of Social Dysfunction and Oxytocin-Mediated Recovery

Atypical sociability is a hallmark of neurodevelopmental disorders arising from genetic susceptibility and prenatal environmental perturbations affecting diverse brain cell types. Using single-cell transcriptomics, we previously identified selective vulnerability of parvocellular oxytocin (OT) neurons in the paraventricular hypothalamus (PVH) following embryonic exposure to valproic acid (VPA), a teratogen that induces social deficits. Neonatal chemogenetic activation of OT neurons rescued these behavioral abnormalities and partially restored dysregulated gene expression. However, the effects of VPA exposure and OT neuron stimulation on non-neuronal PVH cells remained unclear. Here, we show that VPA induces transcriptional abnormalities in PVH microglia. Spatial transcriptomics revealed altered distributions of PVH microglial subtypes. Notably, neonatal OT neuron stimulation reversed a subset of VPA-induced microglial gene downregulation, while pharmacological manipulation of microglia normalized aberrant OT gene expression in putative parvocellular OT neurons. These findings support bidirectional OT neuron-microglia interactions that may underlie social dysfunction following embryonic VPA exposure. HighlightsO_LIEmbryonic VPA exposure induces potent transcriptional changes in PVH microglia C_LIO_LIPVH microglia comprise two spatially organized subtypes disrupted by VPA C_LIO_LINeonatal OT neuron stimulation restores gene expression in a microglial subtype C_LIO_LIMicroglial manipulation rescues OT ligand in parvocellular PVH neurons C_LI

neuroscience↗

bioRxiv2025

Tracing genome size dynamics in sharks and rays with inclusive sequence analysis by the Squalomix Consortium

Genomes have maintained stable sets of protein-coding genes during evolution, while chromosome organization and genome size vary drastically. Changes in genome size are often attributed to variable amounts of repetitive sequences, including transposable elements. However, it remains poorly understood how such changes were accommodated while maintaining other genomic components. Elasmobranchs, including sharks, rays, and skates, exhibit high among-species variation of genome size and high within-species variation of chromosome length, offering a unique study system to address the question. In this study, we present the first whole genome sequences of the whitebelly skate with remarkably small genome size among elasmobranchs (2.2 Gb), and the red stingray. These chromosome-scale assemblies enabled the assessment of genomic compositions including centromeres and non-coding elements, which revealed notable profiles of tRNA loci and unbiased intragenomic distribution of transposons in elasmobranch genomes. Comparative analyses across these species revealed a shared genomic architecture characterized by correlations of intergenic and intronic sequence lengths with chromosome sizes, with repetitive element accumulation in elongated regions. We analyzed tandemly duplicated genes with high copy number variability. This genome-wide survey revealed the tendency for more frequent tandem gene duplications along with genome size expansion. We document the batoid HoxC cluster in the red stingray genome, which has undergone extensive repetitive element invasion and co-localizes with the HoxB cluster on a sex chromosome. Our study demonstrates an inclusive analysis encompassing both coding and non-coding regions, adaptable to more species in the taxon and a basis for molecular-level understanding on phenotypic diversity of elasmobranchs.

genomics↗

bioRxiv2025

RNA Dynamics Regulate Transcriptional Condensate Vivacity to Drive Gene Coordination

Transcriptional condensates (TCs), enriched with Mediator, orchestrate super-enhancer (SE)-driven gene expression critical for cell identity. However, how their dynamic physical properties shape transcriptional activities remains unclear. Here, we reveal a previously unknown regulatory axis wherein dynamic features of enhancer RNA (eRNA), transcribed but rapidly degraded by the RNA exosome, maintain optimal TC fluidity and stability. Depletion of RNA exosome disrupts TC integrity, altering Mediator and Pol II colocalization, in embryonic stem cells. This TC perturbation attenuates proper transcriptional regulator loading and pause-release regulation, enhances transcriptional noise, and diminishes coordinated eRNA-mRNA expression for SE-associated genes. Multi-omics analyses, live-cell imaging, and computational modeling collectively demonstrate that RNA turnover modulates TC vivacity, facilitating widespread chromatin contacts between SE-containing active A compartments and coordinated transcriptional bursts across SE-associated genes. Our findings establish RNA-dependent condensate dynamics as an essential quality-control mechanism that fine-tunes global transcriptional coordination, maintaining cellular homeostasis and cell identity. HighlightsO_LIRNA exosome is required for the homeostasis of transcriptional condensates (TCs) C_LIO_LIRNA synthesis and decay optimize the fluidity and dynamic properties of TCs C_LIO_LITCs maintain the transcriptional consistency of super-enhancer (SE) genes C_LIO_LITCs support contacts of SE-containing A compartments for coordinated transcription C_LI

molecular biology↗

bioRxiv2025

Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones

Structural variation is increasingly recognized as a pivotal contributor to genomic diversity in marine invertebrates, yet its extent and evolutionary significance remain poorly characterized in many species. Haplotype-phased genome assembly is an excellent method for studying such variations by comparing homologous chromosomes. In this study, we constructed a haplotype-phased genome assembly for the western Pacific abalone, Haliotis gigantea, using high-fidelity (HiFi) long-read sequencing and high-resolution chromosome conformation capture (Hi-C) data. The primary and alternative assemblies each comprised 18 long scaffolds (>50 Mb), consistent with the species diploid chromosome number (2n = 36), and contained 96.5% and 96.2% complete single-copy Metazoa Benchmarking Universal Single-Copy Orthologs genes, respectively, indicating high assembly quality. Comparative analysis of the two haplotypes revealed three homologous chromosomes with large-scale non-syntenic regions caused by extensive segmental duplications, with each enriched in distinct gene domains. These non-syntenic chromosomes likely originated in abalone evolution, as they were conserved across both closely and distantly related species. Our findings highlight the evolutionary importance of non-syntenic structural variation in shaping genome architecture and suggest that such variation may play a broader role in functional diversification across abalones.

genomics↗

bioRxiv2025

Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms

Sex determination has been investigated across vertebrate lineages to reveal stepwise evolution of sex chromosomes and diversity of responsible molecular mechanisms. However, these studies hardly encompass cartilaginous fishes deeply isolated from the rest of vertebrates, which hinders the comprehensive view of vertebrate sex determination. Here, we produced chromosome-scale genome assemblies of egg-laying shark species and comparatively investigated genome sequences and transcriptome profiles across diverse cartilaginous fishes. Sex chromosome identification, supported by cytogenetic experiments, elucidated the homology of X chromosomes between sharks and rays as well as an extensively degenerating Y chromosome harboring no male-specific genes. These sex chromosomes scarcely included orthologs of previously documented sex determining genes. Transcriptomic analyses combined with histology of embryonic gonads revealed female-biased expressions of X-linked genes including those implicated in TGF-{beta} and IGF signaling pathways, which are attributed to their incomplete dosage compensation. Our findings indicate that sharks and rays share the oldest vertebrate sex chromosomes that originated around 300 million years ago and the dosage-dependent sex determination mechanism comprised of distinct molecules from other vertebrates. This study highlights the antiquity of sex chromosomes and uniqueness of sex determination mechanisms in sharks and rays, which advance our understanding on evolutionary plasticity of vertebrate sex determination.

evolutionary biology↗

bioRxiv2025

The Greenland shark genome: insights into deep-sea ecology and lifespan extremes

The Greenland shark (Somniosus microcephalus) is known for its slow metabolism and deep-sea habitat. It is considered the longest-lived vertebrate on Earth, with an estimated lifespan of 392{+/-}120 years. Despite its remarkable longevity and lifestyle, there have been no genomic studies on this species. Here, we report the first, chromosome-level assembly of the Greenland shark genome, which is 5.9 Gb in size with an N50 length of 233 Mb, and contains 37,125 predicted genes with a completeness score of 86.5%. We found that the copy numbers of three gene families (TNF, TLR, LRRFIP), which are involved in activating the NF-{kappa}B signaling pathway, are significantly increased in the Greenland shark compared to short-lived shark species. In the rhodopsin of this deep-sea dweller, we detected amino acid substitutions that result in spectral tuning for the so-called blue shift, suggesting adaptive evolution to dim-light vision. We also elucidate the dynamics of the effective population size (Ne) of the Greenland shark and its close relative, the Pacific sleeper shark (Somniosus pacificus). These genomic analyses offer new insights into the molecular basis of the exceptional longevity of the Greenland shark and highlight potential genetic mechanisms that could inform future research into longevity.

genomics↗

bioRxiv2024

Engineered acetylation patterns drive large-scale chromatin organization in vitro

Chromatin organization plays a crucial role in gene regulation [1, 2, 3], but disentangling the contributions of various epigenetic components to gene-scale chromatin structure remains challenging. While in vitro chromatin reconstitution enables controlled studies on the effect of bio-chemical factors on the structure, current methods are either limited to short arrays or lack control over histone modification patterns. Here we directly test how histone modification affects higher-order chromatin architecture by characterizing gene-scale reconstituted chromatin using single-molecule microscopy and in vitro Hi-C. We reconstitute 20-kilobase chromatin arrays with histone modification patterns controlled at 12-nucleosome resolution, achieving complete assembly of 96 nucleosomes in the designed order as confirmed by atomic force microscopy and longread sequencing. Observing end-to-end fluctuations of the reconstituted arrays, we find that increasing the density of acetylated nucleosomes leads to larger structural fluctuations with longer relaxation times, consistent with the predictions of a polymer model with hydrodynamic interactions. We demonstrate through in vitro Hi-C how acetylation reduces contact frequency between nucleosomes and induces open conformations. In heterogeneously modified arrays, differential contact probabilities between acetylated and unmodified regions lead to distinct structural domains. The results establish the physical principles by which histone modifications directly modulate chromatin architecture through altered nucleosome-nucleosome interactions, providing a quantitative framework for understanding and engineering genome organization.

biophysics↗

bioRxiv2024

Silver chimaera genome assembly and identification of the holocephalan sex chromosome sequence

Cartilaginous fishes are divided into holocephalans and elasmobranchs, and comparative studies involving them are expected to elucidate how variable phenotypes and distinctive genomic properties were established in those ancient vertebrate lineages. To date, molecular-level studies on holocephalans have concentrated on the family Callorhinchidae, with a chromosome-scale genome assembly of Callorhinchus milii available. In this study, we focused on the most species-rich holocephalan family Chimaeridae and sequenced the genome of its member, silver chimaera (Chimaera phantasma). We report the first chromosome-scale genome assembly of the Chimaeridae, with high continuity and completeness, which exhibited a large intragenomic variation of chromosome lengths, which is correlated with intron size. This pattern is observed more widely in vertebrates and at least partly accounts for cross-species genome size variation. A male-female comparison identified a silver chimaera genomic scaffold with a double sequence depth for females, which we identify as an X chromosome fragment. This is the first DNA sequence-based evidence of a holocephalan sex chromosome, suggesting a male heterogametic sex determination system. This study, allowing the first chromosome-level comparison among holocephalan genomes, will trigger in-depth understanding of the genomic diversity among vertebrates as well as species population genetic structures based on the genome assembly of high completeness.

genomics↗

bioRxiv2023

Chromosomal DNA sequences of the Pacific saury genome: versatile resources for fishery science and comparative biology

Pacific saury (Cololabis saira) is a commercially important small pelagic fish species in Asian. In this study, we conducted the first-ever whole genome sequencing of this species, with single molecule, real-time (SMRT) sequencing technology. The obtained high-fidelity (HiFi) long-read sequence data, which amount to approximately 30 folds of its haploid genome size that was measured with quantitative PCR (1.17 Gb), were assembled into contigs. Scaffolding with Hi-C reads yielded a whole genome assembly containing 24 chromosome-scale sequences, with a scaffold N50 length of 47.7 Mb. Screening of repetitive elements including telomeric repeats was performed to characterize possible factors that need to be resolved towards telomere-to-telomere sequencing. The larger genome size than in medaka, a close relative in Beloniformes, is at least partly explained by larger repetitive element quantity, which is reflected in more abundant tRNAs, in the Pacific saury genome. Protein-coding regions was predicted using transcriptome data, which resulted in 22,274 components. Retrieval of Pacific saury homologs of aquaporin (AQP) genes known from other teleost fishes validated high completeness and continuity of the genome assembly. These resources are available at https://treethinkers.nig.ac.jp/saira/ and will assist various molecular-level studies in fishery science and comparative biology.

genomics↗

bioRxiv2023

Meta-analysis of gonadal transcriptomes in protogynous fishes provides novel perspective into sex change machinery

Protogyny, being capable of changing from female to male during their lifetime, is prevalent in 20 families of teleosts but is believed to have evolved within specific evolutionary lineages. Therefore, shared regulatory factors governing the sex change process are expected to be conserved across protogynous fishes. However, a comprehensive understanding of this mechanism remains elusive. To identify these factors, we conducted a meta-analysis using gonadal transcriptome data from seven species. We curated data pairs of ovarian tissue and transitional gonad, and employed ratios of expression level as a unified criterion for differential expression, enabling a meta-analysis across species. Our approach revealed that classical sex change-related genes exhibited differential expression levels between the ovary and transitional gonads, consistent with previous reports. These results validate our methodologys robustness. Additionally, we identified novel genes not previously linked to gonadal sex change in fish. Notably, changes in the expression levels of acetoacetyl-CoA synthetase and apolipoprotein Eb, which are involved in cholesterol synthesis and transport, respectively, suggest that the levels of cholesterol, a precursor of steroid hormones crucial for sex change, are decreased upon sex change onset in the gonads. This implies a potential universal influence of cholesterol dynamics on gonadal transformation in protogyny.

zoology↗

bioRxiv2023

Shark and ray genome size estimation: methodological optimization for inclusive and controllable biodiversity genomics

Estimate of nuclear DNA content serves as an independent tool for validating the completeness of whole genome sequences and investigating the among-species variation of genome sizes, but for some species, the requirement of fresh cells makes this tool highly inaccessible. Here we focused on elasmobranch species (sharks and rays), and using flow cytometry or quantitative PCR (qPCR), estimated the nuclear DNA contents of brownbanded bamboo shark, white spotted bamboo shark, zebra shark, small-spotted catshark, sandbar shark, slendertail lanternshark, megamouth shark, red stingray, and ocellate spot skate. Our results revealed their genome sizes spanning from 3.40 pg (for ocellate spot skate) to 13.34 pg (for slendertail lanternshark), in accordance with the huge variation of genome sizes already documented for elasmobranchs. Our improved qPCR-based method enabled accurate genome size estimation without using live cells, which has been a severe limitation with elasmobranchs. These findings and our methodology are expected to contribute to better understanding of the diversity of genome sizes in elasmobranchs even including species with limited availability of fresh tissue materials. It will also help validate the completeness of already obtained or anticipated whole genome sequences.

genomics↗

bioRxiv2022

Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotypic organization

Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here, we report the chromosome-scale genome assembly for the zebra shark Stegostoma tigrinum, an endangered species that has the smallest genome sequenced to date among sharks (3.71 Gb), as well as for the whale shark Rhincodon typus. Our analysis employing a male-female comparison identified an X chromosome, the first genomically characterized shark sex chromosome. The X chromosome harbors a Hox C cluster whose intact linkage has not been shown for an elasmobranch fish. The sequenced shark genomes exhibit a gradualism of chromosome length with remarkable length-dependent characteristics--shorter chromosomes tend to have higher GC content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length, which resemble the edges of longer chromosomes. This pattern of intragenomic heterogeneity, previously recognized as peculiar to species with so-called microchromosomes, occurs in more vertebrates including elasmobranchs. We challenge the traditional binary classification of karyotypes as with and without microchromosomes, as even without microchromosomes, shorter chromosomes tend to have higher contents of GC and simple tandem repeats and harbor shorter and more rapid-evolving genes. Such characteristics also appear on the edges of longer chromosomes. Our investigation of elasmobranch karyotypes underpins their unique characteristics and provides clues for understanding how vertebrate karyotypes accommodate intragenomic heterogeneity to realize a complex readout.

evolutionary biology↗

bioRxiv2022

Single cell transcriptomics of ferrets reveal a common temporal pattern of progenitors in brain development of gyrencephalic mammals

The diversity of neural stem cells is a hallmark of the cerebral cortex development in gyrencephalic mammals, such as Primates and Carnivora. Among them, ferrets are a good model for mechanistic studies. However, information on their neural progenitor cells (NPC), termed radial glia (RG), is limited. Here, we surveyed the temporal series of single-cell transcriptomes of progenitors regarding ferret corticogenesis and, found a conserved diversity and temporal trajectory between human and ferret NPC, despite the large timescale difference. We found truncated RG (tRG) in ferret cortical development, a progenitor subtype previously described in humans. The combination of in silico and in vivo analyses identified that tRG differentiate into both ependymal and astrogenic cells. Via transcriptomic comparison, we predict that this is also the case in humans. Our findings suggest that tRG plays a role in the formation of adult ventricles, thereby providing the architectural bases for brain expansion.

developmental biology↗

bioRxiv2021

Single-cell transcriptome atlas of Drosophila gastrula 2.0

During development, positional information directs cells to specific fates, leading them to differentiate with their own transcriptomes and express specific behaviors and functions. However, the mechanisms underlying these processes in a genome-wide view remain ambiguous, partly because the single-cell transcriptomic data of early developing embryos containing both accurate spatial and lineage information is still lacking. Here, we report a new single-cell transcriptome atlas of Drosophila gastrulae, divided into 65 transcriptomically distinct clusters. We found that the expression profiles of plasma-membrane-related genes, but not those of transcription factor genes, represented each germ layer, supporting the nonequivalent contribution of each transcription factor mRNA level to effector gene expression profiles at the transcriptome level. We also reconstructed the spatial expression patterns of all genes at the single-cell stripe level as the smallest unit. This atlas is an important resource for the genome-wide understanding of the mechanisms by which genes cooperatively orchestrate Drosophila gastrulation.

developmental biology↗

bioRxiv2021

Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu fish

Recent studies have revealed a surprising diversity of sex chromosomes in vertebrates. However, the detailed mechanism of their turnover is still elusive. To understand this process, it is necessary to compare closely related species in terms of sex-determining genes and the chromosomes harboring them. Here, we explored the genus Takifugu, in which one strong candidate sex-determining gene, Amhr2, has been identified. To trace the processes involved in transitions in the sex determination system in this genus, we studied 12 species and found that while the Amhr2 locus likely determines sex in the majority of Takifugu species, three species have acquired sex-determining loci at different chromosomal locations. Nevertheless, the generation of genome assemblies for the three species revealed that they share a portion of the male-specific supergene that contains a candidate sex-determining gene, GsdfY, along with genes that potentially play a role in male fitness. The shared supergene span approximately 100 kb and are flanked by two duplicated regions characterized by CACTA transposable elements. These results suggest that the shared supergene has taken over the role of sex-determining locus from Amhr2 in lineages leading to the three species, and repeated translocations of the supergene underlie the turnover of sex chromosomes in these lineages. These findings highlight the underestimated role of a mobile supergene in the turnover of sex chromosomes in vertebrates. SignificanceAlthough turnover of sex chromosomes is very common in many vertebrate lineages, the transition process is still elusive. We studied the sex-determining region (SDR) of 12 congeneric fish species. We found that while nine species retained their ancestral SDR, three species had acquired derived SDRs. Although the derived SDRs resided in three different chromosomes, they harbored a shared supergene flanked by two putative transposable elements. The results highlight the underestimated role of a mobile supergene in turnover of sex chromosomes in vertebrates.

genomics↗