Biology subjects

Kawaguchi, A.

Publications and source records attributed to Kawaguchi, A..

11 recordsLinked to original sources

bioRxiv2026

Near-complete genome assembly of the African turquoise killifish enables locus-level profiling of transposable element expression

Tandem repeats (TRs) and transposable elements (TEs) occupy substantial fractions of eukaryotic genomes, yet how repeat detection programs affect downstream expression analyses remains poorly explored. Here, we present an improved chromosome-scale assembly of the African turquoise killifish, Nothobranchius furzeri. The assembly matches experimentally estimated genome size and chromosome number. It resolves highly expanded TRs that occupy up to 28.0% of the whole genome. Using this assembly and other complete vertebrate genome assemblies, we compared TR and TE-derived regions across combinations of TR detection programs and TE consensus library construction workflows under a standardized TE classification scheme. Choices in TR detection reshaped the apparent TE landscape. TE workflows shared a broad core of TE-derived regions but recovered complementary sets of age- and sex-associated TE loci, evaluated with a sex-balanced killifish multi-tissue aging cohort. Together, the combinatorial use of adaptable programs supports robust, locus-aware detection of complex repeats across genome assemblies.

genomics↗

bioRxiv2026

Inhibition of the gut ceramidase Asah2 decelerates the vertebrate ageing rate

The pace of ageing varies markedly among vertebrate species and individuals. However, the mechanisms underlying these differences in ageing rates remain unclear. Here, we show that the activity of the gut ceramidase Asah2 determines species- and strain-specific rates of vertebrate ageing. Comparative genomic analyses of vertebrate species and strains with different ageing rates reveal an association between low Asah2 activity and increased lifespan. Using the ultra-short-lived killifish Nothobranchius furzeri as a model, we demonstrate that knockout of Asah2 (asah2 KO) extends lifespan and attenuates systemic ageing phenotypes, including declines in locomotor activity, abnormal protein accumulation in the brain, and accumulation of senescent cells in the liver. asah2 KO elevates levels of ceramide species with long-chain fatty acids in the intestine, and supplementation with these ceramide species suppresses ageing phenotypes and extends lifespan in wild-type fish. asah2 KO and ceramide supplementation alter gut microbiota composition, and asah2 KO-derived microbiota transplantation attenuates ageing phenotypes, suggesting that reduced Asah2 activity prevents ageing through intestinal ceramide-mediated modulation of the microbiota. Given the evolutionary conservation of the Asah2 gene and its age-dependent upregulation in fish and humans, Asah2 and ceramides may act as ageing accelerators and decelerators, respectively, across animal species.

developmental biology↗

bioRxiv2025

ATAC-seq of Low-Input and Cryopreserved Primordial Germ Cells Reveals Functional Enhancers

Cell fate specification during development is orchestrated by dynamic changes in gene expression, driven by the accessibility of cis-regulatory elements. To profile such functional regulatory elements at the genome-wide level, bulk ATAC-seq is a powerful method. Yet, its application has still been technically limited in rare cell types. Here, we optimized and titrated the ATAC-seq protocol for cultured chicken primordial germ cells (PGCs) and obtained high-quality chromatin accessibility profiles from as few as 200 cells, even after cryopreservation. Integrative analysis of our ATAC-seq with published RNA-seq and tissue ATAC-seq datasets identified over 10,000 PGC-specific accessible chromatin regions (ACRs), many absent from somatic tissues. Reporter assays demonstrated activity of selected enhancers in cultured PGCs, while transcriptome integration revealed preferential association of PGC-specific ACRs with genes highly expressed at embryonic day 2.5. In vivo transplantation confirmed that these enhancers are active in an early-stage-specific manner, but become silenced upon gonadal settlement. In conclusion, this streamlined method provides a practical and cost-effective approach to the epigenomic analysis of scarce cell populations, facilitating future investigations in developmental biology, germline research, and beyond.

developmental biology↗

bioRxiv2025

The chicken retrovirus-like gene ENS-1/ERNI and its LTR Soprano are involved in primordial germ cell development.

Cultured chicken primordial germ cells (PGCs) are attractive tools for reproductive biology and for preserving and modifying genetic resources. However, it remains difficult to establish cell lines from some breeds or females. In the present study, we performed transcriptome analyses of cultured PGCs from different breeds and found that the expression of the Galliformes-specific endogenous retrovirus-like gene ENS-1/ERNI correlated with the establishment efficiency of PGC lines. CRISPRi targeting the ENS-1/ERNI long terminal repeat (LTR) sequence (Soprano) broadly reduced homeostasis-related genes including ribosome, endoplasmic reticulum, and oxidative phosphorylation. These PGCs exhibited abnormal cell cycle arrest under DNA-damaged conditions, suggesting involvement in the quality control mechanisms of chicken PGCs. Furthermore, when transplanted into blastoderms, these PGCs showed a reduction in colonization of the genital ridges. These results indicate the involvement of Soprano LTR and ENS-1/ERNI in the development of chicken PGCs and their adaptation to the in vitro environment.

cell biology↗

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↗

bioRxiv2022

The shh limb enhancer is activated in patterned limb regeneration but not in hypomorphic limb regeneration in Xenopus laevis

Xenopus young tadpoles regenerate a limb with the anteroposterior (AP) pattern, but metamorphosed froglets regenerate a hypomorphic limb after amputation. The key gene for AP patterning, shh, is expressed in a regenerating limb of the tadpole but not in that of the froglet. Genomic DNA in the shh limb-specific enhancer, MFCS1 (ZRS), is hypermethylated in froglets but hypomethylated in tadpoles: shh expression may be controlled by epigenetic regulation of MFCS1. Is MFCS1 specifically activated for regenerating the AP-patterned limb? We generated transgenic Xenopus laevis lines that visualize the MFCS1 enhancer activity with a GFP reporter. The transgenic tadpoles showed GFP expression in hoxd13- and shh-expressing domains of developing and regenerating limbs, whereas the froglets showed no GFP expression in the regenerating limbs despite having hoxd13 expression. Genome sequence analysis and co-transfection assays using cultured cells revealed that Hoxd13 can activate Xenopus MFCS1. These results suggest that MFCS1 activation correlates with regeneration of AP-patterned limbs and that re-activation of epigenetically inactivated MFCS1 would be crucial to confer the ability to non-regenerative animals for regenerating a properly patterned limb.

developmental biology↗

bioRxiv2022

Calcium signals tune AMPK activity and mitochondrial homeostasis in dendrites of developing neurons

The growth of dendritic arbors in developing neurons is known to be regulated by neuronal activity, which is thought as one of the mechanisms of neural circuit optimization. Here we demonstrate that activity-dependent calcium signaling controls mitochondrial homeostasis and dendritic outgrowth via AMP-activated protein kinase (AMPK) in developing hippocampal neurons. AMPK deficiency phenocopies the inhibition of neuronal activity, inducing dendritic hypotrophy with abnormally elongated mitochondria. In growing dendrites, AMPK is activated by neuronal activity and dynamically oscillates in synchrony with calcium spikes, and this AMPK oscillation is inhibited by CaMKK2 knockdown. AMPK activation leads to phosphorylation of MFF and ULK1, which initiate mitochondrial fission and mitophagy, respectively. Dendritic mitochondria in AMPK-depleted neurons exhibit impaired fission and mitophagy and display multiple signs of dysfunction. Thus, AMPK activity is finely tuned by the calcium-CaMKK2 pathway and regulates mitochondrial homeostasis by facilitating removal of damaged components in rapidly growing neurons during normal brain development.

neuroscience↗

bioRxiv2022

Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration

The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed "positional information". How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program.

developmental biology↗

bioRxiv2022

Border-associated macrophages transventricularly infiltrate the early embryonic cerebral wall to differentiate into microglia

The relationships between microglia and macrophages, especially their lineage segregation outside the yolk sac, have been recently explored, providing a model in which a conversion from macrophages seeds microglia during brain development. However, spatiotemporal evidence to support such microglial seeding and to explain how it occurs has not been obtained. By cell tracking via slice culture, intravital imaging, and Flash tag-mediated labeling, we found that a group of intraventricular macrophages belonging to border-associated macrophages (BAMs), which were abundantly observed along the inner surface of the mouse cerebral wall at embryonic day 12, frequently entered the brain wall. Immunohistochemistry of the tracked cells showed that postinfiltrative BAMs acquired microglial properties while losing a macrophage phenotype. We also found that the intraventricular BAMs were supplied transepithelially from the roof plate. Thus, this study demonstrates that the "roof plate[->]ventricle[->]cerebral wall" route is an essential path for microglial colonization into the embryonic mouse brain.

neuroscience↗

bioRxiv2022

G307S DNAM-1 mutation exacerbates autoimmune encephalomyelitis via enhancing CD4+ T cell activation

Although rs763361, which causes a non-synonymous glycine-to-serine mutation at residue 307 (G307S mutation) of the DNAM-1 immunoreceptor, is a single-nucleotide polymorphism (SNP) associated with autoimmune disease susceptibility, little is known about how the SNP is involved in pathogenesis. Here, we established CD4+ T cells expressing wild-type or G307S DNAM-1 and showed that the costimulatory signal from G307S DNAM-1 induced greater pro-inflammatory cytokine production and cell proliferation than that from wild-type DNAM-1. The G307S mutation also enhanced the recruitment of the tyrosine kinase Lck and augmented tyrosine phosphorylation at residue 322 (Tyr322) of DNAM-1. However, conversion of Tyr322 of DNAM-1 to phenylalanine (Y322F mutation) canceled the enhanced activation of CD4+ T cell transfectants expressing G307S DNAM-1. Adoptive transfer of myelin-antigen-specific CD4+ T cells expressing G307S DNAM-1 into mice exacerbated experimental autoimmune encephalomyelitis compared with the transfer of cells expressing wild-type DNAM-1. These findings suggest that rs763361 is a gain-of-function mutation that enhances DNAM-1-mediated costimulatory signaling for proinflammatory responses.

immunology↗

bioRxiv2020

Potent mouse monoclonal antibodies that block SARS-CoV-2 infection

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has developed into a global pandemic since its first outbreak in the winter of 2019. An extensive investigation of SARS-CoV-2 is critical for disease control. Various recombinant monoclonal antibodies of human origin that neutralize SARS-CoV-2 infection have been isolated from convalescent patients and will be applied as therapies and prophylaxis. However, the need for dedicated monoclonal antibodies in molecular pathology research is not fully addressed. Here, we produced mouse anti-SARS-CoV-2 spike monoclonal antibodies that exhibit not only robust performance in immunoassays including western blotting, ELISA, immunofluorescence, and immunoprecipitation, but also neutralizing activity against SARS-CoV-2 infection in vitro. Our monoclonal antibodies are of mouse origin, making them compatible with the experimental immunoassay setups commonly used in basic molecular biology research laboratories, and large-scale production and easy distribution are guaranteed by conventional mouse hybridoma technology.

microbiology↗