Biology subjects

Tonosaki, K.

Publications and source records attributed to Tonosaki, K..

5 recordsLinked to original sources

bioRxiv2026

EC1 body controls sperm cell reception via gamete pit formation.

The remarkable efficiency of double fertilization in flowering plants depends on the precise delivery of immotile sperm cells to two female gametes1. Although sperm cells are rapidly released from the pollen tube, how they are accurately directed to their fertilization site has remained unknown. Here we identify a transient extracellular structure, termed the gamete pit, that forms at the egg cell-central cell (EC-CC) interface immediately after pollen tube discharge and serves as the landing site for sperm cells. Gamete pit formation is enabled by localized dissociation of the EC-CC interface, mediated by extracellular protein assemblies designated EC1 bodies. These structures contain extracellular deposits enriched in EGG CELL 1 (EC1) peptides2, including amyloid-like assemblies. Loss of EC1 bodies prevented gamete pit formation, causing sperm-cell backflow or catastrophic over-penetration of pollen tube contents into the central cell. Surprisingly, ectopic deposition of a heterologous amyloidogenic protein alleviated over-penetration and partially restored fertility. Our findings reveal a mechanism by which extracellular protein assemblies remodel the gamete interface for sperm-cell reception, uncover an unexpected structural role for the conserved gamete-activating peptide EC1, and establish protein-mediated cell-interface remodeling as a fundamental principle underlying double fertilization in flowering plants.

plant biology↗

bioRxiv2026

glmmDMR reveals replicate-level methylation variance as a major determinant of false-positive DMR detection

BackgroundAccurate identification of differentially methylated regions (DMRs) is fundamental to epigenomic research but remains challenging due to biological variability among replicates, heterogeneous effect sizes, and the tendency of adjacent cytosines to share similar methylation states. Many existing methods aggregate methylation measurements before statistical testing or do not explicitly account for replicate-level variability, contributing to elevated false-positive rates. ResultsWe developed glmmDMR, a DMR detection framework that combines generalized linear mixed models with a seed-based strategy for reconstructing DMRs from locally high-confidence signals while explicitly modeling replicate-level variability. Using simulated datasets with known ground-truth DMRs, we demonstrate that false-positive detections are more strongly associated with methylation variance among biological replicates than with the magnitude of methylation differences between groups. glmmDMR achieved higher precision than existing approaches while maintaining competitive recall, particularly for subtle methylation differences. Site-level modeling with beta regression provided the strongest overall performance, and seed-based region construction reduced artificial DMR fragmentation, improving recovery of true DMR boundaries and producing more contiguous, biologically interpretable DMRs. Applied to Arabidopsis thaliana ddm1 methylomes and a rice DEMETER-LIKE DNA demethylase mutant (Osdml3a-1), glmmDMR identified biologically meaningful DMRs, revealing widespread TE-associated hypomethylation and subtle TE-family-specific hypermethylation. ConclusionsReplicate-level methylation variance is an important determinant of DMR detection performance, and explicitly modeling this variance improves discrimination of biologically meaningful methylation changes from high-variance signals. By combining variance-aware statistical modeling with seed-based region construction, glmmDMR provides a robust framework for identifying contiguous, biologically interpretable DMRs across diverse methylome datasets.

genomics↗

bioRxiv2025

DECREASE IN DNA METHYLATION 1-mediated epigenetic regulation maintains gene expression balance required for heterosis in Arabidopsis thaliana

Heterosis, or hybrid vigor, is characterized by superior phenotypic performance in F hybrids compared to their parental lines, and its expression is influenced by both genetic and epigenetic factors. In this study, we investigated the role of epigenetic regulation, particularly DNA methylation mediated by DECREASE IN DNA METHYLATION 1 (DDM1), in early seedling biomass heterosis using hybrids between Arabidopsis thaliana accessions Columbia-0 and C24. Loss of DDM1 function in F hybrids resulted in a significant reduction of rosette diameter, confirming that DDM1 is essential for heterosis. Transcriptomic and epigenomic analyses revealed extensive genotype-specific changes in gene expression and DNA methylation patterns in ddm1 mutants. Notably, ddm1-F hybrids exhibited upregulation of genes categorized into xyloglucan:xyloglucosyl transferase activity and downregulation of genes categorized into circadian rhythm, which may contribute to reduced growth vigor. Whole-genome bisulfite sequencing showed widespread hypomethylation in ddm1 mutants, yet the overlap between differentially methylated and expressed genes was limited, suggesting indirect or context-dependent regulatory effects. Additionally, we examined the role of salicylic acid (SA) in heterosis using SA-deficient mutants and found that variations in endogenous SA levels did not correlate with biomass heterosis under normal conditions. Our findings suggest that heterosis in A. thaliana is dependent on the maintenance of parental epigenetic divergence, particularly in DNA methylation patterns mediated by DDM1. Disruption of DDM1 compromises this epigenetic complementarity, leading to transcriptomic imbalances that reduce heterosis. HighlightLoss of DDM1 reduces biomass heterosis in Arabidopsis thaliana hybrids by disrupting DNA methylation and transcriptome stability, revealing a novel salicylic acid-independent epigenetic mechanism.

plant biology↗

bioRxiv2021

Temporal Changes in Transcripts of MITE Transposable Elements during Rice Endosperm Development

The repression of transcription from transposable elements (TEs) by DNA methylation is necessary to maintain genome integrity and prevent harmful mutations. However, under certain circumstances, TEs are thought to escape from the host defense system and reactivate their transcription. In Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), DNA demethylases target the sequences derived from TEs in the central cell, the progenitor cell for the endosperm in the female gametophyte. This genome-wide DNA demethylation is also observed in the endosperm after fertilization. In this study, we used a custom microarray to survey the transcripts generated from TEs during the rice endosperm development and at selected timepoints in the embryo as a control. The expression patterns of TE transcripts are dynamically up- and downregulated during endosperm development, especially for miniature inverted-repeat transposable elements (MITEs). Surprisingly, some TE transcripts were directionally controlled, while the other DNA transposons and retrotransposons were not. We also discovered the NF-Y binding motif, CCAAT, in the region near the 5' terminal inverted repeat of Youren, one of the transcribed MITEs in the endosperm. Our results uncover dynamic changes in TE activity during endosperm development in rice.

plant biology↗

bioRxiv2021

Cubam receptor-mediated endocytosis in hindgut-derived pseudoplacenta of a viviparous teleost Xenotoca eiseni

Nutrient transfer from mother to the embryo is essential for reproduction in viviparous animals. In the viviparous teleost Xenotoca eiseni belonging to the family Goodeidae, the intraovarian embryo intakes the maternal component secreted into the ovarian fluid via the trophotaenia. Our previous study reported that the epithelial layer cells of the trophotaenia incorporate a maternal protein via vesicle trafficking. However, the molecules responsible for the absorption were still elusive. Here, we focused on Cubam (Cubilin-Amnionless) as a receptor involved in the absorption, and cathepsin L as a functional protease in the vesicles. Our results indicated that the Cubam receptor is distributed in the apical surface of the trophotaenia epithelium and then is taken into the intracellular vesicles. The trophotaenia possesses acidic organelles in epithelial layer cells and cathepsin L-dependent proteolysis activity. This evidence does not conflict with our hypothesis that receptor-mediated endocytosis and proteolysis play roles in maternal macromolecule absorption via the trohotaenia in viviparous teleosts. Such nutrient absorption involving endocytosis is not a specific trait in viviparous fish. Similar processes have been reported in the larval stage of oviparous fish or the suckling stage of viviparous mammals. Our findings suggest that the viviparous teleost acquired trophotaenia-based viviparity from a modification of the intestinal absorption system common in vertebrates. This is a fundamental study to understand the strategic variation of the reproductive system in vertebrates. Summary statementHere, we report that an endocytic pathway is a candidate for nutrient absorption in pseudoplacenta of a viviparous teleost. The trait may have developed from common intestinal mechanism among vertebrates.

zoology↗