Biology subjects

Aoyama, K.

Publications and source records attributed to Aoyama, K..

9 recordsLinked to original sources

bioRxiv2026

Coffee induces chromatin structural changes associated with histone H4K16 hypoacetylation

Histone acetylation plays a critical role in the regulation of chromatin structure and gene expression. Among histone acetylation marks, acetylation of histone H4 at lysine 16 (H4K16ac) is particularly important for the maintenance of chromatin organization. We previously identified a reduction in H4K16ac following coffee treatment through mass spectrometry-based histone modification profiling. In the present study, we investigated the effects of coffee on H4K16ac levels, chromatin structure, and gene expression. Western blotting and immunofluorescence analyses confirmed that coffee treatment reduced H4K16ac levels in a cell type-dependent manner. Notably, H4K16ac was reduced in HCT116 cells, in which H3K27ac was not decreased by coffee treatment. Quantitative analysis of DAPI-stained nuclei revealed a significant increase in the coefficient of variation of nuclear fluorescence intensity following coffee treatment, indicating alterations in chromatin structure. Furthermore, integrative analysis of publicly available H4K16ac chromatin immunoprecipitation sequencing (ChIP-seq) data and previously generated RNA sequencing (RNA-seq) data revealed that H4K16ac-enriched genes exhibited transcriptional changes following coffee treatment in K562 cells, including the downregulation of MYC-associated genes. Together, these findings demonstrate that coffee treatment induces alterations in chromatin structure accompanied by H4K16 hypoacetylation and suggest a potential association between these epigenetic changes and transcriptional regulation.

molecular biology↗

bioRxiv2026

Coffee remodels the global histone acetylation landscape with reduced H3K27ac at the MYC promoter

Coffee consumption has been associated with reduced risks of multiple chronic diseases, including cancer; however, whether coffee regulates the epigenetic landscape remains largely unknown. Here, we show that coffee extensively remodels the histone acetylation landscape in human cells. Quantitative histone modification proteomics revealed a global reduction in active histone acetylation marks following coffee treatment. Mechanistically, coffee reduced the abundance of the histone acetyltransferases GCN5 and MOF, decreased 14-3-3 proteins, promoted the nuclear accumulation of class II histone deacetylases, and induced histone hypoacetylation that was reversed by the histone deacetylase inhibitor trichostatin A. Genome-wide H3K27ac profiling revealed widespread loss of promoter and enhancer acetylation, accompanied by broad transcriptional reprogramming. Integrative analyses of ChIP-seq, RNA-seq, proteomics and biochemical validation consistently demonstrated suppression of the MYC transcriptional program, including reduced MYC expression, decreased H3K27ac at MYC target promoters, downregulation of canonical MYC target genes and attenuation of MYC target gene signatures. Functionally, coffee inhibited cancer cell proliferation with minimal cell death. Collectively, our findings identify whole coffee as a previously unrecognized epigenetic modulator that remodels the histone acetylation landscape in association with suppression of the MYC transcriptional program, providing a molecular framework for understanding the epigenetic basis underlying the anti-tumor effects of coffee.

molecular biology↗

bioRxiv2026

Oncogenic NPM-ALK reprograms the TGM1 1 interactome toward oncogenic signaling and transcriptional states

Oncogenic NPM-ALK drives aberrant signaling networks that promote malignant phenotypes; however, the molecular mechanisms linking oncogenic signaling to downstream cellular programs remain incompletely understood. Among candidate regulatory factors, transglutaminase 1 (TGM1) has not been functionally characterized in this context. Here, we investigated the role of TGM1 in NPM-ALK-expressing cells by combining proximity-dependent proteomics with functional analyses. Using a TurboID- based approach, we mapped the TGM1-associated protein network and identified extensive remodeling of this network upon NPM-ALK expression. Proteomic analyses revealed that NPM-ALK reduced TGM1-associated proteins involved in genome maintenance and DNA repair, while enhancing associations with proteins linked to cytoplasmic translation and PI3K-AKT signaling pathways. Consistent with these findings, TGM1 deficiency impaired cell proliferation without significantly affecting cell viability, indicating a specific role in maximal proliferative capacity. Furthermore, proteomic and functional analyses suggested a link between TGM1 and AKT signaling pathways. Together, these findings suggest that oncogenic NPM-ALK reprograms the TGM1 interactome toward oncogenic signaling and transcriptional states, positioning TGM1 within signaling networks associated with proliferative cellular phenotypes.

molecular biology↗

bioRxiv2026

Ribonuclease L Regulates Antiviral Responsiveness through Cleavage of XBP1 mRNA

During viral infection, viral replication perturbs endoplasmic reticulum (ER) homeostasis and triggers the unfolded protein response (UPR). XBP1s, a transcription factor generated by one branch of the UPR, is known to potentiate both innate and adaptive immunity, but its role in antiviral responses remains incompletely understood beyond its ability to augment type I interferon (IFN) mRNA induction. Here, we show that XBP1s positively regulates the RIG-I-like receptors (RLRs), ribonuclease L (RNase L), and protein kinase R (PKR) pathways, indicating that it enhances all three major antiviral response pathways. We further show that RNase L activation rapidly decreases XBP1 mRNA levels in an RNase activity-dependent manner, leading to a prompt reduction in XBP1s expression. Consistent with this, RNase L deletion significantly increased both thapsigargin-mediated XBP1s induction and XBP1s expression following Japan encephalitis virus infection. Poly(I:C)-induced IFNB mRNA expression was significantly enhanced in RNase L-knockout cells. This enhancement was completely abolished by RNase L reconstitution. XBP1 knockdown also significantly attenuated IFNB mRNA expression in RNase L-knockout cells. These findings suggest a negative-feedback loop in which RNase L suppresses XBP1s, thereby fine-tuning antiviral responsiveness during viral infection. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/713401v1_ufig1.gif" ALT="Figure 1000"> View larger version (19K): org.highwire.dtl.DTLVardef@112d312org.highwire.dtl.DTLVardef@df79a9org.highwire.dtl.DTLVardef@1ac571borg.highwire.dtl.DTLVardef@18ac610_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

A coral peptide has bactericidal activity against a global marine pathogen, Vibrio coralliilyticus

Scleractinian corals and their associated microorganisms, including endosymbiotic dinoflagellates and bacteria, constitute coral holobionts. Rising seawater temperatures weaken coral symbiotic relationships, thereby increasing susceptibility to infectious diseases and leading to disease outbreaks and subsequent population declines. The temperature-dependent coral pathogen, Vibrio coralliilyticus, poses one of the greatest threats to coral reefs because of global warming. However, coral immune defenses against this pathogen are poorly understood. We previously identified coral genes responding to V. coralliilyticus exposure by transcriptomic analysis of the reef-building coral, Acropora digitifera. Here, bioinformatic analysis identified digitiferin, a coral antimicrobial peptide (AMP), in the genome of A. digitifera. Recombinant digitiferin showed antibacterial activity against both Gram-positive and -negative bacteria. A 3D structural model and direct microscopic observations revealed that digitiferin damaged bacterial cell membranes by forming pores; however, initial growth inhibition tests in 1.5 % (w/v) NaCl showed no effect on pathogens. Because we found that digitiferin is secreted from epithelial cells into mucus and shows salt sensitivity, we hypothesized that it is active against pathogens in low-salt environments. We then investigated whether it showed antibacterial activity against pathogens in low-salt, moderate-osmolality conditions, using mannitol for osmoregulation instead of NaCl. The results showed that digitiferin exhibits bactericidal activity against V. coralliilyticus under salt-free conditions. To the best of our knowledge, this is the first study to characterize a scleractinian AMP that kills V. coralliilyticus. These findings contribute to a better understanding of coral immunity and may facilitate development of techniques to overcome coral Vibrio disease. SignificanceHealthy coral reefs are one of the most important marine ecosystems, supporting [~]25 % of all marine organisms. Coral reef ecosystems are threatened by coral infectious diseases, as rising seawater temperatures exacerbate pathogen infectivity. Thus, understanding coral immune systems is becoming increasingly important to protect coral reefs. This study reports the discovery of an antimicrobial peptide, digitiferin, from the reef-building coral, Acropora digitifera. Digitiferin is effective against Gram-positive and -negative bacteria, including the major coral pathogen, Vibrio coralliilyticus, and is secreted into mucus from ectodermal granular epithelial cells. As the first antimicrobial peptide known to have bactericidal activity against V. coralliilyticus, this discovery enhances our understanding of coral immunology and coral-pathogen interactions.

microbiology↗

bioRxiv2024

Cryo-electron tomography of the actin cytoskeleton and membrane organization during lamellipodia formation using optogenetics

Lamellipodia are sheet-like protrusions essential for migration and endocytosis, yet the ultrastructure of the actin cytoskeleton during lamellipodia formation remains underexplored. Here, we combined the optogenetic tool PA-Rac1 with cryo-ET to enable ultrastructural analysis of newly formed lamellipodia. We successfully visualized lamellipodia at various extension stages, representing phases of their formation. In minor extensions, several unbundled actin filaments formed "Minor protrusions" at the leading edge. For moderately extended lamellipodia, cross-linked actin filaments formed small filopodia-like structures, termed "mini filopodia." In fully extended lamellipodia, filopodia matured at multiple points, and cross-linked actin filaments running nearly parallel to the leading edge increased throughout the lamellipodia. These observations suggest that actin polymerization begins in specific plasma membrane regions, forming mini filopodia that either mature into full filopodia or detach from the leading edge to form parallel filaments. This actin turnover likely drives lamellipodial protrusion, providing new insights into actin dynamics and cell migration.

cell biology↗

bioRxiv2023

Deciphering mechanisms of UV filter- and temperature-induced bleaching in the coral Acropora tenuis, using ecotoxicogenomics

Coral reefs are at risk of bleaching due to various environmental and anthropogenic stressors such as global warming and chemical pollutants. However, there is little understanding of stressor-specific mechanisms that cause coral bleaching. Therefore, conducting accurate ecotoxicological risk assessments and deciphering modes of action of potentially deleterious ultraviolet (UV) filters (sunscreen compounds) are crucial issues. In this study, we evaluated the toxicity and bleaching effect of benzophenone-3 (BP-3), which is widely used in sunscreen products, on the reef-building coral Acropora tenuis. Furthermore, to understand differences in UV filter- and temperature-induced bleaching, a comparative ecotoxicogenomic approach using RNA-seq was integrated into a toxicity test to clarify differences in gene expression changes induced by BP-3 and heat stress (31{degrees}C). The lethal concentration 50% (LC50) was calculated as 3.9 mg/L, indicating that emission level of BP-3 was properly controlled based on the risk assessment. Differentially expressed genes related to oxidative stress and extracellular matrix organization were involved in coral responses to both BP-3 and heat stress, but their patterns differed. Whereas immune and heat-shock responses were activated in response to heat stress, activation of a drug metabolism pathway and several signal transduction pathways were identified in BP-3 treatment groups. Our study enhances understanding of stress responses in corals induced by UV filters and thermal stress. Using potential gene markers identified in this study for eco-epidemiological surveys of stressed corals, we urgently need to develop effective countermeasures.

ecology↗

bioRxiv2022

Polycomb repressive complex 1.1 coordinates homeostatic and emergency myelopoiesis

Polycomb repressive complex (PRC) 1 regulates stem cell fate by mediating mono-ubiquitination of histone H2A at lysine 119. While canonical PRC1 is critical for hematopoietic stem and progenitor cell (HSPC) maintenance, the role of non-canonical PRC1 in hematopoiesis remains elusive. PRC1.1, a non-canonical PRC1, consists of PCGF1, RING1B, KDM2B, and BCOR. We recently showed that PRC1.1 insufficiency induced by the loss of PCGF1 or BCOR causes myeloid-biased hematopoiesis and promotes transformation of hematopoietic cells in mice. Here we show that PRC1.1 serves as an epigenetic switch that coordinates homeostatic and emergency hematopoiesis. PRC1.1 maintains balanced output of steady-state hematopoiesis by restricting C/EBP-dependent precocious myeloid differentiation of HSPCs and the HOXA9- and {beta}-catenin-driven self-renewing network in myeloid progenitors. Upon regeneration, PRC1.1 is transiently inhibited to facilitate formation of granulocyte-macrophage progenitor (GMP) clusters, thereby promoting emergency myelopoiesis. Moreover, constitutive inactivation of PRC1.1 results in unchecked expansion of GMPs and eventual transformation. Collectively, our results define PRC1.1 as a novel critical regulator of emergency myelopoiesis, dysregulation of which leads to myeloid transformation.

immunology↗

bioRxiv2021

CAMSAP2 organizes a γ-tubulin-independent microtubule nucleation centre

Microtubules are dynamic polymers consisting of {beta}-tubulin heterodimers. The initial polymerization process, called microtubule nucleation, occurs spontaneously via {beta}-tubulin. Since a large energy barrier prevents microtubule nucleation in cells, the {gamma}-tubulin ring complex is recruited to the centrosome to overcome the nucleation barrier. However, detachment of a considerable number of microtubules from the centrosome is known to contribute to fundamental processes in cells. Here, we present evidence that minus-end-binding calmodulin-regulated spectrin-associated protein 2 (CAMSAP2) serves as a strong nucleator for microtubule formation from soluble {beta}-tubulin independent of {gamma}-tubulin. CAMSAP2 significantly reduces the nucleation barrier close to the critical concentration for microtubule polymerization by stabilizing the longitudinal contacts among {beta}-tubulins. CAMSAP2 clusters together with {beta}-tubulin to generate nucleation intermediates, from which numerous microtubules radiate, forming aster-like structures. Our findings suggest that CAMSAP2 supports microtubule growth by organizing a nucleation centre as well as by stabilizing microtubule nucleation intermediates.

cell biology↗