Biology subjects

Fujiwara, S.

Publications and source records attributed to Fujiwara, S..

7 recordsLinked to original sources

bioRxiv2026

WRN deficiency generates oncogenic rearrangements at TA-rich tandem repeats

Werner syndrome, a premature-aging disorder caused by inherited loss of the WRN helicase, predisposes to a narrow set of cancers, including melanoma and sarcoma, through mechanisms that have been unclear. WRN resolves the secondary structures that TA-dinucleotide repeats form, a role established for the expanded repeats of mismatch-repair-deficient cancers. We show that WRN loss also destabilizes native, unexpanded TA-rich tandem repeats, which become fragile sites where chromosomes break and rearrange. In melanoma these rearrangements recurrently produce an identical 15.7Mb-long deletion that transcriptionally activates TERT, the earliest driver of these tumors, and separately disrupt tumor suppressors such as CDKN2A/B and NF1. The same class of rearrangement occurs in WRN-deficient cancers of other types. WRN deficiency is thus a source of instability at TA-rich tandem repeats that generates oncogenic rearrangements.

cancer biology↗

bioRxiv2026

Coordinated Temporal Dynamics of Glucocorticoid Receptor Binding and Chromatin Landscape Drive Transcriptional Regulation

Glucocorticoid receptor (GR) signaling elicits diverse transcriptional responses through dynamic and context-dependent interactions with chromatin. Here, we define a temporally resolved and mechanistically integrated framework for GR-mediated gene regulation. Time-resolved analyses identify three conserved classes of GR chromatin binding (sustained, transient, and late), distinguished by differences in motif strength, chromatin accessibility, and cofactors engagement. Early GR binding preferentially occurs at high-affinity glucocorticoid response elements (GREs) within pre-accessible regulatory regions, whereas late binding is associated with weaker motifs and requires chromatin remodeling activity. Enhancer activation, marked by H3K27ac deposition, closely tracks GR occupancy, supporting a model in which GR recruits acetyltransferase activity to drive coordinated enhancer activation. Concurrently, GR-centered interaction networks are dynamically reconfigured, and motif enrichment analyses identify distinct transcription factor signatures across binding classes, including AP-1/JUNB at transient sites and CEBP family members at late-binding regions. Integration of chromatin binding, chromatin interaction, and transcriptomic datasets reveals that temporal and combinatorial GR occupancy is functionally linked to gene expression programs. Distinct GR binding clusters are nonrandomly associated with specific transcriptional trajectories, including sustained, transient, and late gene induction. Moreover, combinatorial occupancy across multiple regulatory elements correlates quantitatively with transcriptional output, indicating that GR functions not as a simple binary regulator, but as an integrator of multilayered regulatory inputs. These findings support a unified model in which temporal binding dynamics, chromatin state, and combinatorial enhancer activity collectively encode transcriptional specificity, providing a general framework for stimulus-responsive nuclear receptor signaling.

molecular biology↗

bioRxiv2024

STRESS GRANULE-RELATED GENES DURING EMBRYOGENESIS OF AN INVERTEBRATE CHORDATE

Control of global protein synthesis through the assembly of stress granules (SGs) represents a strategy adopted by eukaryotic cells to face various stress conditions. TIAR, TTP and G3BP are key components of SGs, allowing the regulation of mRNA stability and thus controlling not only stress responses but also cell proliferation and differentiation. In the present work we aimed to investigate the role of tiar, ttp and g3bp during embryogenesis of the solitary ascidian Ciona robusta, both in physiological and stress conditions. We carried out CRISPR/Cas9 knockout to evaluate the effects on normal embryonic development, and gene reporter assays to study time and tissue specificity of gene expression, together with whole mount ISH and qRT-PCR. To induce acute stress conditions, we used iron and cadmium as "essential" and "non-essential" metals, respectively. Our results highlight, for the first time, the importance of tiar, ttp and g3bp in the control of development of mesendodermal tissue derivatives during embryogenesis of an invertebrate chordate. HIGHLIGHTS- Mesenchyme, nervous cells, and endoderm are the embryonic regions mainly transcribing cr-tiarx1, cr-ttp and cr-g3bp2 during metal stress conditions. - Only cr-ttp transcription is regulated at mid gastrula stage. - The highest transcription levels are reached in hatching larvae after iron exposure. - cr-tiarx1, cr-ttp and cr-g3bp2 knockouts resulted in impaired embryogenesis.

developmental biology↗

bioRxiv2023

Tight junction membrane proteins regulate the mechanical resistance of the apical junctional complex

Epithelia must be able to resist mechanical force to preserve tissue integrity. While intercellular junctions are known to be important for the mechanical resistance of epithelia, the roles of tight junctions (TJs) remain to be established. We previously demonstrated that epithelial cells devoid of the TJ membrane proteins claudins and JAM-A completely lack TJs and exhibit focal breakages of their apical junctions. Here, we demonstrate that apical junctions undergo spontaneous fracture when claudin/JAM-A-deficient cells are exposed to mechanical stress. The junction fracture was accompanied by actin disorganization, and actin polymerization was required for apical junction integrity in the claudin/JAM-A-deficient cells. Further deletion of CAR resulted in the disruption of ZO-1 molecule ordering at cell junctions, accompanied by severe defects in apical junction integrity. These results demonstrate that TJ membrane proteins regulate the mechanical resistance of the apical junctional complex in epithelial cells. SummaryTight junction membrane proteins claudins, JAM, and CAR coordinately regulate the nanometer-scale organization of ZO-1 molecules, and are required for the mechanical resistance of apical junctions in epithelial cells.

cell biology↗

bioRxiv2022

Transcription factors that specify cell fate activate cell cycle regulator genes to determine cell numbers in ascidian larval tissues

In animal development, most cell types stop dividing before terminal differentiation; thus, cell cycle control is tightly linked to cell differentiation programs. Although cell cycle control in animal development has been studied extensively, such links are not well understood. In ascidian embryos, cell lineages do not vary among individuals, and rounds of the cell cycle are determined according to cell lineages. In the present study, we first showed that maternal factors promote approximately 10 rounds of cell division without zygotic gene expression. Notochord and muscle cells stop dividing after fewer than 10 rounds of cell division, and we show that a Cdk inhibitor (Cdkn1.b) is responsible. Cdkn1.b is also necessary for epidermal cells to stop dividing. In contrast, mesenchymal and endodermal cells divided more than 10 times, and Myc, which encodes a proto-oncogenic transcription factor, is responsible for maintaining cell cycle progression in these tissues. Expression of Cdkn1.b in notochord and muscle is controlled by the same developmental programs that specify the developmental fate of notochord and muscle. Likewise, expression of Myc in mesenchyme and endoderm was under control of the same developmental programs that specify the developmental fate of mesenchyme and endoderm. Because these transcription factors that regulate Cdkn1.b and Myc are essential factors for fate specification of these tissues, cell fate specification and cell cycle control are linked by those transcription factors. In other words, ectodermal, mesodermal, and endodermal tissues in ascidian embryos control the cell cycle through Cdkn1.b and Myc, which are under the control of transcription factors that specify cell fate.

developmental biology↗

bioRxiv2021

Cross-scale Analysis of Temperature Compensation in the Cyanobacterial Circadian Clock System

Clock proteins maintain constant enzymatic activity regardless of temperature, even though thermal fluctuation is accelerated as temperature increases. We investigated temperature influences on the dynamics of KaiC, a temperature-compensated ATPase in the cyanobacterial circadian clock system, using quasielastic neutron scattering. The frequency of picosecond to sub-nanosecond incoherent local motions in KaiC was accelerated very slightly in a temperature-dependent manner. Our mutation studies revealed that internal motions of KaiC include several contributions of opposing temperature sensitivities. To take advantage of this balancing effect, the motional frequency of local dynamics in KaiC needs to exceed [~]0.3 ps-1. Some of the mutation sites may be in a pathway through which the motional frequency in the C-terminal domain of KaiC is fed back to the active site of ATPase in its N-terminal domain. The temperature-compensating ability at the dynamics level is likely crucial for circadian clock systems, into which the clock proteins are incorporated, to achieve reaction- or even system-level temperature compensation of the oscillation frequency.

biophysics↗

bioRxiv2017

A spontaneously blinking fluorescent protein for simple single laser super-resolution live cell imaging

Super-resolution imaging techniques based on single molecule localization microscopy (SMLM) broke the diffraction limit of optical microscopy in living samples with the aid of photoswitchable fluorescent probes and intricate microscopy systems. Here, we developed a fluorescent protein, SPOON, which can be switched-off by excitation light illumination and switched-on by thermally-induced dehydration resulting in an apparent spontaneous blinking behavior. This unique property of SPOON provides a simple SMLM-based super-resolution imaging platform which requires only a single 488 nm laser.

biophysics↗