Biology subjects

Fujiwara, N.

Publications and source records attributed to Fujiwara, N..

6 recordsLinked to original sources

bioRxiv2026

Two closely related RNA helicases, UAP56 and URH49, couple mRNA splicing and export pathways with their distinct complexes

Transcription and mRNA processing are integrated into appropriate mRNA export pathway(s) enabling fine-tuned gene expression. The closely related RNA helicases, UAP56 and URH49, form distinct complexes known as the apo-TREX and the apo-AREX complexes, respectively, which remodel into the ATP-TREX complexes, thus forming multiple mRNA export pathways. However, the mechanisms by which helicases and their complexes shape these pathways remain unclear. Here, we showed that UAP56 and URH49 play general roles in mRNA splicing ahead of export. Further analyses revealed three patterns of splicing regulation and their association with mRNA export: Type I, in which both helicases redundantly or synergistically regulate splicing within the same transcripts, associated with cooperative mRNA export; Type II, in which either helicase preferentially regulates splicing in distinct transcripts; and Type III, in which the helicases exert opposing splicing effects within the same transcripts. Type II and III regulation was associated with selective mRNA export. Moreover, we demonstrated that the distinct complex formation influenced the splicing patterns regulated by the two helicases. Our findings reveal an additional layer of transcriptome regulation mediated by UAP56, URH49, and their complexes, extending beyond their canonical roles in mRNA export.

molecular biology↗

bioRxiv2026

Ile35 residue of SOD1 plays a key role in aggregate formation and eye degeneration in a Drosophila model of ALS

{middle dot}The pathophysiology of ALS caused by mutant SOD1 remains unclear. {middle dot}We previously demonstrated, using the BioID2-EGFP sandwich expression system in cultured cells, that the Ile35 residue of ALS-linked mutant SOD1 promotes its aggregate formation. {middle dot}However, the precise role of the SOD1 Ile35 residue in aggregate formation and neurodegeneration in vivo remained unclear. {middle dot}Drosophila expressing BioID2-G93A-EGFP demonstrated aggregate formation and eye degeneration with reduced eye size, whereas those expressing BioID2-G93A/I35S-EGFP showed less of these phenotypes. {middle dot}These findings highlight the crucial role of the Ile35 residue of ALS-linked SOD1 in aggregate formation and neurodegeneration in vivo.

neuroscience↗

bioRxiv2026

Human club cells derived from pluripotent stem cells reveal new insights into epithelial lineage plasticity through structural and functional validation

Airway epithelial homeostasis relies on multiple specialized cell types, with club cells playing central roles in maintaining epithelial integrity and regulating inflammation. Environmental insults such as allergens, viral infections, or pollutants preferentially damage club cells, impairing epithelial repair and contributing to pulmonary diseases. However, the functional properties of club cells remain incompletely defined, and tractable human models are lacking. Herein, we establish a robust platform to differentiate human pluripotent stem cells (hPSCs) into club cells exhibiting their hallmark secretory features, appropriate epithelial organization, and functional properties. Single-cell transcriptomic analyses and lineage trajectory inference revealed unexpected epithelial plasticity: hPSC-derived club cells give rise to multiciliated epithelial cells through a deuterosomal intermediate--a previously uncharacterized trajectory. Additionally, a distinct club cell subset exhibited transcriptional features indicative of neuroendocrine and goblet cell differentiation potential. This study uncovers club cell plasticity and establishes a hPSC-based platform for studying airway development, regeneration and disease modeling.

cell biology↗

bioRxiv2025

Focused acoustic-radiation-force microscopy for live-cell selective nucleus deformation and nucleus viscoelasticity measurement

Acoustic-radiation-force (ARF) microscopy was developed for non-invasive, selective mechanical stimulation to a single live-cell nucleus and long-term measurement of its mechanical properties. High-frequency focused ultrasound wave achieved a spatially confined ARF field around target nucleus, and its cyclic deformation was induced by amplitude modulation on the ultrasound wave, which was captured by a dark-field microscopy. This method was applied to human mesenchymal stem cells, revealing their extremely high mechanical homeostasis.

biophysics↗

bioRxiv2023

Shell protein composition specified by NEAT1 domains dictates the formation of paraspeckles as distinct membraneless organelles

Many membraneless organelles (MLOs) formed through phase separation play crucial roles in various cellular processes. Although these MLOs co-exist in cells, how they maintain their independence without coalescence or engulfment remains largely unknown. Here, we investigated the molecular mechanism by which paraspeckles with core-shell architecture scaffolded by NEAT1_2 lncRNAs exist as distinct MLOs. We identified NEAT1 deletion mutants that assemble paraspeckles that are incorporated into nuclear speckles. Several paraspeckle proteins, including SFPQ, HNRNPF, and BRG1, prevent this incorporation and thus contribute to the segregation of paraspeckles from nuclear speckles. Shell localization of these proteins in the paraspeckles, which is determined by NEAT1_2 lncRNA domains, is required for this segregation process. Conversely, U2-related spliceosomal proteins are involved in internalizing the paraspeckles into nuclear speckles. This study shows that the paraspeckle shell composition dictates the independence of MLOs in the nucleus, providing insights into the importance of the shell in defining features and functions of MLOs.

cell biology↗

bioRxiv2023

Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease

Somatic mutations in non-malignant tissues accumulate with age and insult, but whether these mutations are adaptive on the cellular or organismal levels is unclear. To interrogate mutations found in human metabolic disease, we performed lineage tracing in mice harboring somatic mosaicism subjected to non-alcoholic steatohepatitis (NASH). Proof-of-concept studies with mosaic loss of Mboat7, a membrane lipid acyltransferase, showed that increased steatosis accelerated clonal disappearance. Next, we induced pooled mosaicism in 63 known NASH genes, allowing us to trace mutant clones side-by-side. This in vivo tracing platform, which we coined MOSAICS, selected for mutations that ameliorate lipotoxicity, including mutant genes identified in human NASH. To prioritize new genes, additional screening of 472 candidates identified 23 somatic perturbations that promoted clonal expansion. In validation studies, liver-wide deletion of Bcl6, Tbx3, or Smyd2 resulted in protection against NASH. Selection for clonal fitness in mouse and human livers identifies pathways that regulate metabolic disease. HighlightsO_LIMosaic Mboat7 mutations that increase lipotoxicity lead to clonal disappearance in NASH. C_LIO_LIIn vivo screening can identify genes that alter hepatocyte fitness in NASH. C_LIO_LIMosaic Gpam mutations are positively selected due to reduced lipogenesis. C_LIO_LIIn vivo screening of transcription factors and epifactors identified new therapeutic targets in NASH. C_LI

cell biology↗