Biology subjects

Habuchi, S.

Publications and source records attributed to Habuchi, S..

3 recordsLinked to original sources

bioRxiv2026

Evolution of mechanical chromatin insulators from selfish genetic elements

Genomes require physical boundaries to separate active and repressed chromatin, a function traditionally attributed to insulator proteins. Here, we show that genomic insulation can also emerge from physical properties encoded directly within the DNA polymer. In C. elegans, transcription-coupled mutational bias remodels Helitron transposon minisatellites to match the DNA helical repeat. The resulting 10-bp periodicity (PATCs) encodes intrinsic curvature, creating topologically responsive DNA elements that favor local deformation under supercoiling, disrupt canonical nucleosome organization, and protect germline genes from progressive and heritable silencing. Rather than acting as short protein-binding motifs, Helitron-derived PATCs form extended barrier elements that limit the stabilization of repressive chromatin. Comparative analyses suggest that related sequence-encoded mechanical signatures recur across Metazoa, including at Drosophila insulators, human CTCF sites, and active human LINE-1 retrotransposons. Thus, sequence-encoded mechanics provide an evolutionarily accessible substrate for chromatin insulation--a physical layer of genome organization that can be co-opted by host genomes to protect gene expression, and potentially retained by selfish elements for their own persistence.

molecular biology↗

bioRxiv2025

Combined TIRF and 3D Super-Resolution Microscopy for Nanoscopic Spatiotemporal Characterization of Adhesion Molecules on Microvilli

The homing of hematopoietic stem/progenitor cells (HSPCs) and leukemic cells is a multistep process governed by complex spatiotemporal interactions between adhesion molecules under shear stress. While the molecular and biological mechanisms of this process have been extensively studied, the precise spatial and temporal organization of adhesion molecules that influences homing efficiency remains relatively poorly understood. In particular, the roles of the cell surface topography and its morphological changes during homing in shaping the spatial organization of adhesion molecules remain elusive. This is partly due to the lack of imaging techniques that simultaneously capture both nanoscopic cell surface morphology and the spatial distribution of the adhesion molecules. Here, we develop a microfluidics-based super-resolution (SR) imaging platform that enables the three-dimensional (3D) mapping of the cell surface morphology and the spatial distribution of the adhesion molecules during HSPC and leukemic cell rolling by integrating total internal reflection fluorescence microscopy (TIRFM) with single-molecule localization microscopy (SMLM). We reconstruct the cell surface morphology, which is critical to the homing, using TIRFM, and precisely overlay the spatial distribution of adhesion molecules, including CD44, PSGL-1, and actin cytoskeleton, determined by 3D-SMLM, on the topographic map. We show distinct nanoscopic localizations of adhesion molecules on the microvilli of HSPCs/leukemic cells and their reorganization under shear stress during cell rolling, at a spatial resolution of approximately 30 nm. The approach offers a powerful means to elucidate the complicated interplay between cell surface morphology and ligand-receptor interactions. TOC graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/672391v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@19e513eorg.highwire.dtl.DTLVardef@e7dd0corg.highwire.dtl.DTLVardef@617295org.highwire.dtl.DTLVardef@1a9ae0a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2020

Spatial confinement and temporal dynamics of selectin ligands enable stable hematopoietic stem cell rolling

Hematopoietic stem/progenitor cell (HSPC) and leukemic cell homing is an important biological phenomenon that occurs through key interactions between adhesion molecules. Tethering and rolling of the cells on endothelium, the crucial initial step of the adhesion cascade, is mediated by interactions between selectins expressed on endothelium to their ligands expressed on HSPCs/leukemic cells in flow. Although multiple factors that affect the rolling behavior of the cells have been identified, molecular mechanisms that enable the essential slow and stable cell rolling remain elusive. To investigate the molecular mechanisms of cell rolling, an experimental platform that enables molecular level characterization of the adhesion molecules in the context of space, time, and force is required. Here, using a microfluidics-based single-molecule live cell fluorescence imaging, we reveal that unique spatiotemporal dynamics of selectin ligands on the membrane tethers and slings, which are distinct from that on the cell body, play an essential role in the rolling of the cell. Our results suggest that the spatial confinement of the selectin ligands to the tethers and slings together with the rapid scanning of a large area by the selectin ligands, increases the efficiency of selectin-ligand interactions during cell rolling, resulting in slow and stable rolling of the cell on the selectins. Our findings provide novel insights and contribute significantly to the molecular-level understanding of the initial and essential step of the homing process.

biophysics↗