Sakata, R. | bioRxiv Science

bioRxiv2026

Full-thickness spatial transcriptomics of the human uterus reveals basalis niche architecture and regeneration gradients during menstrual breakdown

The human endometrium (uterine lining) undergoes cyclical breakdown and scarless regeneration during each menstrual cycle, representing an exceptional model of adult tissue renewal. Regeneration is driven primarily by progenitor cells retained within the deep, basalis compartment during menstruation, yet the full-depth spatiotemporal dynamics of this process have remained understudied due to anatomical and technical limitations. Here, we map spatial gene-expression gradients across the full thickness of the human endometrium, from the myometrial-endometrial boundary to the luminal surface, using high-resolution spatial transcriptomics integrated with single-cell transcriptomics. We profile more than ten million cells from biopsies, hysterectomy samples and menstrual fluid, enriching for the menstrual and proliferative phases, which are underrepresented in previous studies. We show that endometrial breakdown, regeneration and rapid luminal re-epithelialisation are concurrent rather than temporally separated, organised across distinct tissue compartments, revealing a mode of tissue renewal in which shedding and repair operate simultaneously. Continuous basalis-to-luminal transcriptional gradients link progenitor identity, niche signalling, and tissue remodelling, defining a coordinated regenerative axis spanning the full tissue depth. We resolve the basalis epithelial niche at unprecedented molecular resolution, identifying for the first time a discrete, predominantly quiescent progenitor-like epithelial subset and specialised supporting SFRP5+ fibroblasts, both characterised by WNT inhibition, alongside lymphoid aggregates, forming a multi-component architecture that persists after menopause, consistent with a long-lived regenerative reservoir. Together, these findings establish spatial transcriptional gradients as a central organising principle of endometrial renewal, providing a molecular framework for understanding disorders of menstruation, implantation failure, and impaired tissue repair.

cell biology↗

bioRxiv2025

AT-hook-dependent DNA loop extrusion by STAG1 drives 3D genome folding

Cohesin, a ring-shaped complex composed of Smc1, Smc3, Scc1 and STAG, is essential for sister chromatid cohesion and the regulation of three-dimensional (3D) genome architecture. At the single-molecule level, cohesin extrudes DNA loops, a process thought to drive higher-order genome folding. In vertebrates, cohesin incorporates either STAG1 or STAG2. Although both support sister chromatid cohesion, they differentially regulate 3D genome organization. However, the mechanistic basis for these differences has remained unclear. Here we show, using single-molecule assays, that cohesin-STAG1 extrudes DNA loops more efficiently than cohesin-STAG2, despite comparable ATPase activity and topological DNA entrapment. We identify an AT-hook motif unique to the STAG1 N-terminus as the element that promotes loop extrusion without altering ATPase activity or DNA binding. In human somatic cells, the AT-hook is required for stable cohesin-chromatin association during G1 phase but is dispensable for sister chromatid cohesion. Mutation of this motif markedly impairs TAD and chromatin loop formation. These findings highlight AT-hook as a critical determinant that distinguishes STAG1 from STAG2 by promoting DNA loop extrusion and stabilizing cohesin-chromatin interactions in interphase through a mechanism distinct from the one underlying sister chromatid cohesion.

molecular biology↗