Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism of Xist

The fundamental process of X-chromosome inactivation (XCI) involves silencing one X chromo-some in female mammals by the Xist gene within the X-inactivation center (Xic). While experiments have identified key regulatory elements controlling Xist expression, mechanistic details are unknown. By combining nucleosome-resolution and coarse-grained polymer modeling, we reveal multiscale Xic reorganization during XCI driven by loop extrusion and epigenetic modifications, including methylation. At the nucleosome level, inactive X shows differential gene organization, where Xite is buried and compacted but Xist folds into a fragmented open structure; clutch patterns also change upon inactivation, and changes in methylation (in Xite) and NFRs (in Xist) explain the reorganization. At the megabase scale, our simulations reveal spatial rewiring: Linx -Tsix contacts are disrupted, isolating Tsix from its activator, while Xist, Jpx, and Ftx coalesce into an active compartment. This hierarchical and differential reorganization creates a chromatin architecture with an active domain for Xist favoring its expression, while a repressed Xite prevents Tsix reactivation. These general principles of how 3D genome organization directs development have implications for diseases related to XCI and extend beyond XCI to gene regulation broadly.