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

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