SWING domains prime chromatin for nuclear body mediated gene regulation

Abstract

Nuclear speckles have long been recognized as RNA-rich nuclear bodies, yet their role in genome organization and gene regulation remains incompletely understood. Using a rapid dTAG-mediated degradation system to simultaneously deplete SON and SRRM2--the core structural components of nuclear speckles--we identify a novel class of genomic regions, which we term SWING regions. Upon speckle disruption, SWING regions relocate to the nuclear periphery and acquire repressive histone marks such as H3K9me3, accompanied by gene downregulation, particularly of genes involved in developmental pathways. Consistent with this, depletion of Lamin A reduces lamina association of SWING regions and enhances their association with nuclear speckles, supporting a bidirectional balance between these two nuclear compartments. Notably, human mutations in SON and SRRM2 are associated with neurodevelopmental disorders characterized by intellectual disability and global developmental delay. Patient-derived cells bearing such mutations similarly exhibit SWING-region relocalization and gene repression, underlining a role for speckles in developmental gene regulation. We also report that drug-induced speckle rejuvenation partially rescues aberrant SWING-region localization to the nuclear lamina in patient-derived cells and iPSCs with acute depletion of SON. These findings identify SWING regions as an intermediate chromatin state positioned between nuclear speckles and the lamina, maintained by opposing functions from both structures. Our work reveals a mechanism underlying the contribution of nuclear bodies to 3D genome organization, highlights the importance of nuclear speckles and SWING regions in developmental regulation, and provides a potential therapeutic intervention in speckle dysfunction. Impact StatementIdentification of nuclear speckles as determinants of specific 3D genome organization. Demonstration of functional interactions between opposing nuclear structures (speckle versus lamina) through SWING regions. Establishment of developmental and human disease relevance of speckle-mediated genome organization. Providing potential avenues for therapeutic intervention in speckleopathies.