A multiomics atlas of the Arabidopsis nuclear envelope

The nuclear envelope (NE) is a critical regulatory interface that preserves genome integrity and mediates nucleocytoplasmic transport, yet its compositional and functional landscape in plants remains poorly defined. Here, we present a multiomics atlas of the Arabidopsis NE. By integrating proximity-labeling proteomics with single-cell/single-nucleus transcriptomics, we uncover distinct NE coexpression networks that dynamically shape NE composition and function in cell type–specific manners, enabling adaptation to diverse physiological and environmental demands. Notably, this analysis revealed that nuclear pore complex (NPC) biogenesis is transcriptionally restricted primarily to proliferative cells, whereas the protein complex exhibits remarkable stability and persists throughout cellular differentiation despite the absence of sustained high-level transcription. This supports an “assembly-and-maintenance” model in which NPCs are predominantly assembled during cell division and subsequently maintained as exceptionally long-lived structures throughout developmental progression. Together, this atlas provides a high-resolution framework for plant nuclear organization and establishes the NE as a spatiotemporally regulated hub central to plant growth, development, and responses to stimuli.