A multi-omics atlas of the plant nuclear envelope

The nuclear envelope (NE) proteins play a pivotal role in maintaining nuclear integrity and orchestrating nucleocytoplasmic communication. Increasing evidence suggests that NE proteins interact with a wide array of other proteins, implying functions far beyond membrane compartmentalization. However, the full composition and functional landscape of plant NE proteins remain largely uncharted. Here, we used proximity-labeling proteomics to generate a comprehensive map of the Arabidopsis NE proteome, identifying nearly 700 unique integral and associated NE proteins. Compositional analyses revealed that the NE not only functions as a hub for chromatin organization and transcriptional regulation but also tied to mRNA processing, membrane trafficking, and lipid metabolism. By integrating these proteomic data with single-cell and single-nucleus RNA sequencing, we uncovered a range of NE-associated functional modules exhibiting specificity across tissues, cell types, and developmental stages. Together, our results highlight the fundamental and multifaceted roles of the plant NE and provide new insights into its conserved and lineage-specific functions across eukaryotic evolution.