Extended Data Fig. 1: Nuclear basket proxiome reveals robust association of NPC with the spliceosome.

a, Schematic diagrams illustrating the DNA constructs carried by transgenic Arabidopsis plants utilized for proximity labeling (PL) proteomics. The positions of FG repeats are marked with red stars on Nup50a and CG1. b, Bubble plot presenting the reanalysis of PL proteomic data obtained using different Nups as bait. The left side displays LFQ intensity values of Nup50a protein, while the right side features a heatmap showing normalized peptide spectrum match (PSM) values of Nup50a. Controls for Nup82 and Nup93a are biotin-treated NEAP1-BioID2 sample (Ctrl 1) and mock-treated YFP-BioID2 sample (Ctrl 2). For GBPL3, non-transformant plants (NT) served as control (Ctrl 1). Controls for KAKU4, Nup188, and PNET1 were NT plants (Ctrl 1) and mock-treated YFP-BioID2 samples (Ctrl 2). For CG1 and Nup54, NT plants (Ctrl 1) and mock-treated transgenic plants (Ctrl 2) were used as controls. c, Scatter plot showing candidates identified in the Nup82 proxiome. Known nucleoporins and nucleoskeleton proteins are labeled. Controls for ratiometric analysis included NEAP1-BioID2 and mock samples. Three biological replicates were utilized for each sample. Significantly enriched protein candidates, denoted by red dots, were selected using cutoffs p-value < 0.01, fold-change > 4, and PSM > 1. On the right, GO enrichment analysis and heatmaps displaying averaged PSM values of known nucleoporins and other candidates in the Nup82 proxiome are presented. d, GO enrichment analysis of the integrated nuclear basket proxiome consisting of 423 proteins. Representative GO terms are displayed. e, Gene expression patterns of Nup82, Nup50a, KAKU4, and GBPL3 in different tissues and developmental stages of Arabidopsis. Transcriptomic data were retrieved from the TraVA database (Transcriptome Variation Analysis, http://travadb.org/). For protein candidates identified by proximity labeling, statistical tests were two-sided t-tests without adjustment (b and c). Statistical tests used for GO analysis in (c and d) were one-sided Fisher’s Exact tests with multiple comparison adjustments.