Our previous work identified the inner basket of the NPC as a physical activation/protection station for force-tethered, epigenetically silenced genes. Here we show that a specific nucleopore-to-gene-promoter interaction (Nup-PI) is an early physiological event of gene activation. Nup-PI was discovered with chromatin endogenous cleavage (ChEC) experiments that mapped in vivo the genomic interaction sites of the nucleoporin Nup2p fused to microccocal nuclease (Nup2-MN). Strong Nup-PI, cleavage by Nup2-MN, is observed at the promoters of the GAL genes and at HXK1 upon activation of these genes with galactose. Nup-PI at the GAL locus requires Gal4p and the UASg and TATA box elements but not SAGA and active transcription. The physical, activation-dependent interaction of the GAL locus with the NPC basket was confirmed by imaging. Chromosome-wide ChEC studies indicated that Nup-PI occurs at numerous genes. The data identify the NPC basket as a new, integral participant in gene expression.