Gene expression profiling of human DLD-1 cells after instant depletion of basket nucleoporins

We used RNA-seq approach to distinguish roles of basket nucleoporins Nup153, Nup50, and Tpr in transcription and nucleocytoplasmic trafficking. AID-mediated depletion of BSK-NUPs caused rapid and drastic changes in transcriptomic profiles within two hours of auxin addition. Changes upon Tpr nucleoporin loss were distinct from Nup153 and Nup50, but similar to changes upon loss of export factor NXF1 and GANP subunit of the TREX-2 mRNA export complex. Altogether, we demonstrated a unique role of Tpr nucleoporin in regulating genes expression through mRNA export. Overall design: We performed RNA-Seq analyses on human DLD-1 cells that we specifically depleted of the basket nucleoporins using Auxin-Inducible Degron system.