Nucleoporin TPR is an integral component of the TREX-2 mRNA export pathway

Abstract

Nuclear pore complexes (NPCs) are important for cellular functions beyond nucleocytoplasmic trafficking, including genome organization and gene expression. This multi-faceted nature and the slow turnover of NPC components complicates investigations of how individual nucleoporins act in these diverse processes. To address this question, we apply an Auxin-Induced Degron (AID) system to distinguish roles of basket nucleoporins NUP153, NUP50 and TPR. Acute depletion of TPR causes rapid and pronounced changes in transcriptomic profiles. These changes are dissimilar to shifts observed after loss of NUP153 or NUP50, but closely related to changes caused by depletion of mRNA export receptor NXF1 or the GANP subunit of the TRanscription-EXport-2 (TREX-2) mRNA export complex. Moreover, TPR depletion disrupts association of TREX-2 subunits (GANP, PCID2, ENY2) to NPCs and results in abnormal RNA transcription and export. Our findings demonstrate a unique and pivotal role of TPR in gene expression through TREX-2- and/or NXF1-dependent mRNA turnover.

The Nuclear Pore Complex and mRNA Export in Cancer

“…For instance, during neurogenesis, a neuron-specific transcript STX1b undergoes splicing, export, and translation, while in non-neuronal cells, these RNAs are not spliced correctly, leading to nuclear retention and degradation, which is TPR-dependent [ 65 ]. Additionally, the TPR protein is tethered to the NPC via Nup153 [ 66 ], although there is some disagreement if this is required [ 67 ] (and references therein). Disruption of the TPR–Nup153 interaction leads to the leakage of intron-containing RNAs into the cytoplasm, showcasing the mRNA surveillance activity of the nuclear basket [ 63 ].…”

“…Disruption of the TPR–Nup153 interaction leads to the leakage of intron-containing RNAs into the cytoplasm, showcasing the mRNA surveillance activity of the nuclear basket [ 63 ]. The TREX2 component GANP requires TPR for association with the NPC [ 67 ]. Indeed, depletion of Tpr more closely mirrored loss of NXF1 or GANP than did depletion of other nuclear basket components Nup153 or Nup50, also highlighting that basket components can have differential impacts on mRNA export [ 67 ].…”

“…The TREX2 component GANP requires TPR for association with the NPC [ 67 ]. Indeed, depletion of Tpr more closely mirrored loss of NXF1 or GANP than did depletion of other nuclear basket components Nup153 or Nup50, also highlighting that basket components can have differential impacts on mRNA export [ 67 ]. Cell cycle-driven changes to the NPC also contribute to changes in mRNA export.…”

The Nuclear Pore Complex consists of two independent scaffolds

“…1a). We also used CRISPR/Cas9 to program the cells for TIR-1 protein expression under the control of the ubiquitously expressed RCC1 gene 16 . TIR-1 is necessary for specific, auxin-dependent degradation of AID-tagged proteins 17 , 18 .…”

“…Tagged NUP160, NUP133 and NUP96 nucleoporins (green) with and without Auxin treatment (4 hours, 1mM). Regulator of Chromosome Condensation 1 protein (RCC1) tagged with Infra-red Fluorescent Protein (IFP), RCC1::IFP, serves as a chromatin marker and is shown in magenta 16 . (Scale bar = 5 μm.…”