Exon junction complex and nuclear pore complex components preferentially govern the nuclear export of spliced lncRNAs

Long non-coding RNAs (lncRNAs) are crucial regulators of gene expression, but how spliced lncRNAs destined for the cytoplasm are exported from the nucleus remains unclear. Using LINC00998 and ANCR as cytoplasmic lncRNA reporters, in vivo-assembled lncRNPs were purified via MS2-MBP-based affinity purification, and proteins in the lncRNPs were identified by mass spectrometry. An siRNA screen followed by RNA FISH showed that while knockdown of the TREX-TAP pathway components UAP56 and TAP blocked the export of both lncRNAs and mRNAs, depletion of ALYREF, the exon junction complex (EJC) core protein eIF4A3, or the nuclear pore complex (NPC) component NUP98 preferentially impaired lncRNA export without significantly affecting spliced mRNAs. This lncRNA-biased retention phenotype was also observed upon depletion of other EJC components, Y14 or MAGOH/MAGOHB, and at least 9 additional NPC components. In contrast, depletion of NUP160 or NUP205 caused strong retention of spliced lncRNAs and partial retention of spliced mRNAs. Consistent with these findings, stable knockdown of eIF4A3 and NUP98 predominantly increased nuclear accumulation of endogenous lncRNAs, whereas NUP160 depletion affected both RNA classes. Overall, our results demonstrate that although spliced lncRNAs utilize the canonical mRNA export machinery, they exhibit a distinct and preferential dependency on specific EJC and NPC components.