Dual modes of ZFC3H1 confer selectivity in nuclear RNA sorting

The export and degradation pathways compete to sort nuclear RNAs, yet the default pathway remains unclear. Sorting of mature RNAs to degradation, facilitated by the exosome co-factor poly(A) exosome targeting (PAXT), is particularly challenging for their resemblance to mRNAs intended for translation. Here, we unveil that ZFC3H1, a core PAXT component, is co-transcriptionally loaded onto the first exon/intron of RNA precursors (pre-RNAs). Interestingly, this initial loading does not lead to pre-RNA degradation, as ZFC3H1 adopts a “closed” conformation, effectively blocking exosome recruitment. As processing progresses, RNA fate can be reshaped. Longer RNAs with more exons are allowed for nuclear export. By contrast, short RNAs with fewer exons preferentially recruit transient PAXT components ZC3H3 and RBM26/27 to the 3′ end, triggering ZFC3H1 “opening” and subsequent exosomal degradation. Together, the decoupled loading and activation of ZFC3H1 pre-configures RNA fate for decay while still allowing a switch to nuclear export, depending on mature RNA features. [Display omitted] •ZFC3H1 is prevalently loaded onto the 5′ end of pre-RNAs in an inactive mode•ZFC3H1 loaded on pre-RNAs prevents dysregulated mRNA export•Long multi-exonic RNAs are sorted for export, while short intron-few RNAs for decay•Short RNAs favorably recruit ZC3H3 and RBM26/27 to the 3′ end, activating ZFC3H1 Fan et al. report that poly(A) exosome targeting (PAXT) presets decay as the default RNA fate at an early stage of transcription. This fate can be reshaped to export or remain as decay based on exon number and mature transcript length. This degradation-centric model ensures both the rapid degradation of unwanted RNAs and the efficient export of functional mRNAs.