Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome

Summary During gene expression, RNA export factors are mainly known for driving nucleo-cytoplasmic transport. While early studies suggested that the exon junction complex (EJC) provides a binding platform for them, subsequent work proposed that they are only recruited by the cap binding complex to the 5′ end of RNAs, as part of TREX. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are recruited to the whole mRNA co-transcriptionally via splicing but before 3′ end processing. Consequently, Alyref alters splicing decisions and Chtop regulates alternative polyadenylation. Alyref is recruited to the 5′ end of RNAs by CBC, and our data reveal subsequent binding to RNAs near EJCs. We demonstrate that eIF4A3 stimulates Alyref deposition not only on spliced RNAs close to EJC sites but also on single-exon transcripts. Our study reveals mechanistic insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome.
Graphical Abstract
Highlights • 5′ cap binding complex CBC acts as a transient landing pad for Alyref • Alyref is deposited upstream of the exon-exon junction next to the EJC • Alyref can be deposited on introns and regulate splicing • Chtop is mainly deposited on 3′ UTRs and influences poly(A) site choices
TREX plays a pivotal role in RNA export, though the mechanisms governing its deposition on RNA are obscure. Viphakone et al. show that the cap binding and exon junction complexes drive the ordered deposition of TREX throughout the body of RNA. In doing so, TREX regulates processing of the RNA.