Global RNA-binding profile of the mRNA export adaptor ALYREF

The TREX complex (TREX) plays key roles in nuclear export of mRNAs. However, little is known about its transcriptome-wide binding targets. We used individual cross-linking and immunoprecipitation (iCLIP) to identify the binding sites of ALYREF, an mRNA export adaptor in TREX, in human cells. As expected, iCLIP reads are mainly mapped to exons of mRNAs. Globally, ALYREF binding shows two apparent enrichments on the mRNA, one is near the 5’ end and the other is very close to the 3’ end. In addition, numerous middle exons harbor ALYREF binding sites. CBP80 and PABPN1 mainly affect ALYREF binding at the 5’ and the 3’ region, respectively. Interestingly, we found that the 3’ processing factor CstF64 directly interacts with ALYREF and is required for the overall binding of ALYREF on the mRNA. Sequence analysis led to the identification of multiple ALYREF iCLiP