UC San Diego

FMRP binds and regulates translation of neuronal mRNAs. Loss of FMRP causes aberrant expression of proteins, which results in Fragile X syndrome. Three promising RNA sequence/structure motifs have been proposed to specifically bind FMRP's RNA-binding domains. The KH1/2 domain-binding motifs have not been thoroughly tested for direct binding to FMRP. An in vitro selected RNA G-quadruplex (GQ) has been shown to directly bind the RGG motif, but it is unclear whether this specific GQ structure is an accurate model of the RNA GQ structures FMRP may bind in vivo.

Here we quantified binding of human FMRP variants containing different RNA-binding domains to a set of model RNAs representing the three proposed RNA motifs. We find human FMRP variants containing the KH1 and KH2 domains bind (UGGA)4 with sub-micromolar affinity, while the RGG domain alone binds (UGGA)4 with tenfold lower affinity. Surprisingly, FMRP cannot bind (GACG)4 at all. Both the PolyG18 and UG4U GQ model RNAs bound with nanomolar affinities specifically to the RGG motif. The RGG domain alone bound with equal or higher affinity to both RNAs compared to the full-length and N-terminus truncated variants, suggesting that the RNA GQ is recognized and bound by the RGG motif with little contribution from the KH1 and KH2 domains.