Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs

How heterogeneous nuclear ribonucleoprotein (RNP) F regulates alternative splicing is unclear. Solution structures of three quasi RNA recognition motifs (qRRMs) bound to G-tract RNA now reveal an unusual binding mode, confirmed by mutagenesis and isothermal titration calorimetry analysis. Binding and splicing assays suggest that hnRNP F prevents RNA structure formation. The heterogeneous nuclear ribonucleoprotein (hnRNP) F is involved in the regulation of mRNA metabolism by specifically recognizing G-tract RNA sequences. We have determined the solution structures of the three quasi–RNA-recognition motifs (qRRMs) of hnRNP F in complex with G-tract RNA. These structures show that qRRMs bind RNA in a very unusual manner, with the G-tract 'encaged', making the qRRM a novel RNA binding domain. We defined a consensus signature sequence for qRRMs and identified other human qRRM-containing proteins that also specifically recognize G-tract RNAs. Our structures explain how qRRMs can sequester G-tracts, maintaining them in a single-stranded conformation. We also show that isolated qRRMs of hnRNP F are sufficient to regulate the alternative splicing of the Bcl-x pre-mRNA, suggesting that hnRNP F would act by remodeling RNA secondary and tertiary structures.