Transcriptome-wide mapping of RNA:protein interactions of seven SR proteins and NXF1 in P19 cells by iCLIP

We used GFP-tagged SR proteins expressed at endogenous levels and iCLIP to identify and compare endogenous RNA targets of individual SR proteins, map the preferential sites of binding, compare binding pattern and binding motifs between family members and to NXF1 and quantify binding of SR proteins and NXF1 to spliced versus unspliced RNAs to study the role of SR proteins in mRNA export via NXF1. For each GFP-tagged SR proteins and NXF1, 3 to 6 biological replicates were subjected to the iCLIP procedure with UV-crosslinking at 254 nm. An anti-GFP antibody as used for IPs. As negative control served samples prepared from a P19 cell line expressing only GFP-NLS fusion protein.