Both cCL and PAR-CL protocols can be applied to the dual fluorescence RNA-binding assay. Comparison of the performance of cCL and PAR-CL in the dual fluorescence RNA-binding assay. eGFP, MOV10–YFP, and H2B–eGFP cell lines were induced for 16 h. Protein–RNA complexes were cross-linked applying cCL or PAR-CL. After lysis, control samples were RNase-treated and immunoprecipitated using GFP-multiTrap. The graphs show relative green (eGFP/YFP) and red (Tred) fluorescence levels (A) and their ratios normalized to RNase-treated samples (B). The graphs were generated from two biological and three technical replicates (total of six immunoprecipitations). (***) P < 0.001. Horizontal red and green lines represent averaged Tred or eGFP background signal, respectively, extracted from control samples.
