Figure 3

Validation of the mRNA-protein associations identified by microarray analysis. (a) RT-PCR amplification of putative U2AF⁶⁵ associated mRNAs and a nonassociated mRNA (glucose-6-phosphate dehydrogenase [G6PD]) from immunoprecipitation (RIP), mock-imunoprecipitation (Mock), and input samples. For each target, the primer localization and expected size of amplified spliced products is indicated. (b) Comparison of microarray quantification and independent real time-PCR quantification of the enrichment index (log2 immunoprecipitation/input) of selected target mRNAs from anti-U2AF⁶⁵ or anti-PTB immunoprecipitation experiments. Points falling in the positive (+/+) or negative (-/-) sectors of the plot reveal an agreement between microarray and quantitative real-time PCR experiments. The SMARCA2 and MAPK8 mRNA were found to be enriched only in microarray experiments. IP, immunoprecipitation; PTB, polypyrimidine tract binding protein; RT-PCR, reverse transcription polymerase chain reaction; U2AF, U2 small nuclear RNP auxiliary factor.