Identification of Functional Targets Reveals that the Suppression of Pumilio mediated mRNA Decay Increases Cell Resistance to DNA Damage in Human Cells

RNA-binding proteins (RBPs) play a pivotal role in gene expression by modulating the stability of transcripts; however, the identification of functional targets remains difficult, even for RBPs with a high specific binding ability, such as mammalian PUMILIO proteins (PUMs). To understand the role of RBPs in biological processes and diseases, we present a systematic approach to define the functional targets of an RBP and determine the stimulus that modulates RBP-mediated mRNA decay. We applied our method to investigate PUM function and identified 49 functional target mRNAs of PUM1. Moreover, in silico screening indicated that DNA damage reagents inhibit PUM1-mediated mRNA decay, thus enhancing cell viability. Finally, we applied our method to UPF1 and showed that UPF1-mediated mRNA decay was activated by rapamycin. Thus, our study establishes a systematic and un-biased strategy to identify the biological role of RBPs through the identification and analysis of transcripts directly regulated by RBPs.