Identification of Pumilio (PUM) bound RNAs in early embryos of Drosophila melanogaster

We previously identified PUM’s target RNAs using a phage-displayed synthetic antibody (Fab-PUM7) to immunoprecipitate (IP) PUM and its bound transcripts followed by hybridization to microarrays (Laver et al. 2015, PMID 25962635). To comprehensively identify PUM’s targets and the specific isoforms that are bound by PUM, here we used a different synthetic antibody, Fab-PUM4 (Na, Laver et al. 2016 PMID ), and a control, Fab-hEGFR-C1, to IP from 0-3 hr Drosophila embryo extract followed by next-generation sequencing of copurifying RNA.