CPEB inducible knock-down in a H.D. Myz cell line

Messenger RNA stability, localization, and translation are largely determined by sequences in their 3′ untranslated regions (3’UTRs), which recruit regulatory proteins and RNAs. More than half of the mammalian genes generate multiple mRNA isoforms differing in their 3′UTRs and therefore in their regulatory elements. The Cytoplasmic Polyadenylation Element Binding protein 1 (CPEB1) binds to cognate sites in 3’ UTRs and regulates translation. CPEB1 can shuttle to the nucleus and we report its co-localization with splicing factors. CPEB1 knock down leads to changes in alternative splicing, and we show that alternative 3’ splice site linked to alternative polyadenylation of the bub-3 pre-mRNA, important for cell proliferation, is regulated by CPEB1 at least in part by preventing 3’ splice site recognition by U2AF. RNA-Seq experiments reveal that CPEB1 mediates 3’ UTR shortening of hundreds of mRNAs, leading to changes in their translation efficiency. Three total RNA from three biological replicates were labeled and hybridized versus its own control in direct and dye-swap hybridizations.