Choice of alternative polyadenylation sites, mediated by the rna-binding protein Elavl3, plays a role in differentiation of inhibitory neuronal progenitors

Alternative polyadenylation (APA) is a widespread mechanism involving about half of the expressed genes, resulting in varying lengths of the 3 ′ untranslated region (3 ′ UTR). Variations in length and sequence of the 3 ′ UTR may underlie changes of post-transcriptional processing, localization, miRNA targeting and stability of mRNAs. During embryonic development a large array of mRNAs exhibit APA, with a prevalence of the longer 3 ′ UTR versions in differentiating cells. Little is known about polyA+ site usage during differentiation of mammalian neural progenitors. Here we exploit a model of adherent neural stem (ANS) cells, which homogeneously and efficiently differentiate into GABAergic neurons. RNAseq data shows a global trend towards lengthening of the 3 ′ UTRs during differentiation. Enriched expression of the longer 3 ′ UTR variants of Pes1 and Gng2 was detected in the mouse brain in areas of cortical and subcortical neuronal differentiation, respectively, by two-probes fluorescent in situ hybridization (FISH). Among the coding genes upregulated during differentiation of ANS cells we found Elavl3, a neural-specific RNA-binding protein homologous to Drosophila Elav. In the insect, Elav regulates polyA+ site choice while interacting with paused Pol-II promoters. We tested the role of Elavl3 in ANS cells, by silencing Elavl3 and observed consistent changes in 3 ′ UTR length and delayed neuronal differentiation. These results indicate that choice of the polyA+ site and lengthening of 3 ′ UTRs is a possible additional mechanism of posttranscriptional RNA modification involved in neuronal differentiation.