GSE119073
Choice of alternative polyadenylation sites, mediated by the RNA-binding protein Elavl3, plays a role in differentiation of inhibitory neuronal progenitors
Alternative polyadenylation is a widespread mechanism involving about half of the expressed genes, resulting in varying lengths of the 3' UTR and changes of the post-transcriptional processing, localization, miRNA targeting and stability of mRNAs. During neuronal differentiation a variety of mRNAs change the length of their 3' UTR, promoting the longer version of the transcripts. 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 long 3' UTR variants of Pes1 and Gng2 was detected in areas of cortical and subcortical neuronal differentiation, respectively, in the mouse brain by two-probes FISH analyses. In Drosophila the choice of polyA+ site has been shown to be regulated by the RNA-binding protein Elav, which inhibits polyadenylation at proximal sites while interacting with paused Pol-II promoters. Among the coding genes upregulated during differentiation of ANS cells we found Elavl3, a neural-specific RNA-binding protein homologous to Drosophila Elav. The silencing of Elavl3 in ANS cells resulted in impaired elongation of the 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. Overall design: We studied the transcriptome in four time points during in vitro neuronal differentiation of murine neural stem cells. We had different numbers of biological replicates for each time point, specifically: T0-3 replicates, T1-3 replicates, T2-4 replicates, T3 2 replicates.