Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors

Abstract

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.

Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt

“…Given that the majority of gene expression changes as measured by mRNA levels are gradual and do not sharply distinguish stem cells from progenitor cell states, we investigated whether other transcriptomic signatures better delineate the rapid transitions of loss of stemness and early commitment. As alternative pre-mRNA processing has been shown to be important in the differentiation of embryonic stem cells, we asked whether there are differences in alternative splicing and polyadenylation [29][30][31][32][33][34][35][36][37][38] . We used two computational pipelines, rMATS Turbo and MAJIQ, to analyze the RNA-seq data to identify significant changes in mRNA-splicing patterns among the six cell populations ( Fig.…”

“…This process might not be limited to the intestine but may be a general feature of somatic stem cell differentiation. There are known mRNA processing changes during loss of pluripotency in mouse embryonic stem cells [29][30][31][32][33][34][35][36][37][38] , and changes in RNA processing have been identified in various disease states. However, very little is known regarding global changes in RNA processing during normal adult tissue homeostasis and especially during the earliest changes that occur during loss-of-stemness.…”

Vapor Cannabis Exposure Promotes Genetic Plasticity in the Rat Hypothalamus

“…However, more extended distal APA sites (p sites, by 3%) and more extended exonic APA sites (e sites, by 9%), but less exonic APA sites (c sites, by 8%) and less distal sites (o sites, by 4%) were triggered by cannabis exposure. It has been proposed that use of distal Poly A sites preferentially place longer transcripts under negative regulatory control by miRNAs, whereas the loss of distal APAs spares transcripts from miRNA regulation 54 . Our data show that novel use of genome sequences (extended exonic APA sites and extended distal sites) was reduced by cannabis exposure.…”

Unveiling ncRNA regulatory axes in atherosclerosis progression

“…3′UTR regions of mRNAs are highly polymorphic in length and sequence, variations that may underlie changes in miRNA targeting and stability of the involved mRNAs [79]. Length polymorphisms of 3′UTRs are due to two different mechanisms: alternative splicing of untranslated exons, which is shared with most RNAs, and alternative polyadenylation, which seems to be mostly restricted to mRNAs, lincRNAs and NATs [80].…”