Context-dependent modulation of Pol II CTD phosphatase SSUP-72 regulates alternative polyadenylation in neuronal development

Abstract

Alternative polyadenylation (APA) is widespread in neuronal development and activity-mediated neural plasticity. However, the underlying molecular mechanisms are largely unknown. We used systematic genetic studies and genome-wide surveys of the transcriptional landscape to identify a context-dependent regulatory pathway controlling APA in the Caenorhabditis elegans nervous system. Loss of function in ssup-72, a Ser5 phosphatase for the RNA polymerase II (Pol II) C-terminal domain (CTD), dampens transcription termination at a strong intronic polyadenylation site (PAS) in unc-44/ankyrin yet promotes termination at the weak intronic PAS of the MAP kinase dlk-1. A nuclear protein, SYDN-1, which regulates neuronal development, antagonizes the function of SSUP-72 and several nuclear polyadenylation factors. This regulatory pathway allows the production of a neuron-specific isoform of unc-44 and an inhibitory isoform of dlk-1. Dysregulation of the unc-44 and dlk-1 mRNA isoforms in sydn-1 mutants impairs neuronal development. Deleting the intronic PAS of unc-44 results in increased pre-mRNA processing of neuronal ankyrin and suppresses sydn-1 mutants. These results reveal a mechanism by which regulation of CTD phosphorylation controls coding region APA in the nervous system.[Keywords: pre-mRNA 3 ′ end processing; axon and synapse development; C. elegans; SYDN-1; UNC-44/ankyrin; DLK-1/MAP kinase]

Tissue-specific regulation of alternative polyadenylation represses expression of a neuronal ankyrin isoform in C. elegans epidermal development

“…SSUP-72 regulates tissue-and stage-specific expression of UNC-44L via use of the internal PAS2 Previously, we found that a novel nuclear protein SYDN-1 is required for UNC-44L expression in neurons, acting to inhibit SSUP-72 and a subset of pre-mRNA 3′ end processing factors (Chen et al, 2015). Consistent with these findings, sydn-1(0) mutants displayed greatly decreased expression of UNC-44L:: GFP in the nervous system and in the adult vulva.…”

“…In C. elegans, the unc-44 ankyrin gene extends over 40 kb, and produces multiple mRNA isoforms that are terminated predominantly at three poly(A) sites (designated proximal PAS1, PAS2 and the distal PAS3) (Chen et al, 2015) (Fig. 1A, Fig.…”

“…Our previous studies also showed that a 180 bp deletion in the intron containing PAS2, unc-44( ju1378), results in increased production of unc-44L mRNA in neurons (Chen et al, 2015). To test how PAS2 affects the tissue specificity of UNC-44L expression, we inserted GFP after His6987 in the unc-44( ju1378) deletion locus [ Fig.…”

“…Our previous studies showed that SYDN-1 and SSUP-72 act cellautonomously in neurons (Chen et al, 2015). ssup-72 is expressed in many tissues, whereas the endogenous expression pattern of SYDN-1 has not yet been reported.…”

“…A novel nuclear protein SYDN-1 inhibits SSUP-72, a Ser5 phosphatase for the C-terminal domain of RNA polymerase II. In neurons, this inhibition attenuates the use of an internal polyadenylation site (PAS) in unc-44, allowing downstream pre-mRNA polyadenylation and subsequent production of UNC-44L protein (Chen et al, 2015;Van Epps et al, 2010).…”