PABPN1loss-of-function in oculopharyngeal muscular dystrophy primarily impacts APA-shift in muscle transcripts

Abstract Alternative polyadenylation (APA) at the 3’UTR of transcripts contributes to the cell transcriptome. APA is suppressed by the nuclear RNA binding protein, PABPN1. Aging-associated reduced PABPN1 levels in skeletal muscles lead to muscle wasting. Muscle weakness in oculopharyngeal muscular dystrophy (OPMD) is caused by short alanine expansion in PABPN1 exon1. The expanded PABPN1 forms nuclear aggregates, an OPMD hallmark. Whether the expanded PABPN1 affect APA and how contributes to muscle pathology is unresolved. To investigate these questions, we developed a procedure including RNA library preparation and a simple pipeline calculating ‘APA-shift’ ratio as a readout for PABPN1 function. Using the mouse OPMD model we demonstrate similar results between previously published PAS utilization and ‘APA-shift’ results. Studying APA-shift in two OPMD models and in OPMD patients we show that the expression of the expanded PABPN1 does not correlate with APA-shift. Instead, APA-shift is correlated with reduced expression levels of PABPN1 isoforms, amongst the isoform lacking exon1. Further we show that with our protocol APA-shift is enriched in muscle transcripts, moreover in OPMD patients. We suggest that muscle weakness in OPMD is caused by PABPN1 loss-of-function leading to APA-shift that primarily affects in muscle transcripts.