Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation

Abstract

The choice for a polyadenylation site determines the length of the 3′-untranslated region (3′-UTRs) of an mRNA. Inclusion or exclusion of regulatory sequences in the 3′-UTR may ultimately affect gene expression levels. Poly(A) binding protein nuclear 1 (PABPN1) is involved in polyadenylation of pre-mRNAs. An alanine repeat expansion in PABPN1 (exp-PABPN1) causes oculopharyngeal muscular dystrophy (OPMD). We hypothesized that previously observed disturbed gene expression patterns in OPMD muscles may have been the result of an effect of PABPN1 on alternative polyadenylation, influencing mRNA stability, localization and translation. A single molecule polyadenylation site sequencing method was developed to explore polyadenylation site usage on a genome-wide level in mice overexpressing exp-PABPN1. We identified 2012 transcripts with altered polyadenylation site usage. In the far majority, more proximal alternative polyadenylation sites were used, resulting in shorter 3′-UTRs. 3′-UTR shortening was generally associated with increased expression. Similar changes in polyadenylation site usage were observed after knockdown or overexpression of expanded but not wild-type PABPN1 in cultured myogenic cells. Our data indicate that PABPN1 is important for polyadenylation site selection and that reduced availability of functional PABPN1 in OPMD muscles results in use of alternative polyadenylation sites, leading to large-scale deregulation of gene expression.

Alternative polyadenylation: New insights from global analyses

“…Recent studies suggested that the mutant PABPN1 protein, called trePABPN1, acts as a dominantnegative factor by trapping the wild-type protein in insoluble nuclear inclusion bodies . Global mapping of RNA polyadenylation in trePABPN1-expressing cells and using an OPMD mouse model revealed a systematic shift of the APA profile toward proximal PASs, similar to the effect of PABPN1 loss-of-function (de Klerk et al 2012;Jenal et al 2012). It will be important to understand how the observed aberrant APA pattern contributes to the pathology of OPMD and why only certain muscle cells are affected by this defect.…”

“…Such APA changes are accompanied by the up-regulation of many microRNA target mRNAs, suggesting coupling between APA-and microRNA-mediated gene regulation (Park et al 2011). 39 UTR shortening was also observed in oculopharyngeal muscular dystrophy (OPMD) (de Klerk et al 2012;Jenal et al 2012). This neuromuscular disease is caused by ''prion''-like mutant PABPN1 proteins that have an expanded polyalanine region due to a trinucleotide (GCN) expansion in the PABPN1 gene.…”

Methylation of the nuclear poly(A)-binding protein by type I protein arginine methyltransferases – how and why

“…Experiments in Schizosaccharomyces pombe and mammalian cells (Lemay et al , 2010 ;Lemieux et al , 2011 ;Beaulieu et al , 2012 ) suggest that PABPN1 has an additional function in promoting the activity of the exosome, a protein complex with 3 ′ exonuclease activity involved in many RNA decay and processing reactions both in the nucleus and the cytoplasm. A role of PABPN1 in alternative polyadenylation has also recently been described (de Klerk et al , 2012 ;Jenal et al , 2012 ).…”

Proteasomal activity‐based probes mark protein homeostasis in muscles

“…Immortalized mouse myoblasts, C2C12, were propagated as described in de Klerk et al 23. Immortalized human myoblasts, 7304.1, were cultured according to Anvar et al 24.…”