Poly(A) Tail-Mediated Gene Regulation by Opposing Roles of Nab2 and Pab2 Nuclear Poly(A)-Binding Proteins in Pre-mRNA Decay

Abstract

The 3= end of most eukaryotic transcripts is decorated by poly(A)-binding proteins (PABPs), which influence the fate of mRNAs throughout gene expression. However, despite the fact that multiple PABPs coexist in the nuclei of most eukaryotes, how functional interplay between these nuclear PABPs controls gene expression remains unclear. By characterizing the ortholog of the Nab2/ZC3H14 zinc finger PABP in Schizosaccharomyces pombe, we show here that the two major fission yeast nuclear PABPs, Pab2 and Nab2, have opposing roles in posttranscriptional gene regulation. Notably, we find that Nab2 functions in gene-specific regulation in a manner opposite to that of Pab2. By studying the ribosomal-protein-coding gene rpl30-2, which is negatively regulated by Pab2 via a nuclear pre-mRNA decay pathway that depends on the nuclear exosome subunit Rrp6, we show that Nab2 promotes rpl30-2 expression by acting at the level of the unspliced pre-mRNA. Our data support a model in which Nab2 impedes Pab2/Rrp6-mediated decay by competing with Pab2 for polyadenylated transcripts in the nucleus. The opposing roles of Pab2 and Nab2 reveal that interplay between nuclear PABPs can influence gene regulation. Production of mRNA in eukaryotic cells is a multistep procedure that involves extensive RNA-processing events, such as 5=-end capping, removal of introns by RNA splicing, 3=-end cleavage, and polyadenylation. Polyadenylation has received considerable interest in the past few years, as recent evidence has revealed that polyadenylation can promote RNA turnover in eukaryotic cells (1-5), contrary to the general view that poly(A) tails only contribute positively to gene expression. The extent to which polyadenylation contributes to RNA turnover and the mechanisms that specify this specialized RNA decay pathway remain poorly understood, however.The fundamental role of RNA polyadenylation in gene expression is conferred by the activity of poly(A)-binding proteins (PABPs) that bind to the 3= poly(A) tail of eukaryotic mRNAs. Two evolutionarily conserved RNA recognition motif (RRM)-containing PABPs bind the poly(A) tract of mRNAs in most eukaryotic cells: PABPC1 in the cytoplasm and PABPN1 in the nucleus (6). Biochemical studies on PABPN1 led to a model in which the protein promotes efficient polyadenylation during mRNA synthesis (7). Although a role for PABPN1 in modulating poly(A) tail length is supported by studies in primary mouse myoblasts (8), studies in human cell lines have recently revealed novel functions for PABPN1. One study demonstrated that PABPN1 modulates the use of alternative polyadenylation sites by occluding access to weak polyadenylation signals for a select group of human genes (9, 10). In addition, a recent genome-wide study that addressed the global impact of PABPN1 deficiency on human gene expression uncovered a role for PABPN1 in the negative regulation of long noncoding RNAs (lncRNAs) (11). Interestingly, a 3= poly(A) tail is a prerequisite for PABPN1 to promote lncRNA turnover (11), consistent with a mechanism of ...

The Polyadenosine RNA-binding Protein, Zinc Finger Cys3His Protein 14 (ZC3H14), Regulates the Pre-mRNA Processing of a Key ATP Synthase Subunit mRNA

“…The results from the fractionation studies not only demonstrate that ZC3H14 binds to the ATP5G1 transcript in the nucleus but also provide evidence for a role in ensuring proper pre-mRNA processing of target transcripts prior to exiting the nucleus. These findings are consistent with a recent study in Schizosaccharomyces pombe that demonstrates a role for the fission yeast ortholog of ZC3H14, Nab2, in acting at the level of the unspliced pre-mRNA and preventing degradation by the nuclear exosome to ensure proper maturation of target transcripts (79). We hypothesize that the inability to ensure the proper nuclear processing of the ATP5G1 pre-mRNA results in a significant decrease in the levels of mature ATP5G1 mRNA in the cytoplasm due to rapid degradation of improperly processed ATP5G1 mRNA via NMD.…”

Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex

“…In the first case, the exosome promotes the trimming of the 3 ′ end to generate a mature snoRNA, while in the second, the premRNA is degraded (Lemay et al 2010;Lemieux et al 2011;Lee et al 2013). Our purification of Mtl1 also recovered the Nab2 poly(A)-binding protein (Supplemental Table S1), and a recent purification of Nab2 identified several NURS subunits (Grenier St-Sauveur et al 2013). Nab2 appears to antagonize the action of Pab2, Rrp6, Red1, and Mtl1 in rpl30-2 pre-mRNA degradation by competing with Pab2 for binding to the poly(A) tail (Grenier St-Sauveur et al 2013;Lee et al 2013).…”

“…Our purification of Mtl1 also recovered the Nab2 poly(A)-binding protein (Supplemental Table S1), and a recent purification of Nab2 identified several NURS subunits (Grenier St-Sauveur et al 2013). Nab2 appears to antagonize the action of Pab2, Rrp6, Red1, and Mtl1 in rpl30-2 pre-mRNA degradation by competing with Pab2 for binding to the poly(A) tail (Grenier St-Sauveur et al 2013;Lee et al 2013). Additionally, the gene encoding another NURS subunit, rmn1 + , exhibits a negative genetic interaction with nab2 + (Cho et al 2012).…”

A conserved role for the zinc finger polyadenosine RNA binding protein, ZC3H14, in control of poly(A) tail length

“…Given the interdependent nature of transcription, RNA processing, export, and translation, dNab2/ZC3H14 could play direct roles in functions other than control of poly(A) tail length. Indeed, recent work has defined roles for the S. pombe Nab2 protein in regulated RNA turnover (Grenier St-Sauveur et al 2013) and other studies identified the corresponding C. elegans protein, termed Sut-2, as a suppressor of a Tau toxicity model (Guthrie et al 2009). Understanding the precise molecular functions of RNA-binding proteins, as well as defining their target RNAs, is a significant challenge and a major focus of our ongoing studies of dNab2/ZC3H14.…”