Molecular dissection of mRNA poly(A) tail length control in yeast

Viphakone, Nicolas; Voisinet-Hakil, Florence; Minvielle‐Sebastia, Lionel

doi:10.1093/nar/gkn080

Cited by 52 publications

(69 citation statements)

References 51 publications

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“…Data obtained from biochemical studies and in vitro polyadenylation assays have defined roles for nuclear PABPs in the elongation process of poly(A) polymerase (PAP) and in poly(A) tail length control, suggesting fundamental roles for nuclear PABPs during mRNA polyadenylation in vivo (6,50,51). In S. pombe, however, the current data do not support a role for Pab2 as a general factor required for mRNA polyadenylation.…”

Section: Discussioncontrasting

confidence: 78%

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

St-Sauveur

Soucek

Corbett

et al. 2013

Molecular and Cellular Biology

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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 ...

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Section: Discussioncontrasting

confidence: 78%

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

St-Sauveur

Soucek

Corbett

et al. 2013

Molecular and Cellular Biology

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“…This observation suggests that the signal to stop poly(A) addition is operational in mex67-5 and that there is sufficient Nab2p and Pab1p to limit tail length. Moreover, we find no sign that after prolonged incubation in mex67-5 mutant extract, RNAs are subjected to recleavage, which is a consequence of limited availability of Nab2p in vitro (80). A more likely explanation for the longer tails is that the malformed mRNP blocks recruitment or activation or PAN or its access to the 3Ј end.…”

Section: Vol 29 2009 Release Of 3ј-end Processing Factors 5335mentioning

confidence: 58%

“…The subunits of the complex are largely conserved across eukaryotes, and in the yeast Saccharomyces cerevisiae, this complex can be separated biochemically into three factors: cleavage and polyadenylation factor (CPF), cleavage factor (CF) IA, and Hrp1p (59). The length of the RNA poly(A) tail is restricted by the recruitment of specific poly(A)-binding proteins, such as Nab2p and Pab1p (6,19,22,40,80), and by the action of poly(A)-specific nucleases in the nucleus and the cytoplasm (59). Previous studies showed that 3Ј-end processing factors, with the exception of Hrp1p, Pab1p, and Nab2p, do not shuttle in and out of the nucleus (9, 38, 48).…”

mentioning

confidence: 99%

Assembly of an Export-Competent mRNP Is Needed for Efficient Release of the 3′-End Processing Complex after Polyadenylation

Lykke‐Andersen

Nasser

et al. 2009

Molecular and Cellular Biology

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Before polyadenylated mRNA is exported from the nucleus, the 3-end processing complex is removed by a poorly described mechanism. In this study, we asked whether factors involved in mRNP maturation and export are also required for disassembly of the cleavage and polyadenylation complex. An RNA immunoprecipitation assay monitoring the amount of the cleavage factor (CF) IA component Rna15p associated with poly(A) ؉ RNA reveals defective removal of Rna15p in mutants of the nuclear export receptor Mex67p as well as other factors important for assembly of an export-competent mRNP. In contrast, Rna15p is not retained in mutants of export factors that function primarily on the cytoplasmic side of the nuclear pore. Consistent with a functional interaction between Mex67p and the 3-end processing complex, a mex67 mutant accumulates unprocessed SSA4 transcripts and exhibits a severe growth defect when this mutation is combined with mutation of Rna15p or another CF IA subunit, Rna14p. RNAs that become processed in a mex67 mutant have longer poly(A) tails both in vivo and in vitro. This influence of Mex67p on 3-end processing is conserved, as depletion of its human homolog, TAP/NXF1, triggers mRNA hyperadenylation. Our results indicate a function for nuclear mRNP assembly factors in releasing the 3-end processing complex once polyadenylation is complete.A significant advance in the area of eukaryotic gene expression has been the appreciation of multiple interrelationships between activities needed to get a functional mRNA to the cytoplasm for translation. Coordination occurs at the level of transcription, capping, splicing, 3Ј-end processing, and assembly of the mRNA into a ribonucleoprotein particle (RNP) that can be transported (for reviews, see references 2, 5, 12, 43, 51, and 55). Overseeing all of this is a nuclear mRNA surveillance mechanism which ensures that only correctly formed mRNP reaches the cytoplasm and that defective ones are degraded (for a review, see reference 70).Processing at the mRNA 3Ј end is accomplished by a multisubunit complex that recognizes signals on the nascent RNA, cleaves at the poly(A) site, and adds a poly(A) tract. The subunits of the complex are largely conserved across eukaryotes, and in the yeast Saccharomyces cerevisiae, this complex can be separated biochemically into three factors: cleavage and polyadenylation factor (CPF), cleavage factor (CF) IA, and Hrp1p (59). The length of the RNA poly(A) tail is restricted by the recruitment of specific poly(A)-binding proteins, such as Nab2p and Pab1p (6,19,22,40,80), and by the action of poly(A)-specific nucleases in the nucleus and the cytoplasm (59). Previous studies showed that 3Ј-end processing factors, with the exception of Hrp1p, Pab1p, and Nab2p, do not shuttle in and out of the nucleus (9, 38, 48). Thus, the exported mRNP does not include CF IA and CPF components, yet the signal sequences that stably hold these factors onto the mRNA as it receives its tail are present on the final polyadenylated product. Therefore, a mechanism must ex...

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“…One viable alternative to this "direct-competition" model is one in which addition of a certain length of adenosines to the extending poly(A) tail allows for multiple dNab2/ZC3H14 proteins to bind and induce a conformational change in the RNA that might then displace Pabp2/PABPN1 and inhibit the processivity of the poly(A) polymerase. 32,33 Alternatively, Nab2/dNab2 could also recruit enzymes that actively trim the poly(A) tail. Yeast Nab2 and fly dNab2 both interact genetically with components of the nuclear exosome (our unpublished results and see ref.…”

Section: Mutations In the Conserved Znf Pab Zc3h14 Are Linked To Nsmentioning

confidence: 99%

“…47,48 Given that yeast Nab2 has a minimal binding footprint of roughly 10-15 adenosines (our unpublished data and see ref. 33), and antibodies targeting yeast Nab2 co-immunoprecipitate chromatincontaining genes transcribed by RNA polymerase II or RNA polymerase III, 18 dNab2/ZC3H14 may be able to recognize these short poly(A) tails and trigger exosome recruitment and subsequent RNA turnover (Fig. 2 and inset I).…”

Section: Mutations In the Conserved Znf Pab Zc3h14 Are Linked To Nsmentioning

confidence: 99%

New kid on the ID block

Kelly¹,

Pak²,

Garshasbi³

et al. 2012

RNA Biology

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Polyadenosine RNA binding proteins (Pabs) play critical roles in regulating the polyadenylation, nuclear export, stability and translation of cellular RNAs. Although most Pabs are ubiquitously expressed and are thought to play general roles in post-transcriptional regulation, mutations in genes encoding these factors have been linked to tissue-specific diseases including muscular dystrophy and now intellectual disability (ID). Our recent work defined this connection to ID, as we showed that mutations in the gene encoding the ubiquitously expressed Cys 3 His tandem zinc-finger (ZnF) Pab, ZC3H14 (Zinc finger protein, CCCH-type, number 14) are associated with non-syndromic autosomal recessive intellectual disability (NS-ARID). This study provided a first link between defects in Pab function and a brain disorder, suggesting that ZC3H14 plays a required role in regulating RNAs in nervous system cells. Here we highlight key questions raised by our study of ZC3H14 and its ortholog in the fruit fly Drosophila melanogaster, dNab2 and comment on future approaches that could provide insights into the cellular and molecular roles of this class of zinc fingercontaining Pabs. We propose a summary model depicting how ZC3H14-type Pabs might play particularly important roles in neuronal RNA metabolism.

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Molecular dissection of mRNA poly(A) tail length control in yeast

Cited by 52 publications

References 51 publications

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

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

Assembly of an Export-Competent mRNP Is Needed for Efficient Release of the 3′-End Processing Complex after Polyadenylation

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