Mammalian pre-mRNA 3′ End Processing Factor CF I<sub>m</sub>68 Functions in mRNA Export

Ruepp, Marc-David; Aringhieri, Chiara; Vivarelli, Silvia; Cardinale, Stefano; Paro, Simona; Schümperli, Daniel; Barabino, Silvia M.L.

doi:10.1091/mbc.e09-05-0389

Cited by 51 publications

(69 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Also, several previous studies suggest a coupling between the polyadenylation machinery and mRNA export in mammalian cells (for review, see Zhao et al 1999). More recently, the CPSF6 gene product (the CF I m 68 protein) was reported to stimulate Nxf1-mediated mRNA export (Ruepp et al 2009). It was suggested that the CF I m 68 protein accompanies the RNP complex to the cytoplasm and that it is released in the cytoplasm during the initial stages of translation.…”

Section: Discussionmentioning

confidence: 99%

The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway

Coyle¹,

Bor²,

Rekosh³

et al. 2011

RNA

View full text Add to dashboard Cite

Post-transcriptional regulation of mRNA includes restriction mechanisms to prevent export and expression of mRNAs that are incompletely spliced. Here we present evidence that the mammalian protein Tpr is involved in this restriction. To study the role of Tpr in export of mRNA with retained introns, we used reporters in which the mRNA was exported either via the Nxf1/Nxt1 pathway using a CTE or via the Crm1 pathway using Rev/RRE. Our data show that even modest knockdown of Tpr using RNAi leads to a significant increase in export and translation from the mRNA containing the CTE. In contrast, Tpr perturbation has no effect on export of mRNA containing the RRE, either in the absence or presence of Rev. Also, no effects were observed on export of a completely spliced mRNA. Taken together, our results indicate that Tpr plays an important role in quality control of mRNA trafficked on the Nxf1 pathway.

show abstract

Section: Discussionmentioning

confidence: 99%

The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway

Coyle¹,

Bor²,

Rekosh³

et al. 2011

RNA

View full text Add to dashboard Cite

show abstract

“…We and others have previously demonstrated that members of the cleavage and polyadenylation complex are involved in the processing of histone pre-mRNA in addition to their role in the cleavage and polyadenylation of cellular mRNA (7,23,40,49,51). Moreover, a recent proteomic analysis of the cleavage and polyadenylation complex found the presence of several Integrator proteins (45).…”

Section: Figmentioning

confidence: 97%

A Subset of Drosophila Integrator Proteins Is Essential for Efficient U7 snRNA and Spliceosomal snRNA 3′-End Formation

Ezzeddine

Chen

Waltenspiel

et al. 2011

Molecular and Cellular Biology

116

View full text Add to dashboard Cite

Proper gene expression relies on a class of ubiquitously expressed, uridine-rich small nuclear RNAs (snRNAs) transcribed by RNA polymerase II (RNAPII). Vertebrate snRNAs are transcribed from a unique promoter, which is required for proper 3-end formation, and cleavage of the nascent transcript involves the activity of a poorly understood set of proteins called the Integrator complex. To examine 3-end formation in Drosophila melanogaster, we developed a cell-based reporter that monitors aberrant 3-end formation of snRNA through the gain in expression of green fluorescent protein (GFP). We used this reporter in Drosophila S2 cells to determine requirements for U7 snRNA 3-end formation and found that processing was strongly dependent upon nucleotides located within the 3 stem-loop as well as sequences likely to comprise the Drosophila equivalent of the vertebrate 3 box. Substitution of the actin promoter for the snRNA promoter abolished proper 3-end formation, demonstrating the conserved requirement for an snRNA promoter in Drosophila. We tested the requirement for all Drosophila Integrator subunits and found that Integrators 1, 4, 9, and 11 were essential for 3-end formation and that Integrators 3 and 10 may be dispensable for processing. Depletion of cleavage and polyadenylation factors or of histone pre-mRNA processing factors did not affect U7 snRNA processing efficiency, demonstrating that the Integrator complex does not share components with the mRNA 3-end processing machinery. Finally, flies harboring mutations in either Integrator 4 or 7 fail to complete development and accumulate significant levels of misprocessed snRNA in the larval stages.In eukaryotes, the major transcripts produced by RNA polymerase II (RNAPII) include the polyadenylated [poly (A) ϩ ] mRNAs, the replication-dependent histone mRNAs, and the Sm class of small nuclear RNAs (snRNAs). The 3Ј ends of these three general classes of RNAs are all formed by cotranscriptional cleavage, but each one has a distinct mechanism for 3Ј-end formation (for reviews, see references 29 and 32). In poly(A) ϩ and histone pre-mRNAs there are conserved upstream and downstream sequences that flank the cleavage site; factors bind to these sites and then recruit additional factors that initiate cleavage (53). In the case of poly(A) ϩ pre-mRNA, the upstream element is the canonical AAUAAA polyadenylation signal (PAS) and the downstream sequence is the G/Urich downstream element (DSE). Recognition of the PAS is carried out by the cleavage and polyadenylation specificity complex (CPSF) component CPSF160 via its RNA recognition motifs (RRM) (36), whereas the DSE is bound by the RRM of the cleavage stimulation factor (CstF) component CstF64 (28). Subsequent to this recognition event is recruitment of additional factors that activate the endonucleolytic cleavage between the PAS and the DSE.Histone pre-mRNA contains a distinct set of flanking elements. Upstream of the cleavage site is a conserved stem-loop structure (SL) and downstream a purine-rich element called the ...

show abstract

“…CFI m is composed of a large subunit of 59, 68, or 72 kDa and a small subunit of 25 kDa (CFI m 25, also referred to as CPSF5 or NUDT21) (12,13), both of which contribute to RNA binding (14). The large subunit, encoded by either of two paralogs (CPSF6 and CPSF7), contains an N-terminal RNA Recognition Motif (RRM), an internal polyproline-rich region, and a C-terminal RS/RD alternating charge domain-a structure similar to that of the SR-protein family of splicing regulators.…”

mentioning

confidence: 99%

Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing

Yang

Gilmartin

Doublié

2010

Proc. Natl. Acad. Sci. U.S.A.

130

144

View full text Add to dashboard Cite

Human Cleavage Factor Im (CFI m ) is an essential component of the pre-mRNA 3′ processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI m 25) of the CFI m complex possesses a characteristic α/β/α Nudix fold, CFI m 25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI m 25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI m 25 is the first Nudix protein to be reported to bind RNA in a sequencespecific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap 4 A (diadenosine tetraphosphate) by CFI m 25 suggests a potential role for small molecules in the regulation of mRNA 3′ processing.T he transcriptome complexity of higher eukaryotes requires the coordinate recognition of an array of alternative pre-mRNA processing signals in a developmental and tissue-specific manner (1, 2). The sequences that direct pre-mRNA splicing and 3′ processing are initially recognized within the nascent transcript in a process that is intimately coupled to transcription (3, 4). While the recognition of exons within the pre-mRNA is mediated by both RNA:RNA and protein:RNA interactions (5), the 3′ processing of polyadenylated mRNAs appears to rely solely on the interaction of protein factors (6) with unstructured RNA sequences (7) within the nascent transcript.Vertebrate pre-mRNA 3′ processing signals are recognized by a tripartite mechanism through which a set of short RNA sequences direct the cooperative binding of three multimeric 3′ processing factors, cleavage factor I m (CFI m ), cleavage and polyadenylation specificity factor (CPSF), and cleavage stimulation factor (CstF) (8). CPSF and CstF bind the AAUAAA hexamer and downstream GU-rich elements that flank the poly(A) site, respectively, whereas CFI m interacts with upstream sequences that may function in the regulation of alternative polyadenylation (9-11). SELEX and biochemical analyses have identified the sequence UGUAN (N ¼ A > U > G, C) as the preferred binding site of CFI m (11). In this report we have taken a structural approach to determine the mechanism of sequence-specific RNA binding by CFI m .CFI m is composed of a large subunit of 59, 68, or 72 kDa and a small subunit of 25 kDa (CFI m 25, also referred to as CPSF5 or NUDT21) (12, 13), both of which contribute to RNA binding (14). The large subunit, encoded by either of two paralogs (CPSF6 and CPSF7), contains an N-terminal RNA Recognition Motif (RRM), an internal polyproline-rich region, and a C-termina...

show abstract

Mammalian pre-mRNA 3′ End Processing Factor CF I_m68 Functions in mRNA Export

Cited by 51 publications

References 50 publications

The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway

The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway

A Subset of Drosophila Integrator Proteins Is Essential for Efficient U7 snRNA and Spliceosomal snRNA 3′-End Formation

Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing

Contact Info

Product

Resources

About

Mammalian pre-mRNA 3′ End Processing Factor CF Im68 Functions in mRNA Export

Cited by 51 publications

References 50 publications

The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway

The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway

A Subset of Drosophila Integrator Proteins Is Essential for Efficient U7 snRNA and Spliceosomal snRNA 3′-End Formation

Structural basis of UGUA recognition by the Nudix protein CFI m 25 and implications for a regulatory role in mRNA 3′ processing

Contact Info

Product

Resources

About

Mammalian pre-mRNA 3′ End Processing Factor CF I_m68 Functions in mRNA Export

Structural basis of UGUA recognition by the Nudix protein CFI _m 25 and implications for a regulatory role in mRNA 3′ processing