Multiple factors in the early splicing complex are involved in the nuclear retention of pre-mRNAs in mammalian cells

Takemura, Reiko; Takeiwa, Toshihiko; Taniguchi, Ichiro; McCloskey, Asako; Ohno, Masatomi

doi:10.1111/j.1365-2443.2011.01548.x

Cited by 50 publications

(52 citation statements)

References 41 publications

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“…Interestingly, intron retention is linked to usage of the distal CPA site, which would support the aforementioned fail-safe hypothesis in which the distal CPA site is used when the proximal CPA site is not adequately recognized-most likely due to the perturbation of the well-documented interconnection between splicing and 3 ′ end processing (Proudfoot et al 2002). The mechanism of transcript retention is likely to involve the presence of splice factors that are associated with the incompletely spliced distal APA isoform (Takemura et al 2011). Secondly, our analysis of nuclear and cytoplasmic APA profiles under conditions in which DICER1 is depleted identifies DICER1 as an unexpected regulator of APA at the point of CPA site choice (Fig.…”

Section: Discussionmentioning

confidence: 54%

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation

Neve

Burger

et al. 2015

Genome Res.

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Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we used a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape APA profiles in different subcellular locations. Here, we show that APA isoforms with shorter 3 ′ UTRs tend to be overrepresented in the cytoplasm and appear to be cell-type-specific events. Nuclear retention of longer APA isoforms occurs and is partly a result of incomplete splicing contributing to the observed cytoplasmic bias of transcripts with shorter 3′ UTRs. We demonstrate that the endoribonuclease III, DICER1, contributes to the establishment of subcellular APA profiles not only by expected cytoplasmic miRNA-mediated destabilization of APA mRNA isoforms, but also by affecting polyadenylation site choice.

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Section: Discussionmentioning

confidence: 54%

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation

Neve

Burger

et al. 2015

Genome Res.

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“…4) suggests that the regulation circuitry identified in our study involves interaction of the retained introns with the pre-mRNA splicing machinery. Interestingly, the U1 snRNP and U2AF complexes interacting with the 59ss and the 39ss have been shown to facilitate nuclear retention of incompletely spliced transcripts (Rain and Legrain 1997;Takemura et al 2011). Nuclear retention of incompletely spliced transcripts has additionally been shown to be modulated by cis-regulatory elements.…”

Section: Discussionmentioning

confidence: 99%

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

Yap¹,

Lim²,

Khandelia³

et al. 2012

Genes Dev.

268

295

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Differentiated cells acquire unique structural and functional traits through coordinated expression of lineagespecific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the underlying regulation is not well understood. Here we show that genes encoding critical presynaptic proteins are transcribed at a detectable level in both neurons and nonneuronal cells. However, in nonneuronal cells, the splicing of 39-terminal introns within these genes is repressed by the polypyrimidine tract-binding protein (Ptbp1). This inhibits the export of incompletely spliced mRNAs to the cytoplasm and triggers their nuclear degradation. Clearance of these introncontaining transcripts occurs independently of the nonsense-mediated decay (NMD) pathway but requires components of the nuclear RNA surveillance machinery, including the nuclear pore-associated protein Tpr and the exosome complex. When Ptbp1 expression decreases during neuronal differentiation, the regulated introns are spliced out, thus allowing the accumulation of translation-competent mRNAs in the cytoplasm. We propose that this mechanism counters ectopic and precocious expression of functionally linked neuron-specific genes and ensures their coherent activation in the appropriate developmental context.

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“…One mechanism is spliceosome formation around introns, which is confined to the nucleus because most splicing factors are localized in the nucleus. In this mechanism, the spliceosome itself or one or more spliceosomeassociated factors anchor intron-containing RNAs in the nucleus (5)(6)(7). Another mechanism for the nuclear retention of introncontaining RNAs is the splicing-dependent recruitment of mRNA export-related factors.…”

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confidence: 99%

A Specific Set of Exon Junction Complex Subunits Is Required for the Nuclear Retention of Unspliced RNAs in Caenorhabditis elegans

Shiimori

Inoue

Sakamoto

2013

Molecular and Cellular Biology

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The exon junction complex (EJC) is highly conserved in many organisms and is involved in various steps of mRNA metabolism. During the course of investigating the role of EJC in the germ line sex determination of the nematode Caenorhabditis elegans, we found that depletion of one of the three core subunits (Y14, MAG-1, and eukaryotic translation initiation factor 4III [eIF4AIII]) or one auxiliary subunit (UAP56) of EJC resulted in the cytoplasmic leakage of unspliced RNAs from almost all of the C. elegans protein-coding genes examined thus far. This leakage was also observed with the depletion of several splicing factors, including SF3b, IBP160, and PRP19, all of which genetically interacted with Y14. We also found that Y14 physically interacts with both pre-mRNA and spliceosomal U snRNAs, especially U2 snRNA, and that the interaction was abolished when both IBP160 and PRP19 were depleted. Our results strongly suggest that a specific set of EJC subunits is recruited onto introns and interacts with components of the spliceosome, including U2 snRNP, to provide a critical signal for the surveillance and nuclear retention of unspliced RNAs in C. elegans.T he complete removal of introns from pre-mRNA before mRNA export to the cytoplasm is critical to ensure the proper expression of the protein product in higher eukaryotes. Premature export of intron-containing RNAs gives rise to abnormal protein products that are very harmful to various cell functions, although most of such abnormal RNAs are eliminated by mRNA quality control systems, including nonsense-mediated mRNA decay (NMD) (1-4). Thus, cells must have mechanisms to retain partially spliced pre-mRNA in the nucleus. Indeed, most intron-containing RNAs, except in the case of alternative splicing, are normally localized in the nucleus. One mechanism is spliceosome formation around introns, which is confined to the nucleus because most splicing factors are localized in the nucleus. In this mechanism, the spliceosome itself or one or more spliceosomeassociated factors anchor intron-containing RNAs in the nucleus (5-7). Another mechanism for the nuclear retention of introncontaining RNAs is the splicing-dependent recruitment of mRNA export-related factors. The transcription and export (TREX) complex and exon junction complex (EJC) form on the 5= region of the nascent transcript (8, 9) and 20 to 24 nucleotides upstream from splice junctions (10, 11), respectively. The TREX complex contains the proteins UAP56 and Aly/REF (12, 13), both of which are also subunits of EJC (14-16), suggesting the tight coupling of splicing with mRNA export and the involvement of TREX and EJC for preventing the premature export of unspliced RNAs. Both spliceosome-dependent and export-related-factor-coupled mechanisms for the nuclear retention of intron-containing RNAs may operate concurrently, but the molecular details remain to be elucidated.EJC consists of four core subunits (Y14, Mago-nashi, eukaryotic translation initiation factor 4III [eIF4AIII], and Barentz/ MLN51) and several auxiliary...

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Multiple factors in the early splicing complex are involved in the nuclear retention of pre-mRNAs in mammalian cells

Cited by 50 publications

References 41 publications

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

A Specific Set of Exon Junction Complex Subunits Is Required for the Nuclear Retention of Unspliced RNAs in Caenorhabditis elegans

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