Newly synthesized small nuclear RNAs appear transiently in the cytoplasm

Zieve, Gary W.; Sauterer, Roger; Feeney, Robert J.

doi:10.1016/0022-2836(88)90312-9

Cited by 62 publications

(32 citation statements)

References 46 publications

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“…The levels of LSm (Sm-like)-class snRNAs U6 and U6atac were not decreased in either the SmD1 or SmB/B9 knockdown. agreement with previous studies indicating that the pool of ''Sm-free'' snRNAs is relatively small Zieve et al 1988). Consistent with an important role for Sm core assembly in snRNP stability (Jones and Guthrie 1990), knockdown of SmB/B9 led to a decrease in Sm-class snRNAs (U1, U4, U5, U11, U12, and U4atac), with the exception of U2 (Fig.…”

Section: Knockdown Of Sm Proteins Affects the Levels Of Sm-class Snrnassupporting

confidence: 92%

Regulation of alternative splicing by the core spliceosomal machinery

Saltzman¹,

Pan²,

Blencowe³

2011

Genes Dev.

191

192

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Alternative splicing (AS) plays a major role in the generation of proteomic diversity and in gene regulation. However, the role of the basal splicing machinery in regulating AS remains poorly understood. Here we show that the core snRNP (small nuclear ribonucleoprotein) protein SmB/B9 self-regulates its expression by promoting the inclusion of a highly conserved alternative exon in its own pre-mRNA that targets the spliced transcript for nonsense-mediated mRNA decay (NMD). Depletion of SmB/B9 in human cells results in reduced levels of snRNPs and a striking reduction in the inclusion levels of hundreds of additional alternative exons, with comparatively few effects on constitutive exon splicing levels. The affected alternative exons are enriched in genes encoding RNA processing and other RNA-binding factors, and a subset of these exons also regulate gene expression by activating NMD. Our results thus demonstrate a role for the core spliceosomal machinery in controlling an exon network that appears to modulate the levels of many RNA processing factors.[Keywords: alternative splicing; Sm proteins; snRNP; autoregulation; NMD; exon network] Supplemental material is available for this article. The production of multiple mRNA variants through alternative splicing (AS) is estimated to take place in transcripts from >95% of human multiexon genes Wang et al. 2008). AS represents a mechanism for gene regulation and expansion of the proteome. The most widely studied trans-acting factors regulating AS are proteins of the SR (Ser/Arg-rich) and hnRNP (heterogeneous ribonucleoprotein) families, as well as numerous tissue-restricted AS factors (for review, see Chen and Manley 2009;Nilsen and Graveley 2010). These factors generally regulate AS by recognizing cis-acting sequences in exons or introns and by promoting or suppressing the assembly of the spliceosome at adjacent splice sites. In contrast to these AS regulatory factors, much less is known about how or the extent to which components of the basal or ''core'' splicing machinery modulate splice site decisions.The spliceosome is a large RNP complex that carries out the removal of introns from pre-mRNAs. It comprises the U1, U2, U4/6, and U5 small nuclear RNPs (snRNPs) and several hundred protein factors (for review, see Wahl et al. 2009). Studies in yeast and metazoan systems have indicated that the levels of some of these core splicing components can affect splice site choice. Microarray profiling revealed transcript-specific effects on splicing in yeast strains harboring mutations in or deletions of core splicing components Pleiss et al. 2007). Knockdown of several core splicing factors in Drosophila cells resulted in transcript-specific effects on AS reporters (Park et al. 2004). Deficiency of the snRNP assembly factor SMN (survival of motor neuron) in a mouse model of spinal muscular atrophy (SMA) resulted in tissue-specific perturbations in snRNP levels and splicing defects (Gabanella et al. 2007;Zhang et al. 2008). Tiling microarray profiling analysis of fission yeast...

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Section: Knockdown Of Sm Proteins Affects the Levels Of Sm-class Snrnassupporting

confidence: 92%

Regulation of alternative splicing by the core spliceosomal machinery

Saltzman¹,

Pan²,

Blencowe³

2011

Genes Dev.

191

192

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“…Localization studies of nascent and steadystate snRNAs in mammalian cells using conventional cell fractionation procedures are largely in agreement with data from Xenopus oocytes (Eliceiri 1974;Eliceiri and Sayavedra 1976;Zieve and Penman 1976;Gurney and Eliceiri 1980), as are more recent results (Zieve et al 1988;Feeney et al 1989}. Taken together, the data argue that snRNP biogenesis in mammalian somatic cells and Xenopus oocytes is similar.…”

Section: ' Lg]gaaaa-oohsupporting

confidence: 86%

“…1). In pulse-chase analysis of snRNA synthesis in mammalian cells with two different advanced techniques of cell fractionation (Zieve et al 1988;Feeney et al 1989}, U3 snRNA was also detected in the cytoplasm. Furthermore, because the trimethylation reaction for the spliceosomal snRNAs is believed to be a uniquely cytoplasmic event (Mattaj 1986) and the U3 snRNA cap is trimethylated, U3 snRNA would be expected to undergo this reaction in the cytoplasm.…”

Section: U3 Biogenesis Includes a Cytoplasmic Phasementioning

confidence: 99%

Distinct molecular signals for nuclear import of the nucleolar snRNA, U3.

Baserga¹,

Gilmore-Hebert²,

Yang³

1992

Genes Dev.

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Export to the cytoplasm of U3 RNA transcribed from a rat U3 gene injected into the nucleus of Xenopus oocytes indicates that the biogenesis of U3 RNA, like that of the previously studied Sm-precipitable nucleoplasmic snRNAs (U1, U2, U4, and US), includes a cytoplasmic phase. The regulation of import of the U3 snRNA into the nucleus has been analyzed by injection of synthetic human U3 transcripts into the cytoplasm of Xenopus oocytes. Binding of the major autoantigenic protein of the U3 snRNP, fibriUarin, and cap trimethylation can occur in the cytoplasm, but neither are required for import. The 3'-terminal 13 nucleotides are required for optimal import and cap trimethylation and participate in a phylogenetically conserved U3 structural element, a short 3'-terminal stem. An artificial construct containing the 3'-terminal 13 nucleotides, including the 3'-terminal stem, but only 56 nucleotides of the 217 nucleotides in U3, appears to be sufficient for import. The presence of the 3'-terminal stem in all snRNAs known to be imported suggests that it might be a universal element required for nuclear import.

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“…6C). Since unbound snRNAs are unstable compared to snRNAs in snRNP complexes, quantification of snRNA levels provides insight into snRNP integrity (36,50). Consistent with this, U4 and U5 snRNAs were reduced following immunoprecipitation with the anti-Sm protein Y12 antibody, indicating that U4 and U5 snRNPs are also diminished (Fig.…”

Section: Resultssupporting

confidence: 56%

SmD3 Regulates Intronic Noncoding RNA Biogenesis

Scruggs

Michel

Ory

et al. 2012

Molecular and Cellular Biology

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Accumulation of excess lipid in nonadipose tissues is associated with oxidative stress and organ dysfunction and plays an important role in diabetic complications. To elucidate molecular events critical for lipotoxicity, we used retroviral promoter trap mutagenesis to generate mutant Chinese hamster ovary cell lines resistant to lipotoxic and oxidative stress. A previous report of a mutant from this screen demonstrated that under lipotoxic conditions, small nucleolar RNAs (snoRNAs) in the rpL13a gene accumulate in the cytosol and serve as critical mediators of lipotoxic cell death. We now report a novel, independent mutant in which a single provirus disrupted one allele of the gene encoding the spliceosomal protein SmD3, creating a model of haploinsufficiency. We show that snoRNA expression and the abundance of snoRNA-containing intron lariats are decreased in SmD3 mutant cells, even though haploinsufficiency of SmD3 supports pre-mRNA splicing. The mechanism through which SmD3 regulates the expression of intronic snoRNAs likely involves effects of SmD3 on the levels of small nuclear RNAs (snRNAs) U4 and U5. Our data implicate SmD3 as a critical determinant in the processing of intronic noncoding RNAs in general and as an upstream mediator of metabolic stress response pathways through the regulation of snoRNA expression. Elevations in serum triglycerides and free fatty acids (FA) play an important role in the pathogenesis of diabetic complications. Under physiological conditions, mammalian adipose cells internalize and store large quantities of lipid. However, under pathophysiological conditions, accumulation of fatty acids in nonadipose tissues causes cell dysfunction and cell death that lead to impaired organ function (43). This phenomenon, known as lipotoxicity, contributes to the pathogenesis of heart failure, renal dysfunction, steatohepatitis, and progressive pancreatic insufficiency (1,17,37,38).In vitro models in which the medium of cultured cells is supplemented with excess fatty acid have been used to probe metabolic and signaling pathways involved in the cellular response to lipid overload. In a time-and dose-dependent manner, longchain saturated fatty acids induce apoptosis in a variety of cell types (6,7,21,24,45), and this response is enhanced by high glucose (8). Although lipid overload in nonadipose cells is initially buffered by cytoprotective triglyceride stores (20, 23), when the limited capacity for neutral lipid storage in nonadipose cells is exceeded, excess saturated fatty acids initiate several cellular stress response pathways. Fatty acid-induced endoplasmic reticulum stress can result in reactive oxygen species (ROS) generation (40). Independently, oxidative stress is induced in a variety of cell types through activation of NADPH oxidase, mitochondrial dysfunction due to remodeling of organelle membranes, and excessive cycles of oxidative phosphorylation (16,31,41). Administration of antioxidants to cultured cells and animal models of lipotoxicity mitigate against lipotoxic cell death (4...

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Newly synthesized small nuclear RNAs appear transiently in the cytoplasm

Cited by 62 publications

References 46 publications

Regulation of alternative splicing by the core spliceosomal machinery

Regulation of alternative splicing by the core spliceosomal machinery

Distinct molecular signals for nuclear import of the nucleolar snRNA, U3.

SmD3 Regulates Intronic Noncoding RNA Biogenesis

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