Intron mutations that affect the splicing efficiency of the CYH2 gene of Saccharomyces cerevisiae

Swida, Ulrike; Thüroff, Eduardo; Käufer, Norbert F.

doi:10.1007/bf00333970

Cited by 10 publications

(7 citation statements)

References 19 publications

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“…(28) tations promote mRNA destabilization, whereas 3'-proximal nonsense mutations have little or no effect on mRNA decay rates. This is exemplified by the decay rates of mutant (20,21). Based on this criterion, the CYH2 and RPSIB pre-mRNAs are inefficiently spliced (21)(22)(23) 3.…”

Section: Methodsmentioning

confidence: 99%

“…This is exemplified by the decay rates of mutant (20,21). Based on this criterion, the CYH2 and RPSIB pre-mRNAs are inefficiently spliced (21)(22)(23) 3. RNA blotting analysis ofthe polysomal distribution ofthe MER2 pre-mRNA.…”

Section: Methodsmentioning

confidence: 99%

“…4; RPSIA pre-mRNA also contains an early nonsense codon (Table 2)] or the pre-mRNAs encoded by the ACTI and CRY) genes (data not shown). Unlike the transcripts of the CYH2, RPSIB, and MER2 genes, these three pre-mRNAs are all efficiently spliced (20)(21)(22)(23)(24)29), suggesting that the "escape" of pre-mRNAs from the spliceosome assembly/nuclear retention system into the cytoplasm may vary inversely as a function of splicing efficiency.…”

Section: Methodsmentioning

confidence: 99%

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Stabilization and ribosome association of unspliced pre-mRNAs in a yeast upf1- mutant.

Peltz

Donahue

et al. 1993

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

244

229

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Nonsense-mediated mRNA decay, the accelerated turnover of mRNAs transcribed from genes containing early nonsense mutations, is dependent on the product of the UPFI gene in yeast. Mutations that inactivate UPFI lead to the selective stabilization of mRNAs containing early nonsense mutations but have no effect on the half-lives of almost all other mRNAs. Since the transcripts ofnonsense alleles are not typical cellular constituents, we sought to identify those RNAs that comprise normal substrates of the nonsense-mediated mRNA decay pathway. Many yeast pre-mRNAs contain early in-frame nonsense codons and we considered it possible that a role of this pathway is to accelerate the degradation ofpre-mRNAs present in the cytoplasm. Consistent with this hypothesis, we find that, in a strain lacking UPFI function, the CYH2, RPSIB, and MER2 pre-mRNAs are stabilized 2-to 5-fold and are associated with ribosomes. We conclude that a major source of early nonsense codon-containing cytoplasmic transcripts in yeast is pre-mRNAs and that the UPFI protein may be part ofa cellular system that ensures that potentially deleterious nonsense fragments of polypeptides do not accumulate.In eukaryotes and prokaryotes nonsense mutations in a gene can enhance the decay rate of the mRNA transcribed from that gene (1-12), a phenomenon we describe as nonsensemediated mRNA decay (1). Trans-acting factors that are essential for nonsense-mediated mRNA decay have been identified in experiments that characterized a class of nonsense suppressors in the yeast Saccharomyces cerevisiae. Mutants in the UPFI gene, originally isolated on the basis of their ability to enhance the suppression of a frameshift mutation that led to premature translational termination (13), selectively stabilize mRNAs containing early nonsense mutations without affecting the decay rates of most other mRNAs (ref. 2; S.W.P., A. H. Brown, and A.J., unpublished data).The existence of trans-acting factors that promote rapid decay of nonsense-containing mRNAs raises the question of whether such mRNAs are the sole substrates of these factors-i.e., whether the cell has an apparatus to specifically degrade nonsense-containing mRNAs. It seemed unlikely that the normal function ofthe UPFF gene was anticipatoryi.e., solely involved in the degradation of mRNAs derived from nonsense alleles-so we sought to determine whether these factors have additional substrates. Since introns generally lack contiguous open reading frames, and yeast introns are almost always at the 5' ends of their genes (14), we considered it possible that the UPFI gene product (Upflp) might also be involved in controlling the abundance of yeast pre-mRNAs. If this supposition were correct, the presence of unspliced introns within a pre-mRNA would lead to premature translational termination and accelerated RNA decay in The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate ...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Stabilization and ribosome association of unspliced pre-mRNAs in a yeast upf1- mutant.

Peltz

Donahue

et al. 1993

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

244

229

View full text Add to dashboard Cite

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“…The exons (EX1 and EX2 in Fig. 1A) and intron were based on the relatively inefficiently spliced yeast RPL28/CYH2 gene (Swida et al 1986) to increase the chances that the unspliced transcript levels were detectable. More details, including the cloning strategy and the DNA sequence can be found in the Supplemental Material.…”

Section: Design and Validation Of The Eukaryotic Gene Expression Repomentioning

confidence: 99%

Rapid identification of mRNA processing defects with a novel single-cell yeast reporter

Sorenson

Stevens

2014

RNA

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It has become increasingly evident that gene expression processes in eukaryotes involve communication and coordination between many complex, independent macromolecular machines. To query these processes and to explore the potential relationships between them in the budding yeast Saccharomyces cerevisiae, we designed a versatile reporter using multicolor high-throughput flow cytometry. Due to its design, this single reporter exhibits a distinctive signature for many defects in gene expression including transcription, histone modification, pre-mRNA splicing, mRNA export, nonsense-mediated decay, and mRNA degradation. Analysis of the reporter in 4967 nonessential yeast genes revealed striking phenotypic overlaps between chromatin remodeling, histone modification, and pre-mRNA splicing. Additionally, we developed a copper-inducible reporter, with which we demonstrate that 5-fluorouracil mimics the mRNA decay phenotype of cells lacking the 3 ′ -5 ′ exonuclease Rrp6p. Our reporter is capable of performing high-throughput, rapid, and large-scale screens to identify and characterize genetic and chemical perturbations of the major eukaryotic gene expression processes.

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“…However, no alternative splice sites were detected, suggesting that this mutation did not form alternative splicing isoform. Several reported documents had presented that intron mutations also affected expression and regulation of genes (Swida et al 1986;Zhao et al, 2004;Lai et al, 2009), but this mutation could not affected the expression or regulation of the bovine Six3 gene using real-time quantitative polymerase chain reaction detecting system with different genotypic p=0.04* p=0.04* Note: Means of body weight and average daily gain with different superscript letters (e.g. "a" and "b") show significant difference (LSD test, *p < 0.05).…”

Section: Resultsmentioning

confidence: 99%

Novel genetic variants of sine oculis homeobox homolog 3 gene are associated with body weight and average daily gain in Bos taurus

et al. 2011

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Sine oculis homeobox homolog 3 (Six3) gene is responsible for normal mammalian pituitary development, and its genetic variations or deficiency will cause hypopituitarism, suggesting that this gene is a potential candidate gene for studying association with growth traits in animals. Herein, genetic variants within bovine Six3 gene was screened in 1031 individuals from four Chinese indigenous cattle breeds. Two novel polymorphisms (NC_007309:g.2515G>A and NC_007309:g.2607T>C) locating at positions nt1707 and nt1799 of intron 1 in bovine Six3 gene, were found, and could be genotyped by TaqI ACRS PCR-RFLP and Alw26I PCR-RFLP, respectively. The frequencies of allele "A" of TaqI locus varied from 0.004 to 0.309, as well as the frequencies of allele "C" of Alw26I locus waved from 0.025 to 0.340. Association analysis revealed no significant association of TaqI locus with growth traits in Nanyang breed. However, significant relationships between Alw26I locus and body weight (BW) and average daily gain (ADG) in Nanyang breed was found (p<0.05). The individuals with genotype TC had greater body weight and average daily gain than those with genotype TT at 18 months old. Furthermore, based on combinated genotypes from these two loci, diplotypes was found to be associated with growth traits (p<0.05).The individuals with dihaplotype GG-TC had greater X.-Y. Lan and Y.-T Huai contributed equally to this work. body weight and average daily gain at 18 month-old than those of other dihaplotypes. Therefore, the TaqI and Alw26I genetic variants of bovine Six3 gene were recommended as DNA markers related to growth traits through marker-assisted selection for genetics and breeding in cattle.

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Intron mutations that affect the splicing efficiency of the CYH2 gene of Saccharomyces cerevisiae

Cited by 10 publications

References 19 publications

Stabilization and ribosome association of unspliced pre-mRNAs in a yeast upf1- mutant.

Stabilization and ribosome association of unspliced pre-mRNAs in a yeast upf1- mutant.

Rapid identification of mRNA processing defects with a novel single-cell yeast reporter

Novel genetic variants of sine oculis homeobox homolog 3 gene are associated with body weight and average daily gain in Bos taurus

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