mRNA destabilization triggered by premature translational termination depends on three mRNA sequence elements and at least one trans-acting factor

Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01655.
Genes & Development (Impact Factor: 10.8). 10/1993; 7(9):1737-54. DOI: 10.1101/gad.7.9.1737
Source: PubMed

ABSTRACT Nonsense mutations in a gene can accelerate the decay rate of the mRNA transcribed from that gene, a phenomenon we describe as nonsense-mediated mRNA decay. Using amber (UAG) mutants of the yeast PGK1 gene as a model system, we find that nonsense-mediated mRNA decay is position dependent, that is, nonsense mutations within the initial two-thirds of the PGK1-coding region accelerate the decay rate of the PGK1 transcript < or = 12-fold, whereas nonsense mutations within the carboxy-terminal third of the coding region have no effect on mRNA decay. Moreover, we find that this position effect reflects (1) a requirement for sequences 3' to the nonsense mutation that may be necessary for translational reinitiation or pausing, and (2) the presence of an additional sequence that, when translated, inactivates the nonsense-mediated mRNA decay pathway. This stabilizing element is positioned within the coding region such that it constitutes the boundary between nonsense mutations that do or do not affect mRNA decay. Rapid decay of PGK1 nonsense-containing transcripts is also dependent on the status of the UPF1 gene. Regardless of the position of an amber codon in the PGK1 gene, deletion of the UPF1 gene restores wild-type decay rates to nonsense-containing PGK1 transcripts.

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Available from: Allan Jacobson, Mar 10, 2014
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    • "Reads that mapped within 100 nucleotides upstream of a gene’s start codon and 100 nucleotides downstream of its stop codon were attributed to that gene (see Additional file 2 for allele-specific expression counts for all alleles). Candidates for NMD analysis were selected based on the following criteria: (1) to avoid potential gene-start annotation errors at the 5′ end, the length of the shorter allele must be at least 20% of the longer allele; (2) to ensure that the downstream sequence elements that help to elicit NMD [41] are present, the length of the shorter allele must be less than 80% of the length of the longer allele; (3) to ensure that both alleles are expressed, each must have at least five allele-specific reads in the RNA-seq dataset; (4) to exclude dubious ORFs from assembly 21, the reading frame must start with ATG or a near-cognate start codon (for example, AGG, ACG, and so on). "
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    ABSTRACT: Candida albicans is a ubiquitous opportunistic fungal pathogen that afflicts immunocompromised human hosts. With rare and transient exceptions the yeast is diploid, yet despite its clinical relevance the respective sequences of its two homologous chromosomes have not been completely resolved. We construct a phased diploid genome assembly by deep sequencing a standard laboratory wild-type strain and a panel of strains homozygous for particular chromosomes. The assembly has 700-fold coverage on average, allowing extensive revision and expansion of the number of known SNPs and indels. This phased genome significantly enhances the sensitivity and specificity of allele-specific expression measurements by enabling pooling and cross-validation of signal across multiple polymorphic sites. Additionally, the diploid assembly reveals pervasive and unexpected patterns in allelic differences between homologous chromosomes. Firstly, we see striking clustering of indels, concentrated primarily in the repeat sequences in promoters. Secondly, both indels and their repeat-sequence substrate are enriched near replication origins. Finally, we reveal an intimate link between repeat sequences and indels, which argues that repeat length is under selective pressure for most eukaryotes. This connection is described by a concise one-parameter model that explains repeat-sequence abundance in C. albicans as a function of the indel rate, and provides a general framework to interpret repeat abundance in species ranging from bacteria to humans. The phased genome assembly and insights into repeat plasticity will be valuable for better understanding allele-specific phenomena and genome evolution.
    Genome biology 09/2013; 14(9):R97. DOI:10.1186/gb-2013-14-9-r97 · 10.81 Impact Factor
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    • "Accumulated evidences have shown that all the PTC mRNAs are targeted for degradation in the cytoplasm by a well-characterized specialized mRNA decay pathway called nonsense-mediated decay pathway (NMD) (table 2; see below) (Leeds et al. 1991; Decker and Parker 1993; He et al. 1993; Cui et al. 1999; He and Jacobson 1995; Czaplinski et al. 1998; Hilleren and Parker 1999). Early work demonstrated that relative location of PTC in the transcript body has a very important consequence on the extent of destabilization of PTC-containing mRNA such that a PTC that is located more towards the 5′-proximity of the transcript body is more prone to accelerated decay than the one that harbours the PTC towards its 3′-proximity (Peltz et al. 1993). To explain this position effect the existence of a downstream element (DSE) was proposed (Ruiz-Echevarria and Peltz 1996). "
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    Journal of Biosciences 09/2013; 38(3):615-40. DOI:10.1007/s12038-013-9337-4 · 2.06 Impact Factor
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    • "In this work, we will refer to this allele as gy1-a (NCBI accession KC460320). The reduction in gy1-a transcript abundance is most likely due to the phenomenon termed ''nonsense-mediated mRNA decay'' (Peltz et al. 1993), which has been shown to be a conserved mRNA surveillance pathway in plants (recently reviewed in Chang et al. 2007). "
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