Relationship between mRNA stability and intron presence

Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
Biochemical and Biophysical Research Communications (Impact Factor: 2.3). 04/2007; 354(1):203-8. DOI: 10.1016/j.bbrc.2006.12.184
Source: PubMed


Introns were found to enhance almost every steps of gene expression except increasing mRNA stability. By analyzing the genome-wide data of mRNA stability published by someone previously, we found that human intron-containing genes have more stable mRNAs than intronless genes, and the Arabidopsis thaliana genes with the most unstable mRNAs have fewer introns than other genes in the genome. After controlling for mRNA length, we found mRNA stability is still positively correlated with intron number in human intron-containing genes. But in yeast Saccharomyces cerevisiae, two different datasets on mRNA half-life gave conflicting results. The components of messenger ribonucleoprotein particles recruited during intron splicing may be retained in cytoplasmic mRNPs and act as signals of mRNA stability or simply insulators to avoid mRNA degradation.

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Available from: Deng-Ke Niu, Dec 01, 2014
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    • "In this model, introns are assumed to have deleterious effects, for example, delay in mature mRNA production. On the other hand, the birth of introns could result in beneficial effects such as removal of premature termination codons (PTC) (Catania and Lynch, 2008), enhancement of transcription efficiency or transcript stability (Wang et al., 2007; Rose et al., 2008; Catania and Lynch, 2013) and providing new protein products by alternative splicing (Barrett et al., 2012). "
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    ABSTRACT: Retrogenes are duplicated genes generated via retro-position, which were conventionally believed to contain no introns. However, emerging data showed that a significant number of retrogenes do have introns. Thus, these genes represent an attractive system to study how new genes evolve exon–intron structure. Comparison between par-ental genes and retrogenes revealed that retrogenes mainly evolve chimeric structures by fusing with local host genes or recruiting pre-existing intergenic sequences. Additionally, retrogenes could gain introns by inheriting introns of parental genes or by transforming parental exonic sequences. The functional necessity on intron gain in retrogenes remains largely elusive although limited data suggest that newborn introns play regulatory roles, enable exon shuffling and alternative splicing. Accumulation of population genomic data may help to understand which evolutionary force shapes the fixation of introns in both retrogenes and de novo originated genes given the same intron birth process acts on both type of new genes.
    Full-text · Article · Aug 2014
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    • "To explore the features of mRNAs with different change patterns, mRNA length, untranslated region (UTR) length, GC content as well as the number of introns were analyzed for type I-IV mRNAs. The connection between introns and mRNA stability has been uncovered recently[43-45]. Interestingly, the average intron number for type II genes was higher than for the other genes, but the percentage of intronless genes was lower in this population (Figure S6 in Additional file 1). "
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    ABSTRACT: mRNA degradation is a critical factor in determining mRNA abundance and enables rapid adjustment of gene expression in response to environmental stress. The involvement of processing bodies in stress response suggests a role for decapping-mediated mRNA degradation. However, little is known about the role of mRNA degradation under stressful environmental conditions. Here, we perform a global study of uncapped mRNAs, via parallel analysis of RNA ends (PARE), under cold stress in Brachypodium distachyon. Enrichment analysis indicates that degradation products detected by PARE are mainly generated by the decapping pathway. Endonucleolytic cleavages are detected, uncovering another way of modulating gene expression. PARE and RNA-seq analyses identify four types of mRNA decay patterns. Type II genes, for which light-harvesting processes are over-represented in gene ontology analyses, show unchanged transcript abundance and altered uncapped transcript abundance. Uncapping-mediated transcript stability of light harvesting-related genes changes significantly in response to cold stress, which may allow rapid adjustments in photosynthetic activity in response to cold stress. Transcript abundance and uncapped transcript abundance for type III genes changes in opposite directions in response to cold stress, indicating that uncapping-mediated mRNA degradation plays a role in regulating gene expression. To our knowledge, this is the first global analysis of mRNA degradation under environmental stress conditions in Brachypodium distachyon. We uncover specific degradation and endonucleolytic cleavage patterns under cold stress, which will deepen our understanding of mRNA degradation under stressful environmental conditions, as well as the cold stress response mechanism in monocots.
    Full-text · Article · Aug 2013 · Genome biology
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    • "Some introns can expand protein diversity through alternative splicing (Kalsotra and Cooper 2011). Some introns or elements contained in introns regulate gene expression (Le Hir et al. 2003; Wang et al. 2007; Rose et al. 2008; Parenteau et al. 2011; Rearick et al. 2011). The selective pressure on the loss or gain of these introns is obvious. "
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    ABSTRACT: Despite the prevalence of intron losses during eukaryotic evolution, the selective forces acting on them have not been extensively explored. Arabidopsis thaliana lost half of its genome and experienced an elevated rate of intron loss after diverging from Arabidopsis lyrata. The selective force for genome reduction was suggested to have driven the intron loss. However, the evolutionary mechanism of genome reduction is still a matter of debate. In this study, we found that intron-lost genes have high synonymous substitution rates. Assuming that differences in mutability among different introns are conserved among closely related species, we used the nucleotide substitution rate between orthologous introns in other species as the proxy of the mutation rate of Arabidopsis introns, either lost or extant. The lost introns were found to have higher mutation rates than extant introns. At the genome-wide level, A. thaliana has a higher mutation rate than A. lyrata, which correlates with the higher rate of intron loss and rapid genome reduction of A. thaliana. Our results indicate that selection to minimize mutational hazards might be the selective force for intron loss, and possibly also for genome reduction, in the evolution of A. thaliana. Small genome size and lower genome-wide intron density were widely reported to be correlated with phenotypic features, such as high metabolic rates and rapid growth. We argue that the mutational-hazard hypothesis is compatible with these correlations, by suggesting that selection for rapid growth might indirectly increase mutational hazards.
    Full-text · Article · Mar 2013 · Genome Biology and Evolution
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