Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

Department of Chemistry, Center for Neurosensory Disorders, School of Dentistry, University of North Carolina, Chapel Hill, NC 27599, USA.
Nucleic Acids Research (Impact Factor: 9.11). 04/2011; 39(14):6201-12. DOI: 10.1093/nar/gkr165
Source: PubMed


Catechol-O-methyltransferase (COMT) is a major enzyme controlling catecholamine levels that plays a central role in cognition, affective
mood and pain perception. There are three common COMT haplotypes in the human population reported to have functional effects, divergent in two synonymous and one nonsynonymous
position. We demonstrate that one of the haplotypes, carrying the non-synonymous variation known to code for a less stable
protein, exhibits increased protein expression in vitro. This increased protein expression, which would compensate for lower protein stability, is solely produced by a synonymous
variation (C166T) situated within the haplotype and located in the 5′ region of the RNA transcript. Based on mRNA secondary structure predictions,
we suggest that structural destabilization near the start codon caused by the T allele could be related to the observed increase
in COMT expression. Our folding simulations of the tertiary mRNA structures demonstrate that destabilization by the T allele
lowers the folding transition barrier, thus decreasing the probability of occupying its native state. These data suggest a
novel structural mechanism whereby functional synonymous variations near the translation initiation codon affect the translation
efficiency via entropy-driven changes in mRNA dynamics and present another example of stable compensatory genetic variations
in the human population.

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    • "Functional importance of alternative protein terminal regions is supported by our transcriptome-scale analysis demonstrating that these regions are subject to purifying selection. Our finding of the elevated RNSP in the 5′ grey areas is in good agreement with the reported selection in favour of mRNA folding pattern in the vicinity of translation start codons (47,50,55,74,75) and elevated occupancy of the first protein-coding exons with TF recognition sites across the human exome (56). Thus, nucleotide-level constraints appear to be a major driver of evolution in the upstream translated gene sequences (55,76). "
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    ABSTRACT: Alternative splicing (AS), alternative transcription initiation (ATI) and alternative transcription termination (ATT) create the extraordinary complexity of transcriptomes and make key contributions to the structural and functional diversity of mammalian proteomes. Analysis of mammalian genomic and transcriptomic data shows that contrary to the traditional view, the joint contribution of ATI and ATT to the transcriptome and proteome diversity is quantitatively greater than the contribution of AS. Although the mean numbers of protein-coding constitutive and alternative nucleotides in gene loci are nearly identical, their distribution along the transcripts is highly non-uniform. On average, coding exons in the variable 5′ and 3′ transcript ends that are created by ATI and ATT contain approximately four times more alternative nucleotides than core protein-coding regions that diversify exclusively via AS. Short upstream exons that encompass alternative 5′-untranslated regions and N-termini of proteins evolve under strong nucleotide-level selection whereas in 3′-terminal exons that encode protein C-termini, protein-level selection is significantly stronger. The groups of genes that are subject to ATI and ATT show major differences in biological roles, expression and selection patterns.
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    • "The application of complex trait analysis to human pain genetics research has facilitated the discovery of genes that underlie variability in pain sensitivity and analgesic response (Chou et al. 2006; Compton et al. 2003; Diatchenko et al. 2005, 2006; Fillingim et al. 2005; Indo et al. 1996; Janicki et al. 2006; Klepstad et al. 2004; Nackley et al. 2006; Poulsen et al. 1996; Rakvag et al. 2005; Reyes-Gibby et al. 2007; Sindrup et al. 1990; Tsao et al. 2011; Zubieta et al. 2003). However, human complex trait analyses typically require tens of thousands of individuals to achieve adequate statistical power, in part due to the inherent difficulty of controlling gene–environment interactions in human cohorts (Flint and Eskin 2012). "
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    ABSTRACT: Mouse genetics is a powerful approach for discovering genes and other genome features influencing human pain sensitivity. Genetic mapping studies have historically been limited by low mapping resolution of conventional mouse crosses, resulting in pain-related quantitative trait loci (QTL) spanning several megabases and containing hundreds of candidate genes. The recently developed Diversity Outbred (DO) population is derived from the same eight inbred founder strains as the Collaborative Cross, including three wild-derived strains. DO mice offer increased genetic heterozygosity and allelic diversity compared to crosses involving standard mouse strains. The high rate of recombinatorial precision afforded by DO mice makes them an ideal resource for high-resolution genetic mapping, allowing the circumvention of costly fine-mapping studies. We utilized a cohort of ~300 DO mice to map a 3.8 Mbp QTL on chromosome 8 associated with acute thermal pain sensitivity, which we have tentatively named Tpnr6. We used haplotype block partitioning to narrow Tpnr6 to a width of ~230 Kbp, reducing the number of putative candidate genes from 44 to 3. The plausibility of each candidate gene's role in pain response was assessed using an integrative bioinformatics approach, combining data related to protein domain, biological annotation, gene expression pattern, and protein functional interaction. Our results reveal a novel, putative role for the protein-coding gene, Hydin, in thermal pain response, possibly through the gene's role in ciliary motility in the choroid plexus-cerebrospinal fluid system of the brain. Real-time quantitative-PCR analysis showed no expression differences in Hydin transcript levels between pain-sensitive and pain-resistant mice, suggesting that Hydin may influence hot-plate behavior through other biological mechanisms.
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    • "SNPs in the prothrombin 3′UTR affect post-transcriptional processing and 3′-cleavage/polyadenylation and SNPs in SNCA affect polyadenylation [28], [29]; both of which affect expression. Variants in the 5′UTR of the COMT gene are associated with structural destabilization of the COMT mRNA through differential tertiary structures [30]. Thus, it is possible that the SNPs evaluated in this study which correlated with differential luciferase expression may affect mRNA stability through polyadenylation or other differences resulting in changes to mRNA stability which can be addressed in future studies. "
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    ABSTRACT: Variants in regulatory regions are predicted to play an important role in disease susceptibility of common diseases. Polymorphisms mapping to microRNA (miRNA) binding sites have been shown to disrupt the ability of miRNAs to target genes resulting in differential mRNA and protein expression. () was identified as a locus conferring susceptibility to chemically-induced skin cancer in NIH/Ola by SPRET/Outbred F1 backcrosses. To determine if polymorphisms between the strains which mapped to putative miRNA binding sites in the 3' untranslated region (3'UTR) of genes at influenced expression, we conducted a systematic evaluation of 3'UTRs of candidate genes across this locus. Nine genes had polymorphisms in their 3'UTRs which fit the linkage data and eight of these contained polymorphisms suspected to interfere with or introduce miRNA binding. 3'UTRs of six genes, , , and differentially affected luciferase expression, but did not appear to be differentially regulated by the evaluated miRNAs predicted to bind to only one of the two isoforms. 3'UTRs from four additional genes chosen from the locus that fit less stringent criteria were evaluated. and showed differences and contained polymorphisms predicted to disrupt or create miRNA binding sites but showed no difference in regulation by the miRNAs tested. In summary, multiple 3'UTRs with putative functional variants between susceptible and resistant strains of mice influenced differential expression independent of predicted miRNA binding.
    Preview · Article · Mar 2013 · PLoS ONE
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