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Signs of Selection in Synonymous Sites of the Mitochondrial Cytochrome b Gene of Baikal Oilfish (Comephoridae) by mRNA Secondary Structure Alterations.

Teterina VI, Mamontov AM, Sukhanova LV, Kirilchik SV - Biomed Res Int (2015)

Bottom Line: Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations.Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii).Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure.

View Article: PubMed Central - PubMed

Affiliation: Limnological Institute, Siberian Branch, Russian Academy of Sciences, P.O. Box 278, Irkutsk 664033, Russia.

ABSTRACT
Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations. Most studies focused on prokaryote genomes and the nuclear genomes of eukaryotes while little is known about the regulation of mitochondrial DNA (mtDNA) gene expression. This paper reveals signs of selection in synonymous sites of the mitochondrial cytochrome b gene (Cytb) of Baikal oilfish or golomyankas (Comephoridae) directed towards altering the secondary structure of the mRNA and probably altering the character of mtDNA gene expression. Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii). Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure.

No MeSH data available.


Synonymous mutations in Cytb mapped according to their directions from the central to peripheral haplotypes. Circle sizes and numbers indicate the total number of the mutations as percentages.
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fig2: Synonymous mutations in Cytb mapped according to their directions from the central to peripheral haplotypes. Circle sizes and numbers indicate the total number of the mutations as percentages.

Mentions: TCSB revealed some differences among the studied groups (Figure 2). The direction of mutations within BGa showed strong deviation toward the W→S type. Within BGp, the predominance of W→S mutations was much weaker. The SG group demonstrated the opposite pattern: the direction to W was prevalent. Fisher's exact test failed to show any significant differences between BGa and BGp but we found statistically significant differences between BGp and SG and very statistically significant differences between BGa and SG (two-tailed P values of 0.3073, 0.0147, and 0.0006, resp.). Sliding Window Analysis (SWA) of Cytb showed that, within BGa, W→S mutations dominated over S→W for almost the entire Cytb gene, with two maxima located at ~400 and 600 bp (Figure 3). Thus, the dominance of W→S mutations in this group did not appear to be site- or region-specific. Within SG, the opposite picture was observed; with a few exceptions, S→W mutations dominated. No clear patterns were found within BGp.


Signs of Selection in Synonymous Sites of the Mitochondrial Cytochrome b Gene of Baikal Oilfish (Comephoridae) by mRNA Secondary Structure Alterations.

Teterina VI, Mamontov AM, Sukhanova LV, Kirilchik SV - Biomed Res Int (2015)

Synonymous mutations in Cytb mapped according to their directions from the central to peripheral haplotypes. Circle sizes and numbers indicate the total number of the mutations as percentages.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4465659&req=5

fig2: Synonymous mutations in Cytb mapped according to their directions from the central to peripheral haplotypes. Circle sizes and numbers indicate the total number of the mutations as percentages.
Mentions: TCSB revealed some differences among the studied groups (Figure 2). The direction of mutations within BGa showed strong deviation toward the W→S type. Within BGp, the predominance of W→S mutations was much weaker. The SG group demonstrated the opposite pattern: the direction to W was prevalent. Fisher's exact test failed to show any significant differences between BGa and BGp but we found statistically significant differences between BGp and SG and very statistically significant differences between BGa and SG (two-tailed P values of 0.3073, 0.0147, and 0.0006, resp.). Sliding Window Analysis (SWA) of Cytb showed that, within BGa, W→S mutations dominated over S→W for almost the entire Cytb gene, with two maxima located at ~400 and 600 bp (Figure 3). Thus, the dominance of W→S mutations in this group did not appear to be site- or region-specific. Within SG, the opposite picture was observed; with a few exceptions, S→W mutations dominated. No clear patterns were found within BGp.

Bottom Line: Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations.Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii).Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure.

View Article: PubMed Central - PubMed

Affiliation: Limnological Institute, Siberian Branch, Russian Academy of Sciences, P.O. Box 278, Irkutsk 664033, Russia.

ABSTRACT
Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations. Most studies focused on prokaryote genomes and the nuclear genomes of eukaryotes while little is known about the regulation of mitochondrial DNA (mtDNA) gene expression. This paper reveals signs of selection in synonymous sites of the mitochondrial cytochrome b gene (Cytb) of Baikal oilfish or golomyankas (Comephoridae) directed towards altering the secondary structure of the mRNA and probably altering the character of mtDNA gene expression. Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii). Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure.

No MeSH data available.