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Effects of genetic variations on microRNA: target interactions.

Liu C, Rennie WA, Carmack CS, Kanoria S, Cheng J, Lu J, Ding Y - Nucleic Acids Res. (2014)

Bottom Line: We perform a transcriptome-scale analysis of genetic variants and miRNA:target interactions identified by CLASH.Furthermore, an overwhelming majority of genetic variants within or near miRNA binding sites can alter not only the potential of miRNA:target hybridization but also the structural accessibility of the binding sites and flanking regions.Our data will be valuable for discovering new associations among miRNAs, genetic variations and human diseases.

View Article: PubMed Central - PubMed

Affiliation: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA.

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The histograms of effect measures for common (MAF ≥1%) and rare (MAF <1%) variants in miRNA binding sites (the horizontal axis intervals (a,b], [a,b), (a,b), [a,b] are defined by a<x≤b, a≤x<b, a<x<b, a≤x≤b, respectively, where x is the value of the feature). (A) ΔΔGhybrid; (B) ΔΔGtotal; (C) Δsite_access; (D) Δupstream_access; (E) Δdownstream_access.
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Figure 2: The histograms of effect measures for common (MAF ≥1%) and rare (MAF <1%) variants in miRNA binding sites (the horizontal axis intervals (a,b], [a,b), (a,b), [a,b] are defined by a<x≤b, a≤x<b, a<x<b, a≤x≤b, respectively, where x is the value of the feature). (A) ΔΔGhybrid; (B) ΔΔGtotal; (C) Δsite_access; (D) Δupstream_access; (E) Δdownstream_access.

Mentions: The histograms of ΔΔGhybrid for common and rare variants in miRNA binding sites are shown in Figure 2A. For common variants, 44.3% decrease and 10.5% increase the hybrid stability by at least 1 kcal/mol. For rare variants, 49% decrease and 8.5% increase the hybrid stability by at least 1 kcal/mol. By varying the change in hybrid stability, we also present cumulative distributions of absolute value of ΔΔGhybrid for common and rare variants in miRNA binding sites (Supplementary Figure S2A). These indicate that a majority of variants in miRNA binding sites can alter hybrid stability. In particular, both common and rare variants tend to weaken the miRNA:target hybrid stability (P-values <2.3e−45).


Effects of genetic variations on microRNA: target interactions.

Liu C, Rennie WA, Carmack CS, Kanoria S, Cheng J, Lu J, Ding Y - Nucleic Acids Res. (2014)

The histograms of effect measures for common (MAF ≥1%) and rare (MAF <1%) variants in miRNA binding sites (the horizontal axis intervals (a,b], [a,b), (a,b), [a,b] are defined by a<x≤b, a≤x<b, a<x<b, a≤x≤b, respectively, where x is the value of the feature). (A) ΔΔGhybrid; (B) ΔΔGtotal; (C) Δsite_access; (D) Δupstream_access; (E) Δdownstream_access.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150780&req=5

Figure 2: The histograms of effect measures for common (MAF ≥1%) and rare (MAF <1%) variants in miRNA binding sites (the horizontal axis intervals (a,b], [a,b), (a,b), [a,b] are defined by a<x≤b, a≤x<b, a<x<b, a≤x≤b, respectively, where x is the value of the feature). (A) ΔΔGhybrid; (B) ΔΔGtotal; (C) Δsite_access; (D) Δupstream_access; (E) Δdownstream_access.
Mentions: The histograms of ΔΔGhybrid for common and rare variants in miRNA binding sites are shown in Figure 2A. For common variants, 44.3% decrease and 10.5% increase the hybrid stability by at least 1 kcal/mol. For rare variants, 49% decrease and 8.5% increase the hybrid stability by at least 1 kcal/mol. By varying the change in hybrid stability, we also present cumulative distributions of absolute value of ΔΔGhybrid for common and rare variants in miRNA binding sites (Supplementary Figure S2A). These indicate that a majority of variants in miRNA binding sites can alter hybrid stability. In particular, both common and rare variants tend to weaken the miRNA:target hybrid stability (P-values <2.3e−45).

Bottom Line: We perform a transcriptome-scale analysis of genetic variants and miRNA:target interactions identified by CLASH.Furthermore, an overwhelming majority of genetic variants within or near miRNA binding sites can alter not only the potential of miRNA:target hybridization but also the structural accessibility of the binding sites and flanking regions.Our data will be valuable for discovering new associations among miRNAs, genetic variations and human diseases.

View Article: PubMed Central - PubMed

Affiliation: Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA.

Show MeSH
Related in: MedlinePlus