Mechanisms mediated by 3′-UTR SNPs affecting miRNA targeting.

<p><b>A:</b> Regular binding of the RISC to the target mRNA. <b>B:</b> Binding of the RISC and, thus, miRNA-mediated silencing is inhibited by a change in RNA secondary structure. <b>C:</b> A mutation within the MRE seed site disrupts the ability of a certain miRNA to target a transcript. Here, the opposite effect also applies, i.e. a new MRE seed site is formed by a polymorphism which enables targeting by a miRNA usually not controlling the respective transcript. <b>D:</b> Altered splicing by acceptor or donor splice site gain. The existing splice variants (I and II, grayed) are extended by mutationally introduced additional splice variants: (III) A present acceptor site (A₁) is substituted by a new acceptor site (A<i>_mut</i>), and (IV) a naturally occurring donor site (D₂) is replaced by a new donor site (D<i>_mut</i>). Both effects may lead to a considerable loss of exon sequence (displayed in red) and, thus, RISC binding sites. <b>E:</b> The percentages of classified SNPs mediating the single mechanisms. The greatest amount of functionally annotated 3′-UTR SNPs directly affect MRE sequences, followed by SNPs changing the RNA secondary structure and SNPs with an predicted effect on 3′-UTR splicing.</p

SNPs affecting functional elements with <i>cis</i>-regulatory effects on miRNA regulation.

<p>The first column gives the rs-number of the SNPs, in the second column the HGNC symbol of the affected genes are listed and the third column describes the functional mechanisms which could be assigned to the SNPs. The last column contains all traits associated with the respective SNP.</p

Statistical analysis of 3′-UTR enrichment values and determination of the folding correlation coefficient threshold.

<p><b>A:</b> SNP enrichment in the 3′-UTR in dependency of different LD thresholds. Displayed are the ORs and confidence intervals for five cut-offs. Accumulative 3′-UTR SNP sets were calculated. The fitted distribution (dashed line) points out the stabilization of the OR around a threshold of 0.8. <b>B:</b> SNP enrichment in the 3′-UTR in dependency of the minor allele frequency. Displayed are the ORs and confidence intervals for the 5 different MAF bins. SNP counts were compared within the respective bins. <b>C:</b> Probability distribution of correlation coefficients (<i>p</i>) between wild-type and mutated structures of RBP-binding regions. Below a cut-off for the correlation coefficient of 0.55 (displayed in gray) the probability to observe a change of RNA secondary structure of this scale by chance amounts to less than 5%.</p

Impact of the SNP <i>rs10923</i> on miRNA-mediated repression of <i>SMC4</i>.

<p>Shown is the mRNA:miRNA duplex for the reference allele of <i>rs10923</i> (lower part). The minor allele of the SNP (position adumbrated by the light red box) disrupts the seed complementary region. In the upper part of the figure, the expression pattern of <i>SMC4</i> in lymphoblastoid cells is illustrated. The minor G allele of the polymorphism is significantly () linked to an increased abundance of <i>SMC4</i> transcript. For the illustration of expression values Genevar output was adapted <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036694#pone.0036694-Yang3" target="_blank">[89]</a>.</p

Impact model of mutated SMC4 in primary biliary cirrhosis.

<p>Inflammation follows the autoimmune response leading to the activation of the <i>MAPK</i>-pathway via signal molecules as e.g. <i>TNF-alpha</i>. Transcription factors activated as downstream effect of <i>MAPK</i> activation lead to over-expression of DNA repair genes. The in PBC over-expressed <i>hsa-mir-299-5p</i> is hypothesized to target <i>SMC4</i> at the seed complementary region where <i>rs10923</i> is located. With the major allele, <i>SMC4</i> is silenced, whereas the mutated <i>SMC4</i>-G cannot be bound by <i>hsa-mir-299-5p</i> and therefore is translated without interference. This results in the more frequent association of the <i>Condensin I-PARP1-XRCC1</i> complex contributing to disturbed DNA repair in cirrhosis tissue.</p

Ten Rare, Non-synonymous Variants Shared by Individuals IV:11 and IV:18 of Family PARK_0005.

<p>The rare variants common to the two affected individuals were genotyped in 975 cases and 1014 controls. Penetrance with regard to the PD phenotype was assessed in 6 family members belonging to the same generation as the affected individuals. EA = European American.</p

Assessment of cell viability and subcellular protein localization in fibroblasts.

<p>(A) The presence of <i>PLXNA4</i> p.Ser657Asn do not affect cell viability as assay by live-dead staining and FACS. (B) Immunohistochemistry shows similar subcellular localization of <i>PLXNA4</i> (anti-PLXNA4, Sigma, 1∶500) in fibroblasts with and without the p.Ser657Asn amino acid substitution (scale bar = 50 µm).</p

Pedigree and Linkage Analysis.

<p>(A) Pedigree of family used for exome sequencing. Open symbols indicate unaffected family members, affected individuals are denoted by closed symbols. An arrow denotes the individuals whose exomes were sequenced. Sex was obscured and birth order was altered to protect privacy. A diagonal line indicates a deceased individual. (B) 25 genomic regions on 12 chromosomes with logarithm of the odds (LOD) score≥0.5 were identified by linkage analysis. Green boxes represent genomic regions with LOD≥0.5, yellow stars represent the location of the four candidate genes remaining after frequency assessment (<i>GOLGA4</i>-chr3, <i>PLXNA4</i>-chr7, <i>OGN</i>-chr9, <i>CPNE1</i>-chr20). <i>PLXNA4</i> on chromosome 7 represents the only of the four genes overlapping a genomic region with LOD≥0.5.</p

Qualitative multifactorial interaction network of <i>PLXNA4</i> and genetic factors with known and hypothetical relevance to PD.

<p>Edges obtained from CIDeR are highlighted in blue, PD-specific pathways from KEGG are given in green, red edges denote annotations from OMIM and edges extracted from literature, protein-protein interaction databases or high-confidence predictions are colored black. Undirected protein-protein interactions hold circular ends, directed molecular relations are marked by arcs, whereas general regulations have arrows with no filling, activations have filled arrows and inhibitions have blunted end. Dashed lines indicate indirect effects.</p