The case of the unreliable SNP: recurrent back-mutation of Y-chromosomal marker P25 through gene conversion.

The Y-chromosomal binary marker P25 is a paralogous sequence variant, rather than a SNP: three copies of the P25 sequence lie within the giant palindromic repeats on Yq, and one copy has undergone a C to A transversion to define haplogroup R1b (designated C/C/A). Since gene conversion is known to be active in the palindromic repeats, we reasoned that P25 might be liable to back mutation by gene conversion, yielding the ancestral state C/C/C. Through analysis of a set of binary markers in Y chromosomes in two large samples from Great Britain and the Iberian Peninsula we show that such conversion events have occurred at least twice, and provide preliminary evidence that the reverse conversion event (yielding C/A/A) has also occurred. Because of its inherent instability, we suggest that P25 be used with caution in forensic studies, and perhaps replaced with the more reliable binary marker M269

Val372 shows reduced zinc uptake transport.

<p>(A) Basal zinc content in HeLa cells transiently transfected with different ZIP4 isoforms plus empty CFP vector. Transfected cells were compared with surrounding non-transfected cells. The two isoforms expressing Val372 show significantly reduced intracellular zinc. (B) Zinc uptake upon perfusion with 200 µM ZnSO4 external solution. Graph bars show the maximum transport (Tmax) and the time to reach half of Tmax (t1/2) for the different isoforms that reach the plasma membrane, following the color code on the left. Data are presented as mean ± SEM of 3 different transfections and more than 25 cells per condition. Significance was calculated using ANOVA, with the Ala357-Leu372 isoform as reference (*p<0.05, **p<0.01, ***p<0.001). The two isoforms expressing Val372 show reduced Tmax but no difference in t1/2 when compared to the Leu372 isoforms.</p

List of functionally relevant candidate SNPs in the <i>SLC30A9</i> region.

List of functionally relevant candidate SNPs in the SLC30A9 region.</p

Functional annotation of SNPs with Relate p-value < 0.05 at the <i>SLC30A9</i> region in the YRI population.

Functional annotation of SNPs with Relate p-value SLC30A9 region in the YRI population.</p

For the YRI population, Relate p-values in the <i>SLC30A9</i> region.

For the YRI population, Relate p-values in the SLC30A9 region.</p

Continental allele frequencies and GTEX data for rs7660223.

(A) Continental 1000 Genomes Project Phase 3 allele frequencies as retrieved from Ensembl (https://www.ensembl.org/index.html). (B) Multi-tissue eQTL comparison for rs7660223. (C). Differential SLC30A9 expression in the nucleus accumbens according to the rs7660223 genotypes as available at the GTEX portal (https://www.gtexportal.org/home/). NES, normalized effect sizes. (PDF)</p

Extreme population differentiation of the Leu372Val polymorphism in <i>ZIP4</i> (<i>SLC39A4</i>).

<p>(A) Distribution of F_ST pairwise scores between CEU and YRI in SNPs from the 1000 Genomes data, plotted on a linear and logarithmic scale. The F_ST values and corresponding quantiles of the five common SNPs in ZIP4 are indicated. *The F_ST quantile of rs1871534 (Leu372Val) was 0.99999977. (B) Distribution of F_ST pairwise scores between CHB and YRI in SNPs from the 1000 Genomes data. The F_ST values and corresponding quantiles of the five common SNPs in ZIP4 are indicated. **The F_ST quantile of rs1871534 (Leu372Val) was 0.99999817. (C) Contour map of worldwide frequencies of the Val372 variant at the rs1871534 SNP. A complete list of populations and allele frequencies is available in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004128#pgen.1004128.s010" target="_blank">Table S1</a>.</p

Val372 shows reduced membrane surface expression.

<p>(A) Immunostaining of the different isoforms of ZIP4 in HeLa cells under permeabilizing (left) conditions for total protein visualization and non-permeabilizing (right) conditions for surface protein visualization. Bright field images are provided to show the presence of cells on the field in all conditions. The acrodermatitis enteropathica variants Leu372Pro and Leu372Arg show absence of membrane expression. (B) Surface expression quantification normalized by the total amount of transporter of the different ZIP4 isoforms obtained from 12 independent measurements obtained in 4 different transfections. Data are expressed as mean ± SEM. * P<0.05 and *** P<0.001 <i>vs</i> Ala357-Leu372, one way ANOVA. The two isoforms expressing Val372 show reduced surface expression compared to the Leu372 isoforms.</p

Continental allele frequencies and GTEX data for rs11935648.

(A) Continental 1000 Genomes Project Phase 3 allele frequencies as retrieved from Ensembl (https://www.ensembl.org/index.html). (B) Multi-tissue eQTL comparison for rs11935648. (C). Differential SLC30A9 expression in the nucleus accumbens according to the rs11935648 genotypes as available at the GTEX portal (https://www.gtexportal.org/home/). NES, normalized effect sizes. (PDF)</p

Characterization of the impact on cellular zinc homeostasis of ZnT9 variant overexpression in HEK293 cells.

(A) RT-PCR comparing the expression of several ZTs in basal conditions in cells transfected with ZnT9-50Met, ZnT9-50Val, or an empty vector. 2-(DDCT) plotted using GAPDH as the housekeeping gene (ZIP1, ZIP6, and ZIP7 n = 6; Rest of ZTs n = 3); ** p4 (n = 9); *** p4 conditions (n = 14–20). * p-(DDCT) plotted using GAPDH as the housekeeping gene (n = 5–6) ** p4 conditions (n = 9–12); ** p4 conditions (n = 8–15) * pS1 Data.</p