PMC

Two LCLs of each ERAP2 genotype (AA, AB, and BB) were tested for protein using primary antibodies specific to: A, ERAP2 (goat polyclonal); B, ERAP2 (mouse polyclonal); and C, ß-actin (see ).

The X-axis reflects the absolute frequency of the derived allele, while the Y-axis reflects the frequency of that allele frequency bin in the generated data set. To account for missing data, the frequencies were projected to a sample size of 15 chromosomes. See the SFS of only coding SNPs in .

Circles represent haplotypes, with the areas proportional to the frequency of the haplotype (color-coded by population). The lines connecting the haplotypes have a length proportional to the number of mutations that differentiate the two haplotypes. Reticulations reflect recombinations or recurrent mutations. The ancestral state was inferred using the chimpanzee sequence data. For ERAP2, the four coding diagnostic SNPs are shown as white boxes; one nearly diagnostic SNP, which appears four times in the network due to the reticulations, is marked as thinner horizontal boxes. The ERAP2 haplotype network that includes all SNPs (coding and non-coding) is shown in , and the ERAP2 haplotype network that includes the chimpanzee sequence is shown in .

A, Locations of the four coding diagnostic SNPs across ERAP2 are shown, of which three (in red) were used to test for allele-specific expression. B, The allelic ratio of Haplotype B to Haplotype A ERAP2 cDNA levels, which was measured using these three coding diagnostic SNPs in the indicated heterozygote LCLs treated/untreated with emetine (NMD blocked), are depicted with colored bars. The control represents the allelic ratio measured with genomic DNA (gDNA), expected to be 1.0. The average allelic ratio across all cell lines tested (for a given SNP) is indicated above each set of bars. The error bars represent the standard error of the mean.

A, The genomic organization of the human chromosome 5q15 region containing ERAP1 and ERAP2 is included at the top. The two haplotype-specific ERAP2 spliced forms are shown for Haplotype A (in blue) and Haplotype B (in purple). The different alleles of rs2248374 are shown as a blue or purple base position, respectively. The red boxes represent the premature stop codons in the Haplotype B mRNA. B, PCR amplification of cDNA across the exon 10 splice junction (see ) from the indicated 16 LCLs, with the haplotype status of each cell indicated as homozygote (AA or BB) or heterozygote (AB). A negative control PCR, with no DNA template, was also performed (water).

The distribution of observed levels of surface-expressed HLA-ABC for B cells of AA, AB, and BB individuals are graphically represented as boxplots (the blue box containing the 25th–75th percentile of the distribution, the black horizontal line indicating the median, the red dot reflecting the mean, and black circles representing outliers). Data are shown for two independent experiments (left and right). For each experiment, the significance level of the comparison between AA and BB homozygotes (T-test) is shown within the plot; the significance level of the effect of genotype in the global comparison between AA and BB homozygotes (two-way ANOVA) is shown above. A representative HLA-ABC fluorescence intensity plot is shown in , and the mean fluorescence intensity boxplots of HLA-ABC and CD19 are presented in .