MIPs from HLA-disparate sibships derive from different sets of transcripts regulated by similar miRNomes. (A) Venn diagram showing that MIPs of HLA-disparate sibships derive from different sets of miRNA targets. The WebGestalt analysis program²⁸  was used to identify transcripts significantly enriched in 3′-UTR–binding sites of specific miRNAs among all MIP source transcripts identified in sibships 1 and 2 (P < .05 by hypergeometric test). The total number of MIP source transcripts that are miRNA targets for each sibship are shown in colors. (B) Different sets of MIP source transcripts are predicted to be regulated by mostly the same miRNAs. The WebGestalt analysis program²⁸  was used to identify miRNAs that recognize the 3′-UTR–binding site present in enriched MIP source transcripts. The numbers and percentages of miRNAs are depicted for each category. Total number of miRNAs that target MIP source transcripts in each sibship are shown in colors. (C) miRNA profiling showing that B-LCLs from HLA-disparate sibships have similar miRNA-expression profiles. Human miRNA microarrays were used to assess the expression of 1205 human and 144 viral miRNAs in B-LCLs (2 subjects from each sibship), CD19⁺CD20⁺ cells isolated from PBMCs of one member of sibship 2, and 2 nonlymphoid cell lines (HEK293 and HeLa). Hierarchical clustering was used to calculate the correlation between various profiles (represented by a dendrogram). (D) miRNAs that target MIP source transcripts in B-LCLs are expressed at higher levels in B-LCLs than in other cell types. All miRNAs studied were ranked from high to low according to their expression level in each cell line. Among them, the ranking of each of the 133 miRNAs predicted to regulate MIP source transcripts in B-LCLs was determined in B-LCLs, primary CD19⁺CD20⁺ cells, HEK293 cells, and HeLa cells. Each dot corresponds to 1 miRNA. The median rank is shown for each cell population (red line and values). On average, miRNAs predicted to recognize MIP source transcripts were ranked significantly higher (ie, were more expressed) in B-LCLs than in nonlymphoid cell lines (*P < .05 by 1-way ANOVA and the Bonferroni multiple comparison test). B-LCL-1.1 indicates B-LCLs from subject 1 of sibship 1; B-LCL-1.2, from subject 2 of sibship 1; B-LCL-2.1, from subject 1 of sibship 2; and B-LCL-2.2, from subject 2 of sibship 2.