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. 2010 Jul 5;207(7):1351–1358. doi: 10.1084/jem.20100458

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© 2010 Rasmussen et al.

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Figure 4. — The miR-144/451 locus tunes the expression of many genes. (A) Expression scatterplot showing relative mean expression of Illumina probes in wild-type (x axis) and miR-144/451^−/− (y axis) erythroblasts. Significantly up-regulated genes (red) and down-regulated genes (green) are shown. Expression profiling was performed once with biological quadruplicates of each genotype. (B) Sylamer enrichment landscape plot for all 876 7-nt motifs complementary to canonical mouse miRNA seed regions, either from nt 2–8 (7mer-m8) or from nt 1–7 (7mer-A1). The x axis represents the sorted gene list of 19,600 genes from most up-regulated to most down-regulated in the miR-144/451^−/− erythroblasts. Each 7mer motif was tested for significant enrichment across the 3′ UTRs of genes in this list. The two motifs corresponding to seeds matching miR-451 (red, 7mer-m8; yellow, 7mer-A1) are enriched in the up-regulated genes, peaking at the most up-regulated 588 genes (solid vertical line). Two motifs matching the seed region of miR-144 (blue, 7mer-m8; light blue, 7mer-A1) are also significantly enriched, but to a lesser extent. The horizontal dotted lines represent a Bonferroni-corrected P value threshold of 0.05. (C) Upper region of an empirical cumulative density plot of log fold change for different populations of probes. Those probes whose 3′ UTRs possess miR-144 6-nt seed matches (green), miR-451 6-nt seeds (orange), or both seeds (red) are skewed toward higher positive fold changes in the miR-144/451^−/− erythroblasts, compared with probes whose mapped 3′ UTRs do not contain a seed match (black). (D) qRT-PCR expression analysis of representative miR-144/451 seed-containing deregulated genes identified by Sylamer. Normalized data are plotted as relative fold change in miR-144/451^−/− versus wild-type erythroblasts. Standard error is shown and * indicates significantly up-regulated expression (P < 0.05). Genes are color coded as in C. Data were obtained in two independent experiments measuring biological quadruplicates of each genotype.