FIGURE 4.

Profiling of circRNA expression changes in HuD-OE and HuD-KO mice. (A) Volcano plots representing circRNAs differentially expressed between HuD-KO (Elavl4^–/–) mice and WT littermates. The vertical lines correspond to 2-fold change up and down, respectively, and the horizontal line represents a p-value of 0.05. Values shown in red represent the differentially expressed circRNAs. n = 3 for each genotype (HuD-KO, WT). (B) Volcano Plots representing circRNAs differentially expressed between HuD-OE mice and WT littermates. RNA extracted from HuD-OE and WT mouse striatum was subjected to circRNA array as described in Methods. The vertical lines correspond to 1.5-fold change up and down, respectively, and the horizontal line represents a p-value of 0.05. Values shown in red represent the differentially expressed circRNAs. n = 3 for each genotype (HuD-OE, WT) (C) Identification of common elements between circRNAs bound to HuD and circRNAs whose expression is regulated by HuD. A list of 5 candidate HuD circRNAs for validation was obtained comparing the results of the three different arrays. (D,E) Comparison of circular and linear RNA levels. (D) RNA extracted from HuD-KO and WT mice striatum was subjected to mRNA microarray analysis as described in section “Materials and Methods.” The vertical lines in the volcano plot correspond to 2-fold change up or down, respectively, and the horizontal line represents a p-value of 0.05. Values shown in red or green represent the differentially up- and down-regulated mRNAs. n = 3 for each genotype. (HuD-KO, WT). (E) Graphs showing levels of both circular (top) and linear (bottom) RNA levels in HuD-KO mice vs. WT. Data are Means ± SEM, *p < 0.05, Student’s t-test. (F,G) ceRNA networks. ceRNA analyses were performed as described in sction “Materials and Methods.” circRNA/miRNA/mRNA networks were generated to visualize the interactions for circFoxp1 and circMap1; the ceRNAs of the remaining circRNAs are reported in Supplementary Table 3.