Figure 5

miR-378 in circadian gene regulation.

(a) Comparison of the log2-transformed fold changes of CT10 and CT22 (log₂FC(CT10/CT22)) between Ad-null and Ad-378 of miR-378 circadian targets (Group I and Group III genes in Fig. 4e). The solid grey line represents y = x. The dashed grey lines represent y = x ± 0.5. The colored dots represent the genes with log₂FC(CT10/CT22) differences between Ad-378 and Ad-null larger than 0.5, while the grey nodes represent the genes with the difference less than 0.5. Number of genes in each group is indicated in the bar plot. (b) Comparison of the relative amplitudes (log2-transformed peak to trough ratio) between nascent and mature transcripts of the grey dots in 5a. Red bar represents the genes that do not show relative amplitude changes (difference of the relative amplitude less than 0.5). Black bar represents the genes with relative amplitude changes (difference of the relative amplitude larger than 0.5). Enrichment p-values were calculated by Fisher’s exact test using the relative amplitude differences between nascent and mature transcripts of all mouse genes as the background. (c) The expression patterns of the three genes (Cdkn1a, Eid2 and Por) that showed increased relative amplitudes in nascent transcript comparing to mature transcript and in Ad-378 comparing to Ad-null. The left figures show the expression patterns of nascent and mature transcripts and the right figures show the expression patterns upon miR-378 over-expression. *represents ANOVA p-value for treatment < 0.05. (d) Two gene regulatory motifs formed by miR-378 and circadian TFs (BMAL1/CLOCK, REV-ERBα/β). The green nodes represent the genes peaking around CT10, while the purple nodes represent the genes peaking around CT22.