Figure 1. Transcriptome analysis of Dicer1^−/− oocytes.

(A) M [log₂(fold change)] vs. A [average log₂(expression level)] plot for the Dicer1 Dicer1^+/+ fully-grown GV oocytes. Each dot represents a transcript. Significant expression changes (p-value < 0.001 computed from four replicate experiments) are shown in red. (B) 7-mer motif analysis of up-regulated transcripts. The motifs whose frequency in the 3′-UTRs of up-regulated transcripts is significantly different from the frequency in the entire set of 3′-UTRs are shown in red (see also Experimental Procedures). One of the significantly enriched motifs is complementary to the positions 1–7 of the miR-1195. (C) Comparison of 7-mer motif analyses of Dicer1^−/− oocytes (left panel) and ES cells (right panel, horizontally inverted); most relevant motifs complementary to seeds of most abundant miRNAs in both cell types are highlighted. The most abundant miRNAs in the oocyte and ES cells are shown in red and blue font, respectively. Note that none of the motifs corresponding to abundant maternal miRNAs is enriched more than 1.1 times in 3′ UTRs of transcripts up-regulated in Dicer1^−/− oocytes whereas all four motifs corresponding to miRNAs abundant in ES cells are enriched in Dicer1^−/− ES cells. Posterior probability analysis shows a high significance (1.000) only for the GCACUUU motif. However, posterior probability for the other three motifs corresponding to ES cell miRNAs was one to three orders of magnitude higher than all other motifs, which scored within the statistical background (~ 10⁻⁵, Table S3). Abundance (%) of miRNAs related to individual motifs in both cell types is indicated next to each motif. Dashed lines mark 1.0 and 1.1-fold motif enrichment.