Figure 3
From: Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs
miRNA binding in unannotated exons. Sequencing the RNA captured in the miR-17-5p pull-down revealed several examples of targeting outside annotated exons. The red wiggle plot along the top indicates the number of reads from the RNAseq library that mapped at each position. Illumina microarray probes highlighted in blue showed significant enrichment in the biotin pull-down. (A,B) HMBOX1 (A) encodes a homeobox-containing transcription factor and EEF1E1 (B) a translation elongation factor. Probes detecting these genes were significantly enriched in the pull-down (adjusted P-values: ILMN_1843949, 0.002; ILMN_1725105, 0.03). None of the annotated exons (maroon boxes) contained predicted miR-17-5p sites. However, the RNAseq data suggested that both genes had retained introns that resulted in a longer 3′ UTR, and this region did contain binding sites.