Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance (original) (raw)
Figure 4
Significantly enriched motifs in 3′-UTRs of mRNAs targeted to Ago2 by miR-1 and miR-124.
(A) Analysis of mRNAs associated with Ago2 from cells transfected with FLAG-Ago2 and miR-1 relative to cells transfected with Ago2 alone (1% local FDR). (i) Enrichment of hexamers in 3′-UTRs of miR-1 IP targets compared to 3′-UTRs of all mRNAs passing array filters. Shown are hexamers with at least four contiguous Watson-Crick base pairs to miRNA with a p-value cut-off of 0.001 (binomial test with bonferroni correction). Rank by p-value relative to all 4096 hexamers. Bases in red can form Watson-Crick base pairs with miR-1. (ii) Moving plot of observed/expected ratios of hexamers complementary to miR-1. Frequencies calculated as in (i). (iii) 10mer motif returned by MEME motif finder using 3′-UTR sequences from the miR-1 high confidence target set. For each position in the motif, the combined height of the bases represents the information content at that position, whereas the relative heights of the individual bases represent the frequency of that base at that position. Bases in red can form Watson-Crick base pairs with miR-1. Numbers underneath the logo correspond with miRNA 5′-position, with 1 being the 5′-most miRNA nucleotide. (B) Same as in (A), except for mRNAs associated with Ago2 from cells transfected with FLAG-Ago2 and miR-124 relative to cells transfected with Ago2 alone.