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. Author manuscript; available in PMC: 2015 Jun 19.
Published in final edited form as: Mol Cell. 2014 May 22;54(6):1042–1054. doi: 10.1016/j.molcel.2014.03.049

Figure 2. C. elegans miRNA:Targets (3,600) Derived from Chimeras Reflect Endogenous miRNA Targeting.

Figure 2

(A) Target RNAs were analyzed for complementarity to the seed region of their ligated miRNAs. ~80% of interactions possess the tested complementarities. Shuffled sequences (dinucleotides in target sequences are permuted) served as control. mm = mismatch Mismatches were broadly distributed over all types of nucleotides, including G:U.

(B) Hybridization profile summarized over all interactions. The predicted frequency of a miRNA position to be base paired is plotted along the miRNA length. Duplex structures of miRNA:targets were predicted by RNAhybrid allowing G:U pairing. Shuffled sequences (dinucleotides in target sequences are permuted) and shuffled interactions (targets are swapped between miRNAs) served as control.

(C) Target sites derived from miRNA-chimeras are more often found ligated to miRNAs of the same family than expected by chance (p < 0.0001). Shuffling target sites between miRNA families served as control.

(D) Local frequency of crosslink-induced T to C conversions in target RNAs from interactions with a perfect 2-7 seed match (normalized to local thymidine frequency). Nucleotides hybridized to the seed of the miRNA are strongly indisposed to crosslink with the protein. See also Figure S2.