Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [mRNA expression data]

microRNAs (miRNAs) are essential components of gene regulation, but identification of miRNA targets remains a major challenge. Most target prediction and discovery relies on perfect complementarity of the miRNA seed to the 3’ untranslated region (UTR). However, it is unclear to what extent miRNAs target sites without seed matches. Here, we performed a transcriptome-wide identification of the endogenous targets of a single miRNA—miR-155—in a genetically controlled manner. We found that approximately forty percent of miR-155-dependent Argonaute binding occurs at sites without perfect seed matches. The majority of these non-canonical sites feature extensive complementarity to the miRNA seed with one mismatch. These non-canonical sites confer regulation of gene expression albeit less potently than canonical sites. Thus, non-canonical miRNA binding sites are widespread, often contain seed-like motifs, and can regulate gene expression, generating a continuum of targeting and regulation. We used microarrays to measure changes in gene expression between activated wild type (WT) and miR-155 deficient (155KO) primary CD4 T cells. CD4 T cells were harvested from WT and miR-155 KO mice (Thai et al., 2007) and activated for 3 days in vitro. Each array is from a separate biological replicate, which are cells originating from a separate mouse.