Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [CLIP-seq 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. Argonaute (AGO) HITS-CLIP Libraries generated from wild type and miR-155 knockout activated T cells. AGO HITS-CLIP libraries were generated from activated wild type and miR-155 knockout T cells with two different 3' linkers. Libraries were generated and sequenced with an 11nt index read that contained both a 5nt multiplexing index and a 6nt degenerate barcode. Files have been demultiplexed and the 6nt degenerate barcode has been appended as the first 6 nucleotides of the read.