Identifying microRNA (miRNA) target genes remains a major challenge in understanding the roles miRNAs play in gene regulation. Furthermore, understanding which miRNA-target interactions are the most biologically important is even more difficult. We present CRISPR-based strategies to identify essential miRNA binding sites. First, CRISPR knockout screens can easily be adapted to identify genes whose inactivation suppresses miRNA mutant phenotypes. Second, a custom approach to target individual miRNA binding sites via CRISPR can identify sites whose mutation recapitulates miRNA mutant phenotypes. We emphasize that the latter approach requires a readout of mutational profile (rather than single guide RNA abundance) when applied in a negative selection setting. Overall, the advent of CRISPR technology alongside improving empirical means of miRNA target identification will accelerate our dissection of miRNA gene regulatory networks.
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