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FEBS J. 2020 Jan 23. doi: 10.1111/febs.15218. [Epub ahead of print]

CRISPR screening strategies for microRNA target identification.

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National Institutes of Diabetes and Digestive and Kidney Diseases Intramural Research Program, National Institutes of Health, Bethesda, MD, USA.


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.


CRISPR screens; genetic screens; microRNA target identification; microRNAs; negative selection screens


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