---
title: "Understanding functional miRNA–target interactions in vivo by site-specific genome engineering"
url: "https://phil.ewels.co.uk/publications/2014/bassett-nature-communications"
site: "phil.ewels.co.uk"
author: "Phil Ewels"
section: "Publications"
journal: "Nature Communications"
published: "2014-08-19"
doi: "https://doi.org/10.1038/ncomms5640"
authors: "Andrew R. Bassett, Ghows Azzam, Lucy Wheatley, Charlotte Tibbit, Timothy Rajakumar, Simon McGowan, Nathan Stanger, Philip Andrew Ewels, Stephen Taylor, Chris P. Ponting, Ji-Long Liu, Tatjana Sauka-Spengler, Tudor A. Fulga"
---

# Understanding functional miRNA–target interactions in vivo by site-specific genome engineering

MicroRNA (miRNA) target recognition is largely dictated by short ‘seed’ sequences, and single miRNAs therefore have the potential to regulate a large number of genes. Understanding the contribution of specific miRNA–target interactions to the regulation of biological processes _in vivo_ remains challenging. Here we use transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technologies to interrogate the functional relevance of predicted miRNA response elements (MREs) to post-transcriptional silencing in zebrafish and _Drosophila_. We also demonstrate an effective strategy that uses CRISPR-mediated homology-directed repair with short oligonucleotide donors for the assessment of MRE activity in human cells. These methods facilitate analysis of the direct phenotypic consequences resulting from blocking specific miRNA–MRE interactions at any point during development.

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From the personal website of Phil Ewels, a software developer and bioinformatician in Stockholm, Sweden: https://phil.ewels.co.uk/
The whole site as Markdown: https://phil.ewels.co.uk/llms.txt