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Zhao W, Siegel D, Biton A, Tonqueze OL, Zaitlen N, Ahituv N, Erle DJ. CRISPR-Cas9-mediated functional dissection of 3'-UTRs. Nucleic Acids Res 2017; 45:10800-10810. [PMID: 28985357 PMCID: PMC5737544 DOI: 10.1093/nar/gkx675] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/25/2017] [Indexed: 11/21/2022] Open
Abstract
Many studies using reporter assays have demonstrated that 3′ untranslated regions (3′-UTRs) regulate gene expression by controlling mRNA stability and translation. Due to intrinsic limitations of heterologous reporter assays, we sought to develop a gene editing approach to investigate the regulatory activity of 3′-UTRs in their native context. We initially used dual-CRISPR (clustered, regularly interspaced, short palindromic repeats)-Cas9 targeting to delete DNA regions corresponding to nine chemokine 3′-UTRs that destabilized mRNA in a reporter assay. Targeting six chemokine 3′-UTRs increased chemokine mRNA levels as expected. However, targeting CXCL1, CXCL6 and CXCL8 3′-UTRs unexpectedly led to substantial mRNA decreases. Metabolic labeling assays showed that targeting these three 3′-UTRs increased mRNA stability, as predicted by the reporter assay, while also markedly decreasing transcription, demonstrating an unexpected role for 3′-UTR sequences in transcriptional regulation. We further show that CRISPR–Cas9 targeting of specific 3′-UTR elements can be used for modulating gene expression and for highly parallel localization of active 3′-UTR elements in the native context. Our work demonstrates the duality and complexity of 3′-UTR sequences in regulation of gene expression and provides a useful approach for modulating gene expression and for functional annotation of 3′-UTRs in the native context.
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Affiliation(s)
- Wenxue Zhao
- Lung Biology Center, Department of Medicine, University of California San Francisco, 4th St, San Francisco, CA 94158, USA
| | - David Siegel
- Lung Biology Center, Department of Medicine, University of California San Francisco, 4th St, San Francisco, CA 94158, USA
| | - Anne Biton
- Lung Biology Center, Department of Medicine, University of California San Francisco, 4th St, San Francisco, CA 94158, USA.,Centre de Bioinformatique, Biostatistique et Biologie Intégrative, C3BI, USR 3756 Institut Pasteur et CNRS, 25-28 Rue du Dr Roux, Paris 75015, France
| | - Olivier Le Tonqueze
- Lung Biology Center, Department of Medicine, University of California San Francisco, 4th St, San Francisco, CA 94158, USA
| | - Noah Zaitlen
- Lung Biology Center, Department of Medicine, University of California San Francisco, 4th St, San Francisco, CA 94158, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, 4th St, San Francisco, CA 94158, USA
| | - David J Erle
- Lung Biology Center, Department of Medicine, University of California San Francisco, 4th St, San Francisco, CA 94158, USA
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