1. Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity
- Author
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William Rostain, Theophile Grebert, Danylo Vyhovskyi, Paula Thiel Pizarro, Gatwa Tshinsele-Van Bellingen, Lun Cui, David Bikard, Biologie de Synthèse - Synthetic biology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), European Research Council [677823], European Research Council [101044479], Agence Nationale de la Recherche [ANR-10-LABX-62-IBEID]. Funding for open access charge: Institut Pasteur., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), and European Project: 677823,H2020,ERC-2015-STG,CRISPAIR(2016)
- Subjects
MESH: CRISPR-Cas Systems ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,MESH: Escherichia coli ,MESH: Endonucleases ,[SDV]Life Sciences [q-bio] ,MESH: Promoter Regions, Genetic ,Genetics ,MESH: Genetic Engineering ,MESH: Animals ,MESH: Genes, Bacterial ,MESH: Genome, Bacterial ,MESH: Mammals - Abstract
Genetic tools derived from the Cas9 RNA-guided nuclease are providing essential capabilities to study and engineer bacteria. While the importance of off-target effects was noted early in Cas9’s application to mammalian cells, off-target cleavage by Cas9 in bacterial genomes is easily avoided due to their smaller size. Despite this, several studies have reported experimental setups in which Cas9 expression was toxic, even when using the catalytic dead variant of Cas9 (dCas9). Specifically, dCas9 was shown to be toxic when in complex with guide RNAs sharing specific PAM (protospacer adjacent motif)-proximal sequence motifs. Here, we demonstrate that this toxicity is caused by off-target binding of Cas9 to the promoter of essential genes, with silencing of off-target genes occurring with as little as 4 nt of identity in the PAM-proximal sequence. Screens performed in various strains of Escherichia coli and other enterobacteria show that the nature of toxic guide RNAs changes together with the evolution of sequences at off-target positions. These results highlight the potential for Cas9 to bind to hundreds of off-target positions in bacterial genomes, leading to undesired effects. This phenomenon must be considered in the design and interpretation of CRISPR–Cas experiments in bacteria.
- Published
- 2023