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High-throughput screens of PAM-flexible Cas9 variants for gene knock-out and transcriptional modulation

View ORCID ProfileMateusz Legut, View ORCID ProfileZharko Daniloski, Xinhe Xue, Dayna McKenzie, Xinyi Guo, View ORCID ProfileHans-Hermann Wessels, View ORCID ProfileNeville E. Sanjana
doi: https://doi.org/10.1101/2020.01.22.916064
Mateusz Legut
1New York Genome Center, New York, NY, USA
2Department of Biology, New York University, New York, NY, USA
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  • ORCID record for Mateusz Legut
Zharko Daniloski
1New York Genome Center, New York, NY, USA
2Department of Biology, New York University, New York, NY, USA
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Xinhe Xue
1New York Genome Center, New York, NY, USA
2Department of Biology, New York University, New York, NY, USA
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Dayna McKenzie
1New York Genome Center, New York, NY, USA
2Department of Biology, New York University, New York, NY, USA
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Xinyi Guo
1New York Genome Center, New York, NY, USA
2Department of Biology, New York University, New York, NY, USA
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Hans-Hermann Wessels
1New York Genome Center, New York, NY, USA
2Department of Biology, New York University, New York, NY, USA
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Neville E. Sanjana
1New York Genome Center, New York, NY, USA
2Department of Biology, New York University, New York, NY, USA
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  • ORCID record for Neville E. Sanjana
  • For correspondence: neville@sanjanalab.org
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Abstract

A key limitation of the commonly-used CRISPR enzyme S. pyogenes Cas9 is the strict requirement of an NGG protospacer-adjacent motif (PAM) at the target site, which reduces the number of accessible genomic loci. This constraint can be limiting for genome editing applications that require precise Cas9 positioning. Recently, two Cas9 variants with a relaxed PAM requirement (NG) have been developed (xCas9 and Cas9-NG) but their activity has been measured at only a small number of endogenous sites. Here we devised a high-throughput Cas9 pooled competition screen to compare the performance of both PAM-flexible Cas9 variants and wild-type Cas9 at thousands of genomic loci and across 3 modalities (gene knock-out, transcriptional activation and suppression). We show that PAM flexibility comes at a substantial cost of decreased DNA targeting and cutting. Of the PAM-flexible variants, we found that Cas9-NG outperforms xCas9 regardless of genome engineering modality or PAM. Finally, we combined xCas9 mutations with those of Cas9-NG, creating a stronger transcriptional modulator than existing PAM-flexible Cas9 variants.

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Posted January 23, 2020.
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High-throughput screens of PAM-flexible Cas9 variants for gene knock-out and transcriptional modulation
Mateusz Legut, Zharko Daniloski, Xinhe Xue, Dayna McKenzie, Xinyi Guo, Hans-Hermann Wessels, Neville E. Sanjana
bioRxiv 2020.01.22.916064; doi: https://doi.org/10.1101/2020.01.22.916064
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High-throughput screens of PAM-flexible Cas9 variants for gene knock-out and transcriptional modulation
Mateusz Legut, Zharko Daniloski, Xinhe Xue, Dayna McKenzie, Xinyi Guo, Hans-Hermann Wessels, Neville E. Sanjana
bioRxiv 2020.01.22.916064; doi: https://doi.org/10.1101/2020.01.22.916064

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