Partial DNA-guided Cas9 enables genome editing with reduced off-target activity

Yin, Hao; Song, Chun‐Qing; Suresh, Sneha; Kwan, Suet‐Yan; Wu, Qiongqiong; Walsh, Stephen; Ding, Junmei; Bogorad, Roman L.; Zhu, Lihua Julie; Wolfe, Scot A.; Koteliansky, Victor; Xue, Wen; Langer, Robert; Anderson, Daniel G.

doi:10.1038/nchembio.2559

Cited by 203 publications

(172 citation statements)

References 48 publications

(92 reference statements)

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“…The types of non-canonical gRNA are also continually expanding, including gRNA with DNA nucleotides 33 , chemical modifications 34,35 whose specificity improvement may also arise from DNA unwinding becoming more sensitive to mismatches. Non-canonical gRNAs can expand genome engineering applications a few additional ways.…”

Section: Discussionmentioning

confidence: 99%

Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding

Okafor

Singh

et al. 2019

Preprint

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Cas9 has made a wide range of genome engineering applications possible. However, its specificity continues to be a challenge. Non-canonical gRNAs and new engineered variants of Cas9 have been developed to improve specificity but at the cost of the on-target activity. DNA unwinding is the primary checkpoint before cleavage by Cas9 and was shown to be made more sensitive to sequence mismatches by specificity-enhancing mutations in Cas9. Here we performed single-molecule FRET-based DNA unwinding experiments using various combinations of non-canonical gRNAs and different Cas9s. All engineered Cas9s were less promiscuous than wild type when canonical gRNA was used but HypaCas9 had much-reduced on-target unwinding. Cas9-HF1 and eCas9 showed the best balance between low promiscuity and high on-target activity with canonical gRNA. When extended gRNAs with one or two guanines added were used, Sniper1-Cas9 showed the lowest promiscuity while maintaining high on-target activity. Truncated gRNA generally reduced unwinding and adding a non-matching guanine to the 5' end of gRNA influenced unwinding in a sequence-context dependent manner. Our results are consistent with cell-based cleavage data and provide a mechanistic understanding of how various Cas9/gRNA combinations perform in genome engineering.

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Section: Discussionmentioning

confidence: 99%

Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding

Okafor

Singh

et al. 2019

Preprint

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“…As a result, there was a significant increase in cleavage specificity (0.11~4.15 fold) for chimeric guides ((cr)RNA No. 14,20,21,22,23) that did not induce DNA off-target cleavage ( Figure 4B). For the DNMT1 target gene, consecutive DNA substitutions from the 3′-end of the guide to the eighth nucleotide resulted in less on-target compensation and higher target cleavage specificity than DNA substitutions in the seed region close to the PAM sequence ( Figures 4A, 4B).…”

Section: Target Dna Cleavage Specificity Of Chimeric Dna-rna-guided Cpf1mentioning

confidence: 97%

Enhancement of Target Specificity of CRISPR-Cas12a by Using a Chimeric DNA-RNA Guide

Kim

Lee

Kang

et al. 2020

Preprint

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The CRISPR-Cas9 system is widely used for target-specific genome engineering. Cpf1 is one of the CRISPR effectors that controls target genes by recognizing thymine-rich protospacer adjacent motif (PAM) sequences. Cpf1 has a higher sensitivity to mismatches in the guide RNA than does Cas9; therefore, off-target sequence recognition and cleavage are lower. However, it tolerates mismatches in regions distant from the PAM sequence (TTTN or TTN) in the protospacer, and offtarget cleavage issues may become more problematic when Cpf1 activity is improved for therapeutic purposes. In our study, we investigated off-target cleavage by Cpf1 and modified the Cpf1 (cr)RNA to address the off-target cleavage issue. We developed a CRISPR-Cpf1 that can induce mutations in target DNA sequences in a highly specific and effective manner by partially substituting the (cr)RNA with DNA to change the energy potential of base pairing to the target DNA. A model to explain how chimeric (cr)RNA guided CRISPR-Cpf1 and SpCas9 nickase effectively work in the intracellular genome is suggested. In our results, CRISPR-Cpf1 induces less offtarget mutations at the cell level, when chimeric DNA-RNA guide was used for genome editing. This study has a potential for therapeutic applications in incurable 2 diseases caused by genetic mutation.

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“…HDR enables the insertion of specific point mutations, the addition of in-frame translated epitopes, the performance of sequence-specific knock-in (KI) events of genes, the generation of conditional knock-out (cKO) genetic models, etc.. Once refined to perfection, CRISPR/Cas9-mediated HDR-based genome editing holds immense promise for gene therapy. Indeed, much of the genome-editing community was invested in improving the efficiency and sequence specificity of the CRISPR/Cas9 complexes [11][12][13][14][15][16][17][18][19] . However, several limitations of the technique, such as low efficiency of HDR, off-target effects or genomic rearrangements remain challenging obstacles 20,21 .…”

Section: Introductionmentioning

confidence: 99%

Pervasive head-to-tail insertions of DNA templates mask desired CRISPR/Cas9-mediated genome editing events

Skryabin

Gubar

Seeger

et al. 2019

Preprint

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CRISPR/Cas9 mediated homology-directed DNA repair is the method of choice for precise gene editing in a wide range of model organisms, including mouse and human.Broad use by the biomedical community refined the method, making it more efficient and sequence specific. Nevertheless, the rapidly evolving technique still contains pitfalls. During the generation of six different conditional knock-out mouse models, we discovered that frequently (sometimes solely) homology-directed repair and/or non-homologous end-joining mechanisms caused multiple unwanted head-to-tail

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Partial DNA-guided Cas9 enables genome editing with reduced off-target activity

Cited by 203 publications

References 48 publications

Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding

Single molecule analysis of effects of non-canonical guide RNAs and specificity-enhancing mutations on Cas9-induced DNA unwinding

Enhancement of Target Specificity of CRISPR-Cas12a by Using a Chimeric DNA-RNA Guide

Pervasive head-to-tail insertions of DNA templates mask desired CRISPR/Cas9-mediated genome editing events

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