In-depth assessment of the PAM compatibility and editing activities of Cas9 variants
| Autor: | Weiwei Zhang, Jianhang Yin, Jiazhi Hu, Changchang Xin, Zhengrong Zhang-Ding, Chen Ai, Yuhong Wang, Mengzhu Liu |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Streptococcus pyogenes
AcademicSubjects/SCI00010 media_common.quotation_subject Fidelity C-myc Genes Computational biology Biology Genome 03 medical and health sciences 0302 clinical medicine Genome editing CRISPR-Associated Protein 9 Genetics CRISPR 030304 developmental biology media_common Gene Editing 0303 health sciences Nucleic Acid Enzymes Cas9 Oryza Multiple target Protospacer adjacent motif Mutation CRISPR-Cas Systems Genome Plant 030217 neurology & neurosurgery |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | A series of Cas9 variants have been developed to improve the editing fidelity or targeting range of CRISPR–Cas9. Here, we employ a high-throughput sequencing approach primer-extension-mediated sequencing to analyze the editing efficiency, specificity and protospacer adjacent motif (PAM) compatibility of a dozen of SpCas9 variants at multiple target sites in depth, and our findings validate the high fidelity or broad editing range of these SpCas9 variants. With regard to the PAM-flexible SpCas9 variants, we detect significantly increased levels of off-target activity and propose a trade-off between targeting range and editing specificity for them, especially for the near-PAM-less SpRY. Moreover, we use a deep learning model to verify the consistency and predictability of SpRY off-target sites. Furthermore, we combine high-fidelity SpCas9 variants with SpRY to generate three new SpCas9 variants with both high fidelity and broad editing range. Finally, we also find that the existing SpCas9 variants are not effective in suppressing genome instability elicited by CRISPR–Cas9 editing, raising an urgent issue to be addressed. |
| Databáze: | OpenAIRE |
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