Sequence determinants of improved CRISPR sgRNA design
The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9 fusion-mediated inhibition/activation (CRISPRi/a) are powerful techniques for discovering phenotype-associated gene function. We systematically asses...
| Автори: | , , , , , , , , , , , |
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| Формат: | Стаття |
| Мова: | en_US |
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Cold Spring Harbor Laboratory Press
2016
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| Онлайн доступ: | http://hdl.handle.net/1721.1/100787 https://orcid.org/0000-0003-2782-2509 |
| _version_ | 1826208101955534848 |
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| author | Xu, Han Xiao, Tengfei Chen, Chen-Hao Li, Wei Meyer, Clifford A. Wu, Qiu Wu, Di Cong, Le Zhang, Feng Liu, Jun S. Brown, Myles Liu, X. Shirley |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Xu, Han Xiao, Tengfei Chen, Chen-Hao Li, Wei Meyer, Clifford A. Wu, Qiu Wu, Di Cong, Le Zhang, Feng Liu, Jun S. Brown, Myles Liu, X. Shirley |
| author_sort | Xu, Han |
| collection | MIT |
| description | The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9 fusion-mediated inhibition/activation (CRISPRi/a) are powerful techniques for discovering phenotype-associated gene function. We systematically assessed the DNA sequence features that contribute to single guide RNA (sgRNA) efficiency in CRISPR-based screens. Leveraging the information from multiple designs, we derived a new sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments. Our model confirmed known features and suggested new features including a preference for cytosine at the cleavage site. The model was experimentally validated for sgRNA-mediated mutation rate and protein knockout efficiency. Tested on independent data sets, the model achieved significant results in both positive and negative selection conditions and outperformed existing models. We also found that the sequence preference for CRISPRi/a is substantially different from that for CRISPR/Cas9 knockout and propose a new model for predicting sgRNA efficiency in CRISPRi/a experiments. These results facilitate the genome-wide design of improved sgRNA for both knockout and CRISPRi/a studies. |
| first_indexed | 2024-09-23T14:00:33Z |
| format | Article |
| id | mit-1721.1/100787 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:00:33Z |
| publishDate | 2016 |
| publisher | Cold Spring Harbor Laboratory Press |
| record_format | dspace |
| spelling | mit-1721.1/1007872022-10-01T18:33:01Z Sequence determinants of improved CRISPR sgRNA design Xu, Han Xiao, Tengfei Chen, Chen-Hao Li, Wei Meyer, Clifford A. Wu, Qiu Wu, Di Cong, Le Zhang, Feng Liu, Jun S. Brown, Myles Liu, X. Shirley Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences McGovern Institute for Brain Research at MIT Zhang, Feng The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9 fusion-mediated inhibition/activation (CRISPRi/a) are powerful techniques for discovering phenotype-associated gene function. We systematically assessed the DNA sequence features that contribute to single guide RNA (sgRNA) efficiency in CRISPR-based screens. Leveraging the information from multiple designs, we derived a new sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments. Our model confirmed known features and suggested new features including a preference for cytosine at the cleavage site. The model was experimentally validated for sgRNA-mediated mutation rate and protein knockout efficiency. Tested on independent data sets, the model achieved significant results in both positive and negative selection conditions and outperformed existing models. We also found that the sequence preference for CRISPRi/a is substantially different from that for CRISPR/Cas9 knockout and propose a new model for predicting sgRNA efficiency in CRISPRi/a experiments. These results facilitate the genome-wide design of improved sgRNA for both knockout and CRISPRi/a studies. 2016-01-11T00:31:23Z 2016-01-11T00:31:23Z 2015-08 2015-06 Article http://purl.org/eprint/type/JournalArticle 1088-9051 1549-5469 http://hdl.handle.net/1721.1/100787 Xu, Han, Tengfei Xiao, Chen-Hao Chen, Wei Li, Clifford A. Meyer, Qiu Wu, Di Wu, et al. “Sequence Determinants of Improved CRISPR sgRNA Design.” Genome Res. 25, no. 8 (June 10, 2015): 1147–1157. https://orcid.org/0000-0003-2782-2509 en_US http://dx.doi.org/10.1101/gr.191452.115 Genome Research Creative Commons Attribution http://creativecommons.org/licenses/by-nc/4.0/ application/pdf Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press |
| spellingShingle | Xu, Han Xiao, Tengfei Chen, Chen-Hao Li, Wei Meyer, Clifford A. Wu, Qiu Wu, Di Cong, Le Zhang, Feng Liu, Jun S. Brown, Myles Liu, X. Shirley Sequence determinants of improved CRISPR sgRNA design |
| title | Sequence determinants of improved CRISPR sgRNA design |
| title_full | Sequence determinants of improved CRISPR sgRNA design |
| title_fullStr | Sequence determinants of improved CRISPR sgRNA design |
| title_full_unstemmed | Sequence determinants of improved CRISPR sgRNA design |
| title_short | Sequence determinants of improved CRISPR sgRNA design |
| title_sort | sequence determinants of improved crispr sgrna design |
| url | http://hdl.handle.net/1721.1/100787 https://orcid.org/0000-0003-2782-2509 |
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