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Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array

Bernd Zetsche, Matthias Heidenreich, Prarthana Mohanraju, Iana Fedorova, Jeroen Kneppers, Ellen M. DeGennaro, Nerges Winblad, Sourav R. Choudhury, Omar O. Abudayyeh, Jonathan S. Gootenberg, Wen Y. Wu, David A. Scott, Konstantin Severinov, John van der Oost, Feng Zhang
doi: https://doi.org/10.1101/049122
Bernd Zetsche
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
5Department of Developmental Pathology, Institute of Pathology, Bonn Medical School, Sigmund Freud Street 25, 53127 Bonn, Germany
Matthias Heidenreich
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
Prarthana Mohanraju
6Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708 WE Wageningen, Netherlands
Iana Fedorova
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
8Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
9Peter the Great St.Petersburg Polytechinc University, St. Petersburg, 195251, Russia
Jeroen Kneppers
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
6Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708 WE Wageningen, Netherlands
Ellen M. DeGennaro
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
Nerges Winblad
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
Sourav R. Choudhury
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
Omar O. Abudayyeh
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
7Department of Systems Biology, Harvard Medical School, Boston, MA 02115
Jonathan S. Gootenberg
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
7Department of Systems Biology, Harvard Medical School, Boston, MA 02115
Wen Y. Wu
6Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708 WE Wageningen, Netherlands
David A. Scott
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
Konstantin Severinov
8Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
10Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
11Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
John van der Oost
6Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Stippeneng 4, 6708 WE Wageningen, Netherlands
Feng Zhang
1Broad Institute of MIT and Harvard, Cambridge, MA 02142
2McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
3Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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Abstract

Microbial CRISPR-Cas defense systems have been adapted as a platform for genome editing applications built around the RNA-guided effector nucleases, such as Cas9. We recently reported the characterization of Cpf1, the effector nuclease of a novel type V-A CRISPR system, and demonstrated that it can be adapted for genome editing in mammalian cells (Zetsche et al., 2015). Unlike Cas9, which utilizes a trans-activating crRNA (tracrRNA) as well as the endogenous RNaseIII for maturation of its dual crRNA:tracrRNA guides (Deltcheva et al., 2011), guide processing of the Cpf1 system proceeds in the absence of tracrRNA or other Cas (CRISPR associated) genes (Zetsche et al., 2015) (Figure 1a), suggesting that Cpf1 is sufficient for pre-crRNA maturation. This has important implications for genome editing, as it would provide a simple route to multiplex targeting. Here, we show for two Cpf1 orthologs that no other factors are required for array processing and demonstrate multiplex gene editing in mammalian cells as well as in the mouse brain by using a designed single CRISPR array.

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Posted October 01, 2016.

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Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array
Bernd Zetsche, Matthias Heidenreich, Prarthana Mohanraju, Iana Fedorova, Jeroen Kneppers, Ellen M. DeGennaro, Nerges Winblad, Sourav R. Choudhury, Omar O. Abudayyeh, Jonathan S. Gootenberg, Wen Y. Wu, David A. Scott, Konstantin Severinov, John van der Oost, Feng Zhang
bioRxiv 049122; doi: https://doi.org/10.1101/049122
Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array
Bernd Zetsche, Matthias Heidenreich, Prarthana Mohanraju, Iana Fedorova, Jeroen Kneppers, Ellen M. DeGennaro, Nerges Winblad, Sourav R. Choudhury, Omar O. Abudayyeh, Jonathan S. Gootenberg, Wen Y. Wu, David A. Scott, Konstantin Severinov, John van der Oost, Feng Zhang
bioRxiv 049122; doi: https://doi.org/10.1101/049122

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