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A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants

Nature Plants volume 3, Article number: 17018 (2017) Cite this article

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A Correction to this article was published on 19 June 2017

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR)–Cpf1 has emerged as an effective genome editing tool in animals. Here we compare the activity of Cpf1 from Acidaminococcus sp. BV3L6 (As) and Lachnospiraceae bacterium ND2006 (Lb) in plants, using a dual RNA polymerase II promoter expression system. LbCpf1 generated biallelic mutations at nearly 100% efficiency at four independent sites in rice T0 transgenic plants. Moreover, we repurposed AsCpf1 and LbCpf1 for efficient transcriptional repression in Arabidopsis, and demonstrated a more than tenfold reduction in miR159b transcription. Our data suggest promising applications of CRISPR–Cpf1 for editing plant genomes and modulating the plant transcriptome.

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Figure 1: Comprehensive analysis of AsCpf1 and LbCpf1 activities in rice protoplasts.
Figure 2: Highly efficient genome editing in rice T0 lines by LbCpf1.
Figure 3: Effective transcriptional repression in Arabidopsis by dAsCpf1–SRDX and dLbCpf1–SRDX.

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Acknowledgements

This work was supported by grants including the National Science Foundation of China (31330017, 31271420 and 31371682) and the National Transgenic Major Project (2014ZX0801003B-002) to X.Z. and Y.Z., a Collaborative Funding Grant from North Carolina Biotechnology Center and Syngenta Biotechnology (2016-CFG-8003) and a start-up fund from University of Maryland-College Park to Y.Q., and National Science Foundation (MCB 0209818, DBI 0923827 and 105-1339209) to D.F.V.

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Author notes

  1. Xu Tang and Levi G. Lowder: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biotechnology, School of Life Science and Technology, Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China

    Xu Tang, Xuelian Zheng, Zhaohui Zhong, Yiyi Chen, Qiurong Ren, Qian Li & Yong Zhang

  2. Department of Biology, East Carolina University, Greenville, 27834, North Carolina, USA

    Levi G. Lowder & Elida R. Kirkland

  3. Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China

    Tao Zhang

  4. Department of Plant Science and Landscape Architecture, University of Maryland, College Park, 20742, Maryland, USA

    Aimee A. Malzahn & Yiping Qi

  5. Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, 55455, Minnesota, USA

    Daniel F. Voytas

  6. Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, 20850, Maryland, USA

    Yiping Qi

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  1. Xu Tang
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Contributions

Y.Q., Y.Z. and D.F.V. designed the experiments. Y.Q., L.G.L. and A.A.M. generated all the constructs. X.T. and Y.Z. performed the transient assays in protoplasts and prepared samples for deep sequencing. T.Z., Y.Z. and X.T. analysed the deep sequencing data. X.T., X.Z., Z.Z., Y.C., Q.R. and Q.L. generated stable transgenic rice and analysed the plants. L.G.L. and E.R.K. produced Arabidopsis transcriptional repression data. Y.Q., Y.Z. and D.F.V. wrote the paper with input from other authors. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Yong Zhang or Yiping Qi.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Methods, Supplementary References, Supplementary Figures 1–10, Supplementary Table 1 (Oligos and gBlocks used in this study). (PDF 3235 kb)

Supplementary Table 2

Assembled T-DNA vectors used in this study. (XLSX 11 kb)

Supplementary Table 3

Sample information for high-throughput sequencing. (XLS 14 kb)

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Tang, X., Lowder, L., Zhang, T. et al. A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants. Nature Plants 3, 17018 (2017). https://doi.org/10.1038/nplants.2017.18

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