Brief Communication

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

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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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Author information

Author notes

    • Xu Tang
    •  & Levi G. Lowder

    These authors contributed equally to this work.

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, North Carolina 27834, 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, Maryland 20742, USA

    • Aimee A. Malzahn
    •  & Yiping Qi
  5. Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA

    • Daniel F. Voytas
  6. Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA

    • Yiping Qi

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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.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Yong Zhang or Yiping Qi.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

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

Excel files

  1. 1.

    Supplementary Table 2

    Assembled T-DNA vectors used in this study.

  2. 2.

    Supplementary Table 3

    Sample information for high-throughput sequencing.