Letter | Published:

Optical control of mammalian endogenous transcription and epigenetic states

Nature volume 500, pages 472476 (22 August 2013) | Download Citation

Abstract

The dynamic nature of gene expression enables cellular programming, homeostasis and environmental adaptation in living systems. Dissection of causal gene functions in cellular and organismal processes therefore necessitates approaches that enable spatially and temporally precise modulation of gene expression. Recently, a variety of microbial and plant-derived light-sensitive proteins have been engineered as optogenetic actuators, enabling high-precision spatiotemporal control of many cellular functions1,2,3,4,5,6,7,8,9,10,11. However, versatile and robust technologies that enable optical modulation of transcription in the mammalian endogenous genome remain elusive. Here we describe the development of light-inducible transcriptional effectors (LITEs), an optogenetic two-hybrid system integrating the customizable TALE DNA-binding domain12,13,14 with the light-sensitive cryptochrome 2 protein and its interacting partner CIB1 from Arabidopsis thaliana. LITEs do not require additional exogenous chemical cofactors, are easily customized to target many endogenous genomic loci, and can be activated within minutes with reversibility6,15. LITEs can be packaged into viral vectors and genetically targeted to probe specific cell populations. We have applied this system in primary mouse neurons, as well as in the brain of freely behaving mice in vivo to mediate reversible modulation of mammalian endogenous gene expression as well as targeted epigenetic chromatin modifications. The LITE system establishes a novel mode of optogenetic control of endogenous cellular processes and enables direct testing of the causal roles of genetic and epigenetic regulation in normal biological processes and disease states.

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Acknowledgements

We thank C. Jennings for comments, F. A. Ran for help with illustrations, C. Lin for editing, M. M. Cunniff for technical assistance and W. Yan for computational analysis, and members of the Zhang laboratory for discussion, support and advice. S.K. is supported by a Hubert Schoemaker Fellowship from the McGovern Institute for Brain Research at MIT. M.H. is supported by a postdoctoral fellowship from the Human Frontiers Science Program. G.M.C. is support by a NIH NHGRI CEGS grant (P50-HG005550). F.Z. is supported by a NIH Transformative R01 award (R01-NS073124), a NIH Director’s Pioneer Award (DP1-MH100706), the Keck, McKnight, Vallee, Damon Runyon, Searle Scholars, Klingenstein, and Simons Foundations, Bob Metcalfe and Jane Pauley. Sequence, protocol, and reagent information are available through the Zhang laboratory website at http://www.genome-engineering.org.

Author information

Author notes

    • Silvana Konermann
    •  & Mark D. Brigham

    These authors contributed equally to this work.

Affiliations

  1. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA

    • Silvana Konermann
    • , Mark D. Brigham
    • , Alexandro E. Trevino
    • , Patrick D. Hsu
    • , Matthias Heidenreich
    • , Le Cong
    • , Randall J. Platt
    • , David A. Scott
    • , George M. Church
    •  & Feng Zhang
  2. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

    • Silvana Konermann
    • , Mark D. Brigham
    • , Alexandro E. Trevino
    • , Patrick D. Hsu
    • , Matthias Heidenreich
    • , Le Cong
    • , Randall J. Platt
    • , David A. Scott
    •  & Feng Zhang
  3. School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA

    • Mark D. Brigham
  4. Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA

    • Patrick D. Hsu
  5. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Le Cong
  6. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • George M. Church

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Contributions

S.K., M.D.B. and F.Z. developed the concept and designed experiments. S.K., M.D.B., A.E.T., P.D.H., M.H. and D.A.S. carried out LITE-related experiments and analysed data. L.C. and P.D.H. developed the SID4X effector domain, the P11-targeting TALEs and the abscisic acid induction system. R.J.P. developed the Cas9 transcription activator and repressor systems. S.K., A.E.T., M.D.B., P.D.H. and F.Z. wrote the manuscript with input from M.H., L.C. and G.M.C.

Competing interests

A patent application has been filed relating to this work, and the authors plan on making the reagents widely available to the academic community through Addgene and to provide software tools via the Zhang lab website (http://www.genome-engineering.org).

Corresponding author

Correspondence to Feng Zhang.

Extended data

Supplementary information

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  1. 1.

    Supplementary Information

    This file contains Supplementary Methods, a Supplementary Discussion, Supplementary Tables 1–10, lists of the Supplementary Sequences and the Photostimulation Hardware Control Scripts and Supplementary references.

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DOI

https://doi.org/10.1038/nature12466

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