Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Multidimensional chemical control of CRISPR–Cas9


Cas9-based technologies have transformed genome engineering and the interrogation of genomic functions, but methods to control such technologies across numerous dimensions—including dose, time, specificity, and mutually exclusive modulation of multiple genes—are still lacking. We conferred such multidimensional controls to diverse Cas9 systems by leveraging small-molecule-regulated protein degron domains. Application of our strategy to both Cas9-mediated genome editing and transcriptional activities opens new avenues for systematic genome interrogation.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Multidimensional 'chemical' control of endogenous transcript levels.
Figure 2: Dose and temporal regulation of DD.SpCas9.DD-mediated insertion/deletion (indel) formation.


  1. Doudna, J.A. & Charpentier, E. Science 346, 1258096 (2014).

    Article  Google Scholar 

  2. Hsu, P.D., Lander, E.S. & Zhang, F. Cell 157, 1262–1278 (2014).

    Article  CAS  Google Scholar 

  3. Gantz, V.M. & Bier, E. BioEssays 38, 50–63 (2016).

    Article  Google Scholar 

  4. Chen, B. et al. Cell 155, 1479–1491 (2013).

    Article  CAS  Google Scholar 

  5. Hilton, I.B. et al. Nat. Biotechnol. 33, 510–517 (2015).

    Article  CAS  Google Scholar 

  6. Dominguez, A.A., Lim, W.A. & Qi, L.S. Nat. Rev. Mol. Cell Biol. 17, 5–15 (2016).

    Article  CAS  Google Scholar 

  7. Nuñez, J.K., Harrington, L.B. & Doudna, J.A. ACS Chem. Biol. 11, 681–688 (2016).

    Article  Google Scholar 

  8. Nguyen, D.P. et al. Nat. Commun. 7, 12009 (2016).

    Article  CAS  Google Scholar 

  9. Oakes, B.L. et al. Nat. Biotechnol. 34, 646–651 (2016).

    Article  CAS  Google Scholar 

  10. Iwamoto, M., Björklund, T., Lundberg, C., Kirik, D. & Wandless, T.J. Chem. Biol. 17, 981–988 (2010).

    Article  CAS  Google Scholar 

  11. Miyazaki, Y., Imoto, H., Chen, L.C. & Wandless, T.J. J. Am. Chem. Soc. 134, 3942–3945 (2012).

    Article  CAS  Google Scholar 

  12. Banaszynski, L.A., Chen, L.C., Maynard-Smith, L.A., Ooi, A.G. & Wandless, T.J. Cell 126, 995–1004 (2006).

    Article  CAS  Google Scholar 

  13. Moore, C.L. et al. ACS Chem. Biol. 11, 200–210 (2016).

    Article  CAS  Google Scholar 

  14. Shoulders, M.D., Ryno, L.M., Cooley, C.B., Kelly, J.W. & Wiseman, R.L. J. Am. Chem. Soc. 135, 8129–8132 (2013).

    Article  CAS  Google Scholar 

  15. Perez-Pinera, P. et al. Nat. Methods 10, 973–976 (2013).

    Article  CAS  Google Scholar 

  16. Balboa, D. et al. Stem Cell Rep. 5, 448–459 (2015).

    Article  CAS  Google Scholar 

  17. Konermann, S. et al. Nature 517, 583–588 (2015).

    Article  CAS  Google Scholar 

  18. Zalatan, J.G. et al. Cell 160, 339–350 (2015).

    Article  CAS  Google Scholar 

  19. Zetsche, B., Volz, S.E. & Zhang, F. Nat. Biotechnol. 33, 139–142 (2015).

    Article  CAS  Google Scholar 

  20. Nishimasu, H. et al. Cell 162, 1113–1126 (2015).

    Article  CAS  Google Scholar 

  21. Esvelt, K.M., Smidler, A.L., Catteruccia, F. & Church, G.M. eLife 3, e03401 (2014).

    Article  Google Scholar 

  22. Davis, K.M., Pattanayak, V., Thompson, D.B., Zuris, J.A. & Liu, D.R. Nat. Chem. Biol. 11, 316–318 (2015).

    Article  CAS  Google Scholar 

  23. Tsai, S.Q. & Joung, J.K. Nat. Rev. Genet. 17, 300–312 (2016).

    Article  CAS  Google Scholar 

  24. Zuris, J.A. et al. Nat. Biotechnol. 33, 73–80 (2015).

    Article  CAS  Google Scholar 

  25. Kim, S., Kim, D., Cho, S.W., Kim, J. & Kim, J.S. Genome Res. 24, 1012–1019 (2014).

    Article  CAS  Google Scholar 

  26. Fu, Y. et al. Nat. Biotechnol. 31, 822–826 (2013).

    Article  CAS  Google Scholar 

  27. Schneeberger, K. Nat. Rev. Genet. 15, 662–676 (2014).

    Article  CAS  Google Scholar 

  28. Hsu, P.D. et al. Nat. Biotechnol. 31, 827–832 (2013).

    Article  CAS  Google Scholar 

  29. Ran, F.A. et al. Nat. Protoc. 8, 2281–2308 (2013).

    Article  CAS  Google Scholar 

Download references


This work was supported by the NIH (Director's New Innovator Award 1DP2GM119162 to M.D.S.; grant 1R21AI126239-01 to A.C.), the Edward Mallinckrodt, Jr. Foundation (Faculty Scholar Award to M.D.S.), and the Burroughs Wellcome Fund (Career Award at the Scientific Interface to A.C.). C.L.M. acknowledges the National Science Foundation for a Graduate Research Fellowship. We are grateful to B. Harvey (NIDA) and to I. Slaymaker, F.A. Ran, and B. Wagner (Broad Institute) for helpful discussions. J.K. Joung (Harvard Medical School, Boston, Massachusetts, USA) provided U2OS.eGFP-PEST cells. This work is dedicated to Professor Stuart L. Schreiber on the occasion of his 60th birthday.

Author information

Authors and Affiliations



B.M., C.L.M., B.Z., M.D.S., and A.C. planned research and analyzed data; B.M., C.L.M., B.Z., F.Z., M.D.S., and A.C. designed experiments; B.M., C.L.M., B.Z., and S.E.V. performed experiments; B.M., C.L.M., M.D.S., and A.C. wrote the manuscript; M.D.S. and A.C. supervised research.

Corresponding authors

Correspondence to Matthew D Shoulders or Amit Choudhary.

Ethics declarations

Competing interests

Broad Institute has filed a patent application including work from this paper.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Tables 1–5, Supplementary Figures 1–13 and Supplementary Note. (PDF 3762 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Maji, B., Moore, C., Zetsche, B. et al. Multidimensional chemical control of CRISPR–Cas9. Nat Chem Biol 13, 9–11 (2017).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing