J. Keith Joung, MD, PhD

Joung Laboratory

The Joung laboratory utilizes engineered zinc finger, transcription activator-like effector (TALE), and RNA-guided CRISPR/Cas-based systems to create sequence expression alterations in living cells and organisms.


Program Affiliations

Research Resources

J. Keith Joung, MD, PhD
Professor of Pathology
Harvard Medical School

Associate Chief for Research
The Jim and Ann Orr MGH Research Scholar
Massachusetts General Hospital

Research Summary

The Joung laboratory is developing strategies to reprogram the genome and epigenome of living cells to better understand biology and treat disease. We have developed and optimized molecular tools for customized genome editing that enable scientists to alter the DNA sequence of a living cell—from fruit flies to humans—with great precision. These technologies are based on designer DNA-binding and RNA-guided proteins engineered to recognize and cleave specific genomic sequences. We also use these targeting methodologies to direct various other regulatory elements to enable activation, repression, or alteration of histone modifications of specific genes. These tools have many potential uses in cancer research and may one day lead to more efficient gene therapy capable of correcting disease-related mutations in human cells.


Read more about the Joung Lab from Pathology Basic Science Research Brochure.

Read the Bardeesy Lab's Annual Report in Full


Pathology research report

Group Members

Principal Investigator
J. Keith Joung
The Jim and Ann Orr MGH Research Scholar,
Associate Chief of Pathology, Research

Lab Members

  • James Angstman – Graduate student, Harvard MCO program
  • Maggie Bobbin - Research Fellow
  • Rebecca Cottman – Graduate Student, Harvard BBS program
  • Stacy Francis – Senior Research Technologist
  • Jason Gehrke – Graduate Student, Harvard MCO program
  • Jingyi Gong - HMS/HST Medical Student
  • Benjamin Kleinstiver – Post-doctoral Fellow
  • Nhu Nguyen – Research Technician I
  • Michelle Prew – Research Technician I
  • Ved Topkar - Undergraduate Student, Harvard College
  • Shengdar Tsai – Post-doctoral Fellow
  • Moira Welch - Research Technician I


Research Projects


 The Joung Laboratory develops technologies for genome and epigenome engineering of living cells and organisms using engineered zinc finger, transcription activator-like effector (TALE), and RNA-guided CRISPR-Cas9-based systems and explores their applications for biological research and gene therapy.

Genome Editing Using Targeted Nucleases

Genome editing technology was recently named runner-up for "Breakthrough of the Year" for 2012 and 2013 bySciencemagazine and "Method of the Year" for 2011 byNature Methods. We have previously invented two rapid, robust, and publicly available methods for engineering ZFNs known as OPEN (Oligomerized Pool Engineering; Maeder et al.,Mol Cell2008) and CoDA (Context-Dependent Assembly; Sander et al.,Nat Methods2011). In addition, we have also developed and optimized methods for engineering TALENs including an automated, high-throughput method known as FLASH (Fast Ligation-based Automated Solid-phase High-throughput) assembly (Reyon et al.,Nat Biotechnol.2012). We have also recently described reagents that enable the rapid construction of CRISPR-Cas9 nucleases(Hwang et al.,Nat Biotechnol.2013).

Much of our recent work with genome-editing nucleases has focused on CRISPR-Cas9. We and our collaborators were the first to demonstrate that these nucleases can functionin vivo(Hwang & Fu et al.,Nat Biotechnol. 2013), modifying endogenous genes in zebrafish and the first to show that they can induce significant off-target mutations in human cells (Fu et al.,Nat Biotechnol.2013). To improve the specificities of these nucleases, we have developed two platforms that show greatly reduced off-target effects: one based on the use of truncated guide RNAs (Fu & Sander et al.,Nat Biotechnol.2014) and the other in which we engineered dimerization-dependent CRISPR-Cas9 nucleases (Tsai et al.,Nat Biotechnol. 2014). We recently developed GUIDE-seq, an unbiased, genome-wide method for sensitive detection of CRISPR-Cas9-induced off-target mutations (Tsaiet al.,Nat Biotechnol. 2015). We have also evolved Cas9 variants with novel DNA binding specificities, thereby broadening the targeting range and applications of this platform (Kleinstiver et al.,Nature2015).

Epigenome Editing Using Targeted Transcription Factors

We have recently demonstrated that the TALE and CRISPR RGN platforms can also be utilized to create artificial customizable transcription factors that can robustly alter expression of endogenous human genes (Maeder et al.,Nat Methods2013a; Maeder et al.,Nat Methods2013b). In addition, we have collaborated with the group of Brad Bernstein to develop fusions of the histone demethylase LSD1 with TALE domains that can induce targeted histone alterations at endogenous human enhancers (Mendenhall et al.,Nat Biotechnol. 2013). Finally, we have also developed fusions of engineered TALE domains with the catalytic domain of the TET1 enzyme, enabling the targeted demethylation of CpGs in human cells (Maeder et al.,Nat Biotechnol.2013). We are exploring the use of these and other proteins in both a directed fashion as well as with combinatorial libraries to induce specific phenotypes and cellular states in human cells.

For more information about research concepts, co-authors, and to see a timeline, see Dr. Joung's research profile at the Harvard Clinical and Translational Science Center.


Research Positions

Find information by visiting the Harvard Medical School Molecular Genetic Pathology Training Program, and other Pathology fellowship programs at the Massachusetts General Hospital.


Bibliography of J. Keith Joung via PubMed 

Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT, Zheng Z, Gonzales AP, Li Z, Peterson RT, Yeh JR, Aryee MJ,Joung JK. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature. 2015 Jul 23; 523(7561): 481-5.

Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ,Joung JK. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases.Nat Biotechnol. 2015 Feb; 33(2): 187-97.

Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ,Joung JK. Dimeric CRISPR RNA-guided FokI nucleases for high specific genome editing.Nat Biotechnol., 2014 Jun;32(6): 569-7.

Sander JD,Joung JK. CRISPR-Cas systems for editing, regulating and targeting genomes.Nat Biotechnol., 2014 Apr;32(4):347-55. Review.

Fu Y, Sander JD, Reyon D, Cascio V,Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs.Nat Biotechnol., 2014 Mar;32(3):279-84.

Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR,Joung JK. Efficient genome editing in zebrafish using a CRISPR-Cas system.Nat Biotechnol., 2013 Mar;31(3):227-9.


Contact Us

Joung Laboratory

Massachusetts General Hospital

149 13th Street, 6th Floor Charlestown, MA 02129
  • Phone: 617-726-9462
  • Fax: 617-726-5684

Email: jjoung@partners.org

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