Explore This Lab


The Joung laboratory is developing strategies to reprogram the genomes and epigenomes of living cells to better understand biology and treat disease. We have developed and continue to optimize molecular tools for customized genome editing including engineered zinc finger, transcription activator-like effector (TALE), and RNA-guided CRISPR-Cas-based systems. These platforms 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 lead to more efficient gene therapy capable of correcting disease-related mutations in human cells.

Research Projects

Genome Editing Using Targeted Nucleases and Base Editors

Genome editing technology using CRISPR-Cas nucleases was named “Breakthrough of the Year” for 2015 by Science magazine. We and our collaborators were the first to demonstrate that these nucleases can function in vivo (Hwang & Fu et al., Nat Biotechnol. 2013) to modify endogenous genes in zebrafish embryos and the first to show that they can induce significant off-target mutations in human cells (Fu et al., Nat Biotechnol. 2013). We have led the field in development of unbiased, genome-wide strategies for profiling the specificities of CRISPR-Cas nucleases including the widely used cell-based GUIDE-seq method (Tsai et al., Nat Biotechnol. 2015) and the in vitro CIRCLE-seq method (Tsai et al., Nat Biotechnol. 2017). We have recently shown that CIRCLE-seq can be used to identify Cas9-induced off-targets in vivo (Akcakaya & Bobbin et al., Nature, in press). In addition, we have engineered “high-fidelity” Cas9 variants (Kleinstiver & Pattanayak et al., Nature 2016) and Cas9 variants with novel DNA binding specificities (Kleinstiver et al., Nature 2015; Kleinstiver et al., Nat Biotechnol. 2015). More recently, we have developed a novel base editor architecture that shows improved precision and reduced off-target effects (Gehrke et al., Nat Biotechnol. 2018).

Epigenetic Editing Using Targeted Transcription Factors

We have also performed work showing that the Transcription Activator-Like Effector (TALE) and CRISPR-Cas platforms can also be utilized to create artificial transcription factors that can robustly alter expression of endogenous human genes (Maeder et al., Nat Methods 2013a; Maeder et al., Nat Methods 2013b). 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). More recently, we have shown that the CRISPR-Cpf1(Cas12a) platform can be modified to engineer robust transcriptional activators that can efficiently increase endogenous gene expression in human cells (Tak et al., Nat Methods 2017).

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.

Group Members

Meet our research team:

  • J. Keith Joung, MD, PhD
  • James Angstman 
  • Maggie Bobbin, PhD 
  • Peter Cabeceiras 
  • Rebecca Cottman 
  • Stacy Francis 
  • Julian Grunewald, MD 
  • Joy Horng 
  • Jonathan Hsu 
  • Jay Jun
  • Daniel Kim
  • Benjamin Kleinstiver, PhD 
  • Ibrahim Kurt 
  • Vikram Pattanayak, MD, PhD 
  • Nicholas Perry
  • Karl Petri, MD 
  • Kanae Sasaki 
  • Alexander Sousa 
  • Esther Tak, PhD 
  • Russell Walton 
  • Ronghao Zhou

Selected Publications

Akcakaya P, Bobbin ML, Guo JA, Malagon-Lopez J, Clement K, Garcia SP, Fellows MD, Porritt MJ, Firth MA, Carreras A, Baccega T, Seeliger F, Bjursell M, Tsai SQ, Nguyen NT, Nitsch R, Mayr LM, Pinello L, Bohlooly-Y M, Aryee MJ, Maresca M, Joung JK. In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature 2018, in press.

Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J, Bauer DE, Pinello L, Joung JK. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol. 2018 Jul 30.

Tak YE, Kleinstiver BP, Nuñez JK, Hsu JY, Horng JE, Gong J, Weissman JS, Joung JK. Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors. Nat Methods. 2017; 14(12):1163-1166.

Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK. CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nat Methods. 2017 Jun;14(6):607-614.

Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat Biotechnol. 2016 Aug;34(8):869-74.

Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature. 2016 Jan 28; 529(7587): 490-5.