Joung Laboratory

Overview

The Joung laboratory is developing strategies to reprogram the genome and epigenome of living cells to better understand biology and treat disease. We have created 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. We also use these targeting methodologies to enable activation, repression, or alteration of histone modifications of specific genes. These tools have many potential research uses and have promise for developing therapeutics.

Research Projects

Genome Editing Using Targeted Nucleases and Base Editors

Genome editing technology using CRISPR-Cas9 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 press2018). In addition, we have engineered “high-fidelity” Cas9 variants (Kleinstiver & Pattanayak et al., Nature 2016) and variants with novel DNA binding specificities, (Kleinstiver et al., Nature 2015; Kleinstiver et al., Nat Biotechnol. 2015; Kleinstiver et al., Nat Biotechnol. 2019). More recently, we have developed a novel CRISPR base editor architecture that shows improved precision and reduced off-target effects (Gehrke et al., Nat Biotechnol. 2018) and identified novel RNA off-target effects of CRISPR cytosine and adenine base editors (Grünewald et al., Nature 2019; Grünewald et al., Nat Biotechnol. 2019).

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).

Selected Publications

Grünewald J, Zhou R, Iyer S, Lareau CA, Garcia SP, Aryee MJ, Joung JK. CRISPR DNA base editors with reduced RNA off- target and self-editing activities. Nat Biotechnol. 2019 Sep; 37(9): 1041-1048.

Grünewald J, Zhou R, Garcia SP, Iyer S, Lareau CA, Aryee MJ, Joung JK. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature. 2019 May; 569(7756): 433-437.

Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarfò I, Maus MV, Pinello L, Aryee MJ, Joung JK. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol. 2019 Mar; 37(3): 276-282.

Akcakaya P, Bobbin ML, Guo JA, Malag- on-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 Sep; 561(7723): 416-419.

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 Nov; 36(10): 977-982.

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;14(6):607-614.