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Maeder ML, Stefanidakis M, Wilson CJ, Baral R, Barrera LA, Bounoutas GS, Bumcrot D, Chao H, Ciulla DM, DaSilva JA, Dass A, Dhanapal V, Fennell TJ, Friedland AE, Giannoukos G, Gloskowski SW, Glucksmann A, Gotta GM, Jayaram H, Haskett SJ, Hopkins B, Horng JE, Joshi S, Marco E, Mepani R, Reyon D, Ta T, Tabbaa DG, Samuelsson SJ, Shen S, Skor MN, Stetkiewicz P, Wang T, Yudkoff C, Myer VE, Albright CF, Jiang H. Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10. Nat Med 2019; 25:229-233. [DOI: 10.1038/s41591-018-0327-9] [Citation(s) in RCA: 338] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/07/2018] [Indexed: 12/18/2022]
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Tycko J, Barrera LA, Huston NC, Friedland AE, Wu X, Gootenberg JS, Abudayyeh OO, Myer VE, Wilson CJ, Hsu PD. Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells. Nat Commun 2018; 9:2962. [PMID: 30054474 PMCID: PMC6063963 DOI: 10.1038/s41467-018-05391-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022] Open
Abstract
Therapeutic genome editing with Staphylococcus aureus Cas9 (SaCas9) requires a rigorous understanding of its potential off-target activity in the human genome. Here we report a high-throughput screening approach to measure SaCas9 genome editing variation in human cells across a large repertoire of 88,692 single guide RNAs (sgRNAs) paired with matched or mismatched target sites in a synthetic cassette. We incorporate randomized barcodes that enable whitelisting of correctly synthesized molecules for further downstream analysis, in order to circumvent the limitation of oligonucleotide synthesis errors. We find SaCas9 sgRNAs with 21-mer or 22-mer spacer sequences are generally more active, although high efficiency 20-mer spacers are markedly less tolerant of mismatches. Using this dataset, we developed an SaCas9 specificity model that performs robustly in ranking off-target sites. The barcoded pairwise library screen enabled high-fidelity recovery of guide-target relationships, providing a scalable framework for the investigation of CRISPR enzyme properties and general nucleic acid interactions.
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Affiliation(s)
- Josh Tycko
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Luis A Barrera
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA
- Arrakis Therapeutics, 35 Gatehouse Dr., Waltham, MA, 02451, USA
| | - Nicholas C Huston
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
| | | | - Xuebing Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | | | - Omar O Abudayyeh
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Vic E Myer
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA
| | | | - Patrick D Hsu
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA.
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
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Mann FG, Van Nostrand EL, Friedland AE, Liu X, Kim SK. Deactivation of the GATA Transcription Factor ELT-2 Is a Major Driver of Normal Aging in C. elegans. PLoS Genet 2016; 12:e1005956. [PMID: 27070429 PMCID: PMC4829211 DOI: 10.1371/journal.pgen.1005956] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 03/04/2016] [Indexed: 02/07/2023] Open
Abstract
To understand the molecular processes underlying aging, we screened modENCODE ChIP-seq data to identify transcription factors that bind to age-regulated genes in C. elegans. The most significant hit was the GATA transcription factor encoded by elt-2, which is responsible for inducing expression of intestinal genes during embryogenesis. Expression of ELT-2 decreases during aging, beginning in middle age. We identified genes regulated by ELT-2 in the intestine during embryogenesis, and then showed that these developmental genes markedly decrease in expression as worms grow old. Overexpression of elt-2 extends lifespan and slows the rate of gene expression changes that occur during normal aging. Thus, our results identify the developmental regulator ELT-2 as a major driver of normal aging in C. elegans.
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Affiliation(s)
- Frederick G Mann
- Departments of Genetics and Developmental Biology, Stanford University Medical Center, Stanford, California, United States of America
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Ari E Friedland
- Editas Medicine, Cambridge, Massachusetts, United States of America
| | - Xiao Liu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Stuart K Kim
- Departments of Genetics and Developmental Biology, Stanford University Medical Center, Stanford, California, United States of America
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Friedland AE, Baral R, Singhal P, Loveluck K, Shen S, Sanchez M, Marco E, Gotta GM, Maeder ML, Kennedy EM, Kornepati AVR, Sousa A, Collins MA, Jayaram H, Cullen BR, Bumcrot D. Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications. Genome Biol 2015; 16:257. [PMID: 26596280 PMCID: PMC4657203 DOI: 10.1186/s13059-015-0817-8] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/28/2015] [Indexed: 11/24/2022] Open
Abstract
Background CRISPR-Cas systems have been broadly embraced as effective tools for genome engineering applications, with most studies to date utilizing the Streptococcus pyogenes Cas9. Here we characterize and manipulate the smaller, 1053 amino acid nuclease Staphylococcus aureus Cas9. Results We find that the S. aureus Cas9 recognizes an NNGRRT protospacer adjacent motif (PAM) and cleaves target DNA at high efficiency with a variety of guide RNA (gRNA) spacer lengths. When directed against genomic targets with mutually permissive NGGRRT PAMs, the S. pyogenes Cas9 and S. aureus Cas9 yield indels at comparable rates. We additionally show D10A and N580A paired nickase activity with S. aureus Cas9, and we further package it with two gRNAs in a single functional adeno-associated virus (AAV) vector. Finally, we assess comparative S. pyogenes and S. aureus Cas9 specificity using GUIDE-seq. Conclusion Our results reveal an S. aureus Cas9 that is effective for a variety of genome engineering purposes, including paired nickase approaches and all-in-one delivery of Cas9 and multiple gRNA expression cassettes with AAV vectors. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0817-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Shen Shen
- Editas Medicine, Cambridge, MA, 02142, USA
| | | | | | | | | | - Edward M Kennedy
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Anand V R Kornepati
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | | | | | | | - Bryan R Cullen
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, North Carolina, 27710, USA
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Maeder ML, Shen S, Burnight ER, Gloskowski S, Mepani R, Friedland AE, Jayaram H, Gotta G, Tucker BA, Bumcrot D. 687. Therapeutic Correction of an LCA-Causing Splice Defect in the CEP290 Gene by CRISPR/Cas-Mediated Genome Editing. Mol Ther 2015. [DOI: 10.1016/s1525-0016(16)34296-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Friedland AE, Sousa A, Collins M, Maeder ML, Jayaram H, Welstead GG, Gloskowski S, Bumcrot D. 561. Staphyloccocus aureus Cas9: An Alternative Cas9 for Genome Editing Applications. Mol Ther 2015. [DOI: 10.1016/s1525-0016(16)34170-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Abstract
The clustered, regularly interspaced, short, palindromic repeat (CRISPR)-associated (CAS) nuclease Cas9 has been used in many organisms to generate specific mutations and transgene insertions. Here we describe a method using the S. pyogenes Cas9 in C. elegans that provides a convenient and effective approach for making heritable changes to the worm genome.
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Affiliation(s)
- John A Calarco
- FAS Center for Systems Biology, Harvard University, Northwest Lab Building, 52 Oxford Street, B227.80, Cambridge, MA, 02138, USA.
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Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 2013; 10:741-3. [PMID: 23817069 PMCID: PMC3822328 DOI: 10.1038/nmeth.2532] [Citation(s) in RCA: 649] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/30/2013] [Indexed: 12/12/2022]
Abstract
We report the use of clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated endonuclease Cas9 to target genomic sequences in the Caenorhabditis elegans germ line using single-guide RNAs that are expressed from a U6 small nuclear RNA promoter. Our results demonstrate that targeted, heritable genetic alterations can be achieved in C. elegans, providing a convenient and effective approach for generating loss-of-function mutants.
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Affiliation(s)
| | - Yonatan B. Tzur
- Department of Genetics, Harvard Medical School, Boston MA 02115
| | - Kevin M. Esvelt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge MA 02138
| | | | - George M. Church
- Department of Genetics, Harvard Medical School, Boston MA 02115
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge MA 02138
| | - John A. Calarco
- FAS Center for Systems Biology, Harvard University, Cambridge MA 02138
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Abstract
Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers.
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Affiliation(s)
- Ari E Friedland
- Howard Hughes Medical Institute, Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
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