CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes

Tarasava, Katia; Oh, Eun Joong; Eckert, Carrie A.; Gill, Ryan T.

doi:10.1002/biot.201700586

CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes

Journal Article · Tue Jun 19 00:00:00 EDT 2018 · Biotechnology Journal

DOI:https://doi.org/10.1002/biot.201700586· OSTI ID:1458905

Tarasava, Katia ^[1]; Oh, Eun Joong ^[1]; Eckert, Carrie A. ^[2]; Gill, Ryan T. ^[1]

Univ. of Colorado, Boulder, CO (United States)
Univ. of Colorado, Boulder, CO (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)

In recent years CRISPR-Cas technologies have revolutionized microbial engineering approaches. Genome editing and non-editing applications of various CRISPR-Cas systems have expanded the throughput and scale of engineering efforts, as well as opened up new avenues for manipulating genomes of non-model organisms. As we expand the range of organisms used for biotechnological applications, we need to develop better, more versatile tools for manipulation of these systems. Here we summarize the current advances in microbial gene editing using CRISPR-Cas based tools, and highlight state-of-the-art methods for high-throughput, efficient genome-scale engineering in model organisms Escherichia coli and Saccharomyces cerevisiae. We also review non-editing CRISPR-Cas applications available for gene expression manipulation, epigenetic remodeling, RNA editing, labeling and synthetic gene circuit design. Finally, we point out the areas of research that need further development in order to expand the range of applications and increase the utility of these new methods.

View Accepted Manuscript (DOE)

Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC36-08GO28308

OSTI ID:: 1458905

Alternate ID(s):: OSTI ID: 1557854

Report Number(s):: NREL/JA-2700-71862

Journal Information:: Biotechnology Journal, Journal Name: Biotechnology Journal Journal Issue: 9 Vol. 13; ISSN 1860-6768

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

References (192)

CRISPR-based genome editing and expression control systems in Clostridium acetobutylicum and Clostridium beijerinckii Li, Qi; Chen, Jun; Minton, Nigel P. Biotechnology Journal, Vol. 11, Issue 7 https://doi.org/10.1002/biot.201600053	journal	June 2016
Rapid and marker-free refactoring of xylose-fermenting yeast strains with Cas9/CRISPR: Rapid and Marker-Free Cas9/CRISPR Refactoring Tsai, Ching-Sung; Kong, In Iok; Lesmana, Anastashia Biotechnology and Bioengineering, Vol. 112, Issue 11 https://doi.org/10.1002/bit.25632	journal	June 2015
Current and future prospects for CRISPR-based tools in bacteria: CRISPR-Based Tools in Bacteria Luo, Michelle L.; Leenay, Ryan T.; Beisel, Chase L. Biotechnology and Bioengineering, Vol. 113, Issue 5 https://doi.org/10.1002/bit.25851	journal	October 2015
Gene transcription repression in Clostridium beijerinckii using CRISPR-dCas9 : Gene Transcription in Wang, Yi; Zhang, Zhong-Tian; Seo, Seung-Oh Biotechnology and Bioengineering, Vol. 113, Issue 12 https://doi.org/10.1002/bit.26020	journal	June 2016
Highly efficient editing of the actinorhodin polyketide chain length factor gene in Streptomyces coelicolor M145 using CRISPR/Cas9-CodA(sm) combined system Zeng, Hu; Wen, Shishi; Xu, Wei Applied Microbiology and Biotechnology, Vol. 99, Issue 24 https://doi.org/10.1007/s00253-015-6931-4	journal	August 2015
A novel process for obtaining pinosylvin using combinatorial bioengineering in Escherichia coli Liang, Jing-long; Guo, Li-qiong; Lin, Jun-fang World Journal of Microbiology and Biotechnology, Vol. 32, Issue 6 https://doi.org/10.1007/s11274-016-2062-z	journal	April 2016
Next generation sequencing technology: Advances and applications Buermans, H. P. J.; den Dunnen, J. T. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1842, Issue 10 https://doi.org/10.1016/j.bbadis.2014.06.015	journal	October 2014
CRISPR technologies for bacterial systems: Current achievements and future directions Choi, Kyeong Rok; Lee, Sang Yup Biotechnology Advances, Vol. 34, Issue 7 https://doi.org/10.1016/j.biotechadv.2016.08.002	journal	November 2016
RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex Hale, Caryn R.; Zhao, Peng; Olson, Sara Cell, Vol. 139, Issue 5 https://doi.org/10.1016/j.cell.2009.07.040	journal	November 2009
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression Qi, Lei S.; Larson, Matthew H.; Gilbert, Luke A. Cell, Vol. 152, Issue 5, p. 1173-1183 https://doi.org/10.1016/j.cell.2013.02.022	journal	February 2013
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes Gilbert, Luke A.; Larson, Matthew H.; Morsut, Leonardo Cell, Vol. 154, Issue 2, p. 442-451 https://doi.org/10.1016/j.cell.2013.06.044	journal	July 2013
Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity Ran, F. Ann; Hsu, Patrick D.; Lin, Chie-Yu Cell, Vol. 154, Issue 6, p. 1380-1389 https://doi.org/10.1016/j.cell.2013.08.021	journal	September 2013
Development and Applications of CRISPR-Cas9 for Genome Engineering Hsu, Patrick D.; Lander, Eric S.; Zhang, Feng Cell, Vol. 157, Issue 6 https://doi.org/10.1016/j.cell.2014.05.010	journal	June 2014
Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation Gilbert, Luke A.; Horlbeck, Max A.; Adamson, Britt Cell, Vol. 159, Issue 3 https://doi.org/10.1016/j.cell.2014.09.029	journal	October 2014
Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds Zalatan, Jesse G.; Lee, Michael E.; Almeida, Ricardo Cell, Vol. 160, Issue 1-2 https://doi.org/10.1016/j.cell.2014.11.052	journal	January 2015
Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity Samai, Poulami; Pyenson, Nora; Jiang, Wenyan Cell, Vol. 161, Issue 5 https://doi.org/10.1016/j.cell.2015.04.027	journal	May 2015
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System Zetsche, Bernd; Gootenberg, Jonathan S.; Abudayyeh, Omar O. Cell, Vol. 163, Issue 3, p. 759-771 https://doi.org/10.1016/j.cell.2015.09.038	journal	October 2015
Programmable RNA Tracking in Live Cells with CRISPR/Cas9 Nelles, David A.; Fang, Mark Y.; O’Connell, Mitchell R. Cell, Vol. 165, Issue 2 https://doi.org/10.1016/j.cell.2016.02.054	journal	April 2016
Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA Yamano, Takashi; Nishimasu, Hiroshi; Zetsche, Bernd Cell, Vol. 165, Issue 4 https://doi.org/10.1016/j.cell.2016.04.003	journal	May 2016
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria Peters, Jason M.; Colavin, Alexandre; Shi, Handuo Cell, Vol. 165, Issue 6 https://doi.org/10.1016/j.cell.2016.05.003	journal	June 2016
CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes Komor, Alexis C.; Badran, Ahmed H.; Liu, David R. Cell, Vol. 168, Issue 1-2 https://doi.org/10.1016/j.cell.2016.10.044	journal	January 2017
Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9 Batra, Ranjan; Nelles, David A.; Pirie, Elaine Cell, Vol. 170, Issue 5 https://doi.org/10.1016/j.cell.2017.07.010	journal	August 2017
Markerless chromosomal gene deletion in Clostridium beijerinckii using CRISPR/Cas9 system Wang, Yi; Zhang, Zhong-Tian; Seo, Seung-Oh Journal of Biotechnology, Vol. 200 https://doi.org/10.1016/j.jbiotec.2015.02.005	journal	April 2015
CRISPR–Cas system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains Stovicek, Vratislav; Borodina, Irina; Forster, Jochen Metabolic Engineering Communications, Vol. 2 https://doi.org/10.1016/j.meteno.2015.03.001	journal	December 2015
Diversity, classification and evolution of CRISPR-Cas systems Koonin, Eugene V.; Makarova, Kira S.; Zhang, Feng Current Opinion in Microbiology, Vol. 37 https://doi.org/10.1016/j.mib.2017.05.008	journal	June 2017
CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3 Westra, Edze R.; van Erp, Paul B. G.; Künne, Tim Molecular Cell, Vol. 46, Issue 5 https://doi.org/10.1016/j.molcel.2012.03.018	journal	June 2012
Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis Zhang, Yan; Heidrich, Nadja; Ampattu, Biju Joseph Molecular Cell, Vol. 50, Issue 4 https://doi.org/10.1016/j.molcel.2013.05.001	journal	May 2013
Programmable RNA Shredding by the Type III-A CRISPR-Cas System of Streptococcus thermophilus Tamulaitis, Gintautas; Kazlauskiene, Migle; Manakova, Elena Molecular Cell, Vol. 56, Issue 4 https://doi.org/10.1016/j.molcel.2014.09.027	journal	November 2014
RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus Staals, Raymond H. J.; Zhu, Yifan; Taylor, David W. Molecular Cell, Vol. 56, Issue 4 https://doi.org/10.1016/j.molcel.2014.10.005	journal	November 2014
Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems Leenay, Ryan T.; Maksimchuk, Kenneth R.; Slotkowski, Rebecca A. Molecular Cell, Vol. 62, Issue 1 https://doi.org/10.1016/j.molcel.2016.02.031	journal	April 2016
ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering Gaj, Thomas; Gersbach, Charles A.; Barbas, Carlos F. Trends in Biotechnology, Vol. 31, Issue 7, p. 397-405 https://doi.org/10.1016/j.tibtech.2013.04.004	journal	July 2013
Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology Jusiak, Barbara; Cleto, Sara; Perez-Piñera, Pablo Trends in Biotechnology, Vol. 34, Issue 7 https://doi.org/10.1016/j.tibtech.2015.12.014	journal	July 2016
Beyond Native Cas9: Manipulating Genomic Information and Function Mitsunobu, Hitoshi; Teramoto, Jun; Nishida, Keiji Trends in Biotechnology, Vol. 35, Issue 10 https://doi.org/10.1016/j.tibtech.2017.06.004	journal	October 2017
Advances in Industrial Biotechnology Using CRISPR-Cas Systems Donohoue, Paul D.; Barrangou, Rodolphe; May, Andrew P. Trends in Biotechnology, Vol. 36, Issue 2 https://doi.org/10.1016/j.tibtech.2017.07.007	journal	February 2018
Type III CRISPR-Cas Immunity: Major Differences Brushed Aside Tamulaitis, Gintautas; Venclovas, Česlovas; Siksnys, Virginijus Trends in Microbiology, Vol. 25, Issue 1 https://doi.org/10.1016/j.tim.2016.09.012	journal	January 2017
Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae Jakočiūnas, Tadas; Bonde, Ida; Herrgård, Markus Metabolic Engineering, Vol. 28 https://doi.org/10.1016/j.ymben.2015.01.008	journal	March 2015
Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P(3HB-co-4HB) biosynthesis Lv, Li; Ren, Yi-Lin; Chen, Jin-Chun Metabolic Engineering, Vol. 29 https://doi.org/10.1016/j.ymben.2015.03.013	journal	May 2015
Metabolic engineering of cyanobacteria for photosynthetic 3-hydroxypropionic acid production from CO2 using Synechococcus elongatus PCC 7942 Lan, Ethan I.; Chuang, Derrick S.; Shen, Claire R. Metabolic Engineering, Vol. 31 https://doi.org/10.1016/j.ymben.2015.08.002	journal	September 2015
CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002 Gordon, Gina C.; Korosh, Travis C.; Cameron, Jeffrey C. Metabolic Engineering, Vol. 38 https://doi.org/10.1016/j.ymben.2016.07.007	journal	November 2016
CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production Kim, Seong Keun; Han, Gui Hwan; Seong, Wonjae Metabolic Engineering, Vol. 38 https://doi.org/10.1016/j.ymben.2016.08.006	journal	November 2016
Enhanced protein and biochemical production using CRISPRi-based growth switches Li, Songyuan; Jendresen, Christian Bille; Grünberger, Alexander Metabolic Engineering, Vol. 38 https://doi.org/10.1016/j.ymben.2016.09.003	journal	November 2016
CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production Li, Hung; Shen, Claire R.; Huang, Chun-Hung Metabolic Engineering, Vol. 38 https://doi.org/10.1016/j.ymben.2016.09.006	journal	November 2016
Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae Deaner, Matthew; Alper, Hal S. Metabolic Engineering, Vol. 40 https://doi.org/10.1016/j.ymben.2017.01.012	journal	March 2017
CRISPR/Cas9-coupled recombineering for metabolic engineering of Corynebacterium glutamicum Cho, Jae Sung; Choi, Kyeong Rok; Prabowo, Cindy Pricilia Surya Metabolic Engineering, Vol. 42 https://doi.org/10.1016/j.ymben.2017.06.010	journal	July 2017
CasEMBLR: Cas9-Facilitated Multiloci Genomic Integration of in Vivo Assembled DNA Parts in Saccharomyces cerevisiae Jakočiu̅nas, Tadas; Rajkumar, Arun S.; Zhang, Jie ACS Synthetic Biology, Vol. 4, Issue 11 https://doi.org/10.1021/acssynbio.5b00007	journal	March 2015
CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. coli Cress, Brady F.; Toparlak, Ö. Duhan; Guleria, Sanjay ACS Synthetic Biology, Vol. 4, Issue 9 https://doi.org/10.1021/acssynbio.5b00012	journal	April 2015
CRISPR-Cas9 Based Engineering of Actinomycetal Genomes Tong, Yaojun; Charusanti, Pep; Zhang, Lixin ACS Synthetic Biology, Vol. 4, Issue 9 https://doi.org/10.1021/acssynbio.5b00038	journal	April 2015
Orthogonal Modular Gene Repression in Escherichia coli Using Engineered CRISPR/Cas9 Didovyk, Andriy; Borek, Bartłomiej; Hasty, Jeff ACS Synthetic Biology, Vol. 5, Issue 1 https://doi.org/10.1021/acssynbio.5b00147	journal	September 2015
Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi) Cleto, Sara; Jensen, Jaide VK; Wendisch, Volker F. ACS Synthetic Biology, Vol. 5, Issue 5 https://doi.org/10.1021/acssynbio.5b00216	journal	February 2016
Multiple Gene Repression in Cyanobacteria Using CRISPRi Yao, Lun; Cengic, Ivana; Anfelt, Josefine ACS Synthetic Biology, Vol. 5, Issue 3 https://doi.org/10.1021/acssynbio.5b00264	journal	December 2015
CRISPR/Cas9-Based Efficient Genome Editing in Clostridium ljungdahlii , an Autotrophic Gas-Fermenting Bacterium Huang, He; Chai, Changsheng; Li, Ning ACS Synthetic Biology, Vol. 5, Issue 12 https://doi.org/10.1021/acssynbio.6b00044	journal	June 2016
sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity Chari, Raj; Yeo, Nan Cher; Chavez, Alejandro ACS Synthetic Biology, Vol. 6, Issue 5 https://doi.org/10.1021/acssynbio.6b00343	journal	February 2017
Efficient Transcriptional Gene Repression by Type V-A CRISPR-Cpf1 from Eubacterium eligens Kim, Seong Keun; Kim, Haseong; Ahn, Woo-Chan ACS Synthetic Biology, Vol. 6, Issue 7 https://doi.org/10.1021/acssynbio.6b00368	journal	April 2017
Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas Farzadfard, Fahim; Perli, Samuel D.; Lu, Timothy K. ACS Synthetic Biology, Vol. 2, Issue 10 https://doi.org/10.1021/sb400081r	journal	June 2013
Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae Bao, Zehua; Xiao, Han; Liang, Jing ACS Synthetic Biology, Vol. 4, Issue 5 https://doi.org/10.1021/sb500255k	journal	September 2014
High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System Cobb, Ryan E.; Wang, Yajie; Zhao, Huimin ACS Synthetic Biology, Vol. 4, Issue 6 https://doi.org/10.1021/sb500351f	journal	November 2014
Multiplex gene regulation by CRISPR-ddCpf1 Zhang, Xiaochun; Wang, Jingman; Cheng, Qiuxiang Cell Discovery, Vol. 3, Issue 1 https://doi.org/10.1038/celldisc.2017.18	journal	June 2017
Genome sequence of the human malaria parasite Plasmodium falciparum Gardner, Malcolm J.; Hall, Neil; Fung, Eula Nature, Vol. 419, Issue 6906 https://doi.org/10.1038/nature01097	journal	October 2002
Programming cells by multiplex genome engineering and accelerated evolution Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A. Nature, Vol. 460, Issue 7257, p. 894-898 https://doi.org/10.1038/nature08187	journal	July 2009
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III Deltcheva, Elitza; Chylinski, Krzysztof; Sharma, Cynthia M. Nature, Vol. 471, Issue 7340 https://doi.org/10.1038/nature09886	journal	March 2011
Programmable RNA recognition and cleavage by CRISPR/Cas9 O’Connell, Mitchell R.; Oakes, Benjamin L.; Sternberg, Samuel H. Nature, Vol. 516, Issue 7530 https://doi.org/10.1038/nature13769	journal	September 2014
In vivo genome editing using Staphylococcus aureus Cas9 Ran, F. Ann; Cong, Le; Yan, Winston X. Nature, Vol. 520, Issue 7546 https://doi.org/10.1038/nature14299	journal	April 2015
Engineered CRISPR-Cas9 nucleases with altered PAM specificities Kleinstiver, Benjamin P.; Prew, Michelle S.; Tsai, Shengdar Q. Nature, Vol. 523, Issue 7561 https://doi.org/10.1038/nature14592	journal	June 2015
High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects Kleinstiver, Benjamin P.; Pattanayak, Vikram; Prew, Michelle S. Nature, Vol. 529, Issue 7587 https://doi.org/10.1038/nature16526	journal	January 2016
Structural basis for promiscuous PAM recognition in type I–E Cascade from E. coli Hayes, Robert P.; Xiao, Yibei; Ding, Fran Nature, Vol. 530, Issue 7591 https://doi.org/10.1038/nature16995	journal	February 2016
The crystal structure of Cpf1 in complex with CRISPR RNA Dong, De; Ren, Kuan; Qiu, Xiaolin Nature, Vol. 532, Issue 7600 https://doi.org/10.1038/nature17944	journal	April 2016
The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA Fonfara, Ines; Richter, Hagen; Bratovič, Majda Nature, Vol. 532, Issue 7600 https://doi.org/10.1038/nature17945	journal	April 2016
Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage Komor, Alexis C.; Kim, Yongjoo B.; Packer, Michael S. Nature, Vol. 533, Issue 7603 https://doi.org/10.1038/nature17946	journal	April 2016
Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection East-Seletsky, Alexandra; O’Connell, Mitchell R.; Knight, Spencer C. Nature, Vol. 538, Issue 7624 https://doi.org/10.1038/nature19802	journal	September 2016
CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria Shipman, Seth L.; Nivala, Jeff; Macklis, Jeffrey D. Nature, Vol. 547, Issue 7663 https://doi.org/10.1038/nature23017	journal	July 2017
Enhanced proofreading governs CRISPR–Cas9 targeting accuracy Chen, Janice S.; Dagdas, Yavuz S.; Kleinstiver, Benjamin P. Nature, Vol. 550, Issue 7676 https://doi.org/10.1038/nature24268	journal	September 2017
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage Gaudelli, Nicole M.; Komor, Alexis C.; Rees, Holly A. Nature, Vol. 551, Issue 7681 https://doi.org/10.1038/nature24644	journal	October 2017
Evolved Cas9 variants with broad PAM compatibility and high DNA specificity Hu, Johnny H.; Miller, Shannon M.; Geurts, Maarten H. Nature, Vol. 556, Issue 7699 https://doi.org/10.1038/nature26155	journal	February 2018
RNA-guided editing of bacterial genomes using CRISPR-Cas systems Jiang, Wenyan; Bikard, David; Cox, David Nature Biotechnology, Vol. 31, Issue 3, p. 233-239 https://doi.org/10.1038/nbt.2508	journal	January 2013
High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells Fu, Yanfang; Foden, Jennifer A.; Khayter, Cyd Nature Biotechnology, Vol. 31, Issue 9 https://doi.org/10.1038/nbt.2623	journal	June 2013
CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering Mali, Prashant; Aach, John; Stranges, P. Benjamin Nature Biotechnology, Vol. 31, Issue 9 https://doi.org/10.1038/nbt.2675	journal	August 2013
Improving CRISPR-Cas nuclease specificity using truncated guide RNAs Fu, Yanfang; Sander, Jeffry D.; Reyon, Deepak Nature Biotechnology, Vol. 32, Issue 3 https://doi.org/10.1038/nbt.2808	journal	January 2014
CRISPR-Cas systems for editing, regulating and targeting genomes Sander, Jeffry D.; Joung, J. Keith Nature Biotechnology, Vol. 32, Issue 4 https://doi.org/10.1038/nbt.2842	journal	March 2014
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease Kuscu, Cem; Arslan, Sevki; Singh, Ritambhara Nature Biotechnology, Vol. 32, Issue 7 https://doi.org/10.1038/nbt.2916	journal	May 2014
Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation Doench, John G.; Hartenian, Ella; Graham, Daniel B. Nature Biotechnology, Vol. 32, Issue 12 https://doi.org/10.1038/nbt.3026	journal	September 2014
Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells Chu, Van Trung; Weber, Timm; Wefers, Benedikt Nature Biotechnology, Vol. 33, Issue 5 https://doi.org/10.1038/nbt.3198	journal	March 2015
Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers Hilton, Isaac B.; D'Ippolito, Anthony M.; Vockley, Christopher M. Nature Biotechnology, Vol. 33, Issue 5 https://doi.org/10.1038/nbt.3199	journal	April 2015
Flexible guide-RNA design for CRISPR applications using Protospacer Workbench MacPherson, Cameron Ross; Scherf, Artur Nature Biotechnology, Vol. 33, Issue 8 https://doi.org/10.1038/nbt.3291	journal	June 2015
Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease Dahlman, James E.; Abudayyeh, Omar O.; Joung, Julia Nature Biotechnology, Vol. 33, Issue 11 https://doi.org/10.1038/nbt.3390	journal	October 2015
Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA Richardson, Christopher D.; Ray, Graham J.; DeWitt, Mark A. Nature Biotechnology, Vol. 34, Issue 3 https://doi.org/10.1038/nbt.3481	journal	January 2016
Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library Zhu, Shiyou; Li, Wei; Liu, Jingze Nature Biotechnology, Vol. 34, Issue 12 https://doi.org/10.1038/nbt.3715	journal	October 2016
Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions Kim, Y. Bill; Komor, Alexis C.; Levy, Jonathan M. Nature Biotechnology, Vol. 35, Issue 4 https://doi.org/10.1038/nbt.3803	journal	February 2017
Engineered Cpf1 variants with altered PAM specificities Gao, Linyi; Cox, David B. T.; Yan, Winston X. Nature Biotechnology, Vol. 35, Issue 8 https://doi.org/10.1038/nbt.3900	journal	June 2017
A light-inducible CRISPR-Cas9 system for control of endogenous gene activation Polstein, Lauren R.; Gersbach, Charles A. Nature Chemical Biology, Vol. 11, Issue 3 https://doi.org/10.1038/nchembio.1753	journal	February 2015
A generic strategy for CRISPR-Cas9-mediated gene tagging Lackner, Daniel H.; Carré, Alexia; Guzzardo, Paloma M. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms10237	journal	December 2015
A robust gene-stacking method utilizing yeast assembly for plant synthetic biology Shih, Patrick M.; Vuu, Khanh; Mansoori, Nasim Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13215	journal	October 2016
Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9 Qin, Peiwu; Parlak, Mahmut; Kuscu, Cem Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms14725	journal	March 2017
CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum Jiang, Yu; Qian, Fenghui; Yang, Junjie Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15179	journal	May 2017
Digital logic circuits in yeast with CRISPR-dCas9 NOR gates Gander, Miles W.; Vrana, Justin D.; Voje, William E. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15459	journal	May 2017
Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery Rees, Holly A.; Komor, Alexis C.; Yeh, Wei-Hsi Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15790	journal	June 2017
Gene silencing by CRISPR interference in mycobacteria Choudhary, Eira; Thakur, Preeti; Pareek, Madhu Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms7267	journal	February 2015
Targeted DNA degradation using a CRISPR device stably carried in the host genome Caliando, Brian J.; Voigt, Christopher A. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms7989	journal	May 2015
Orthogonal Cas9 proteins for RNA-guided gene regulation and editing Esvelt, Kevin M.; Mali, Prashant; Braff, Jonathan L. Nature Methods, Vol. 10, Issue 11 https://doi.org/10.1038/nmeth.2681	journal	September 2013
E-CRISP: fast CRISPR target site identification Heigwer, Florian; Kerr, Grainne; Boutros, Michael Nature Methods, Vol. 11, Issue 2 https://doi.org/10.1038/nmeth.2812	journal	January 2014
Highly efficient Cas9-mediated transcriptional programming Chavez, Alejandro; Scheiman, Jonathan; Vora, Suhani Nature Methods, Vol. 12, Issue 4 https://doi.org/10.1038/nmeth.3312	journal	March 2015
Functional annotation of native enhancers with a Cas9–histone demethylase fusion Kearns, Nicola A.; Pham, Hannah; Tabak, Barbara Nature Methods, Vol. 12, Issue 5 https://doi.org/10.1038/nmeth.3325	journal	March 2015
Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach Chari, Raj; Mali, Prashant; Moosburner, Mark Nature Methods, Vol. 12, Issue 9 https://doi.org/10.1038/nmeth.3473	journal	July 2015
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo Moreno-Mateos, Miguel A.; Vejnar, Charles E.; Beaudoin, Jean-Denis Nature Methods, Vol. 12, Issue 10 https://doi.org/10.1038/nmeth.3543	journal	August 2015
Cas9 gRNA engineering for genome editing, activation and repression Kiani, Samira; Chavez, Alejandro; Tuttle, Marcelle Nature Methods, Vol. 12, Issue 11 https://doi.org/10.1038/nmeth.3580	journal	September 2015
Directing cellular information flow via CRISPR signal conductors Liu, Yuchen; Zhan, Yonghao; Chen, Zhicong Nature Methods, Vol. 13, Issue 11 https://doi.org/10.1038/nmeth.3994	journal	September 2016
CRISPR kinetics Rusk, Nicole Nature Methods, Vol. 14, Issue 7 https://doi.org/10.1038/nmeth.4360	journal	July 2017
CRISPR–Cas9-based photoactivatable transcription systems to induce neuronal differentiation Nihongaki, Yuta; Furuhata, Yuichi; Otabe, Takahiro Nature Methods, Vol. 14, Issue 10 https://doi.org/10.1038/nmeth.4430	journal	September 2017
Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform Rock, Jeremy M.; Hopkins, Forrest F.; Chavez, Alejandro Nature Microbiology, Vol. 2, Issue 4 https://doi.org/10.1038/nmicrobiol.2016.274	journal	February 2017
A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants Tang, Xu; Lowder, Levi G.; Zhang, Tao Nature Plants, Vol. 3, Issue 3 https://doi.org/10.1038/nplants.2017.18	journal	February 2017
CRISPR interference (CRISPRi) for sequence-specific control of gene expression Larson, Matthew H.; Gilbert, Luke A.; Wang, Xiaowo Nature Protocols, Vol. 8, Issue 11 https://doi.org/10.1038/nprot.2013.132	journal	October 2013
Genome editing with engineered zinc finger nucleases Urnov, Fyodor D.; Rebar, Edward J.; Holmes, Michael C. Nature Reviews Genetics, Vol. 11, Issue 9 https://doi.org/10.1038/nrg2842	journal	September 2010
Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation Dominguez, Antonia A.; Lim, Wendell A.; Qi, Lei S. Nature Reviews Molecular Cell Biology, Vol. 17, Issue 1 https://doi.org/10.1038/nrm.2015.2	journal	December 2015
Bacterial DNA repair by non-homologous end joining Shuman, Stewart; Glickman, Michael S. Nature Reviews Microbiology, Vol. 5, Issue 11 https://doi.org/10.1038/nrmicro1768	journal	November 2007
An updated evolutionary classification of CRISPR–Cas systems Makarova, Kira S.; Wolf, Yuri I.; Alkhnbashi, Omer S. Nature Reviews Microbiology, Vol. 13, Issue 11, p. 722-736 https://doi.org/10.1038/nrmicro3569	journal	September 2015
Characterizing a thermostable Cas9 for bacterial genome editing and silencing Mougiakos, Ioannis; Mohanraju, Prarthana; Bosma, Elleke F. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01591-4	journal	November 2017
Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system Lian, Jiazhang; HamediRad, Mohammad; Hu, Sumeng Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01695-x	journal	November 2017
Rational modular design of metabolic network for efficient production of plant polyphenol pinosylvin Wu, Junjun; Zhang, Xia; Zhu, Yingjie Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-01700-9	journal	May 2017
Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli Wu, Junjun; Du, Guocheng; Chen, Jian Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep13477	journal	September 2015
CRMAGE: CRISPR Optimized MAGE Recombineering Ronda, Carlotta; Pedersen, Lasse Ebdrup; Sommer, Morten O. A. Scientific Reports, Vol. 6, Article No. 19452 https://doi.org/10.1038/srep19452	journal	January 2016
Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium Pyne, Michael E.; Bruder, Mark R.; Moo-Young, Murray Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep25666	journal	May 2016
Multigene disruption in undomesticated Bacillus subtilis ATCC 6051a using the CRISPR/Cas9 system Zhang, Kang; Duan, Xuguo; Wu, Jing Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep27943	journal	June 2016
Targeting cellular mRNAs translation by CRISPR-Cas9 Liu, Yuchen; Chen, Zhicong; He, Anbang Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep29652	journal	July 2016
tCRISPRi: tunable and reversible, one-step control of gene expression Li, Xin-tian; Jun, Yonggun; Erickstad, Michael J. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep39076	journal	December 2016
Cpf1 Is A Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria Ungerer, Justin; Pakrasi, Himadri B. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep39681	journal	December 2016
One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome Gibson, D. G.; Benders, G. A.; Axelrod, K. C. Proceedings of the National Academy of Sciences, Vol. 105, Issue 51 https://doi.org/10.1073/pnas.0811011106	journal	December 2008
CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells Deng, Wulan; Shi, Xinghua; Tjian, Robert Proceedings of the National Academy of Sciences, Vol. 112, Issue 38 https://doi.org/10.1073/pnas.1515692112	journal	August 2015
One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces Huang, He; Zheng, Guosong; Jiang, Weihong Acta Biochimica et Biophysica Sinica, Vol. 47, Issue 4 https://doi.org/10.1093/abbs/gmv007	journal	March 2015
CasOT: a genome-wide Cas9/gRNA off-target searching tool Xiao, A.; Cheng, Z.; Kong, L. Bioinformatics, Vol. 30, Issue 8 https://doi.org/10.1093/bioinformatics/btt764	journal	January 2014
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases Bae, S.; Park, J.; Kim, J. -S. Bioinformatics, Vol. 30, Issue 10 https://doi.org/10.1093/bioinformatics/btu048	journal	January 2014
Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance Boulton, S. Nucleic Acids Research, Vol. 24, Issue 23 https://doi.org/10.1093/nar/24.23.4639	journal	December 1996
Where does bacterial replication start? Rules for predicting the oriC region Mackiewicz, P. Nucleic Acids Research, Vol. 32, Issue 13 https://doi.org/10.1093/nar/gkh699	journal	July 2004
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways Shao, Zengyi; Zhao, Hua; Zhao, Huimin Nucleic Acids Research, Vol. 37, Issue 2 https://doi.org/10.1093/nar/gkn991	journal	December 2008
Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems Fonfara, Ines; Le Rhun, Anaïs; Chylinski, Krzysztof Nucleic Acids Research, Vol. 42, Issue 4 https://doi.org/10.1093/nar/gkt1074	journal	November 2013
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems DiCarlo, James E.; Norville, Julie E.; Mali, Prashant Nucleic Acids Research, Vol. 41, Issue 7, p. 4336-4343 https://doi.org/10.1093/nar/gkt135	journal	March 2013
Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system Bikard, David; Jiang, Wenyan; Samai, Poulami Nucleic Acids Research, Vol. 41, Issue 15 https://doi.org/10.1093/nar/gkt520	journal	June 2013
Efficient programmable gene silencing by Cascade Rath, Devashish; Amlinger, Lina; Hoekzema, Mirthe Nucleic Acids Research, Vol. 43, Issue 1 https://doi.org/10.1093/nar/gku1257	journal	November 2014
CRISPR-mediated targeted mRNA degradation in the archaeon Sulfolobus solfataricus Zebec, Ziga; Manica, Andrea; Zhang, Jing Nucleic Acids Research, Vol. 42, Issue 8 https://doi.org/10.1093/nar/gku161	journal	March 2014
CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri Oh, Jee-Hwan; van Pijkeren, Jan-Peter Nucleic Acids Research, Vol. 42, Issue 17, p. e131-e131 https://doi.org/10.1093/nar/gku623	journal	July 2014
Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression Luo, Michelle L.; Mullis, Adam S.; Leenay, Ryan T. Nucleic Acids Research, Vol. 43, Issue 1 https://doi.org/10.1093/nar/gku971	journal	October 2014
Harnessing Type I and Type III CRISPR-Cas systems for genome editing Li, Yingjun; Pan, Saifu; Zhang, Yan Nucleic Acids Research, Vol. 44, Issue 4 https://doi.org/10.1093/nar/gkv1044	journal	October 2015
Multiple nucleic acid cleavage modes in divergent type III CRISPR systems Zhang, Jing; Graham, Shirley; Tello, Agnes Nucleic Acids Research, Vol. 44, Issue 4 https://doi.org/10.1093/nar/gkw020	journal	January 2016
Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system Lee, Young Je; Hoynes-O'Connor, Allison; Leong, Matthew C. Nucleic Acids Research, Vol. 44, Issue 5 https://doi.org/10.1093/nar/gkw056	journal	February 2016
Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3′-terminal segment of guide RNA Mekler, Vladimir; Minakhin, Leonid; Semenova, Ekaterina Nucleic Acids Research, Vol. 44, Issue 6 https://doi.org/10.1093/nar/gkw138	journal	March 2016
CRISPR-mediated control of the bacterial initiation of replication Wiktor, Jakub; Lesterlin, Christian; Sherratt, David J. Nucleic Acids Research, Vol. 44, Issue 8 https://doi.org/10.1093/nar/gkw214	journal	April 2016
Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli Cress, Brady F.; Jones, J. Andrew; Kim, Daniel C. Nucleic Acids Research, Vol. 44, Issue 9 https://doi.org/10.1093/nar/gkw231	journal	April 2016
Investigating essential gene function in Mycobacterium tuberculosis using an efficient CRISPR interference system Singh, Atul K.; Carette, Xavier; Potluri, Lakshmi-Prasad Nucleic Acids Research, Vol. 44, Issue 18 https://doi.org/10.1093/nar/gkw625	journal	July 2016
Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation Kuznedelov, Konstantin; Mekler, Vladimir; Lemak, Sofia Nucleic Acids Research, Vol. 44, Issue 22 https://doi.org/10.1093/nar/gkw914	journal	October 2016
AT-rich region and repeated sequences – the essential elements of replication origins of bacterial replicons Rajewska, Magdalena; Wegrzyn, Katarzyna; Konieczny, Igor FEMS Microbiology Reviews, Vol. 36, Issue 2 https://doi.org/10.1111/j.1574-6976.2011.00300.x	journal	March 2012
Identification of a DNA Nonhomologous End-Joining Complex in Bacteria Weller, G. R. Science, Vol. 297, Issue 5587 https://doi.org/10.1126/science.1074584	journal	September 2002
TAL Effectors: Customizable Proteins for DNA Targeting Bogdanove, A. J.; Voytas, D. F. Science, Vol. 333, Issue 6051 https://doi.org/10.1126/science.1204094	journal	September 2011
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity Jinek, M.; Chylinski, K.; Fonfara, I. Science, Vol. 337, Issue 6096, p. 816-821 https://doi.org/10.1126/science.1225829	journal	June 2012
Multiplex Genome Engineering Using CRISPR/Cas Systems Cong, L.; Ran, F. A.; Cox, D. Science, Vol. 339, Issue 6121, p. 819-823 https://doi.org/10.1126/science.1231143	journal	January 2013
Genetic Screens in Human Cells Using the CRISPR-Cas9 System Wang, Tim; Wei, Jenny J.; Sabatini, David M. Science, Vol. 343, Issue 6166 https://doi.org/10.1126/science.1246981	journal	December 2013
The new frontier of genome engineering with CRISPR-Cas9 Doudna, Jennifer A.; Charpentier, Emmanuelle Science, Vol. 346, Issue 6213 https://doi.org/10.1126/science.1258096	journal	November 2014
Genetic circuit design automation Nielsen, A. A. K.; Der, B. S.; Shin, J. Science, Vol. 352, Issue 6281 https://doi.org/10.1126/science.aac7341	journal	March 2016
Rationally engineered Cas9 nucleases with improved specificity Slaymaker, I. M.; Gao, L.; Zetsche, B. Science, Vol. 351, Issue 6268 https://doi.org/10.1126/science.aad5227	journal	December 2015
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector Abudayyeh, Omar O.; Gootenberg, Jonathan S.; Konermann, Silvana Science, Vol. 353, Issue 6299 https://doi.org/10.1126/science.aaf5573	journal	June 2016
RNA editing with CRISPR-Cas13 Cox, David B. T.; Gootenberg, Jonathan S.; Abudayyeh, Omar O. Science, Vol. 358, Issue 6366 https://doi.org/10.1126/science.aaq0180	journal	October 2017
Enhancing the RNA engineering toolkit Yang, Li; Chen, Ling-Ling Science, Vol. 358, Issue 6366 https://doi.org/10.1126/science.aar2400	journal	November 2017
Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase Xu, Tao; Li, Yongchao; Shi, Zhou Applied and Environmental Microbiology, Vol. 81, Issue 13 https://doi.org/10.1128/AEM.00873-15	journal	April 2015
Development of a CRISPR-Cas9 Tool Kit for Comprehensive Engineering of Bacillus subtilis Westbrook, Adam W.; Moo-Young, Murray; Chou, C. Perry Applied and Environmental Microbiology, Vol. 82, Issue 16 https://doi.org/10.1128/AEM.01159-16	journal	June 2016
Coupling the CRISPR/Cas9 System with Lambda Red Recombineering Enables Simplified Chromosomal Gene Replacement in Escherichia coli Pyne, Michael E.; Moo-Young, Murray; Chung, Duane A. Applied and Environmental Microbiology, Vol. 81, Issue 15 https://doi.org/10.1128/AEM.01248-15	journal	May 2015
Editing of the Bacillus subtilis Genome by the CRISPR-Cas9 System Altenbuchner, Josef Applied and Environmental Microbiology, Vol. 82, Issue 17 https://doi.org/10.1128/AEM.01453-16	journal	June 2016
Construction of a Quadruple Auxotrophic Mutant of an Industrial Polyploid Saccharomyces cerevisiae Strain by Using RNA-Guided Cas9 Nuclease Zhang, Guo-Chang; Kong, In Iok; Kim, Heejin Applied and Environmental Microbiology, Vol. 80, Issue 24 https://doi.org/10.1128/AEM.02310-14	journal	October 2014
Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System Jiang, Yu; Chen, Biao; Duan, Chunlan Applied and Environmental Microbiology, Vol. 81, Issue 7, p. 2506-2514 https://doi.org/10.1128/AEM.04023-14	journal	January 2015
Requirements for Pseudomonas aeruginosa Type I-F CRISPR-Cas Adaptation Determined Using a Biofilm Enrichment Assay Heussler, Gary E.; Miller, Jon L.; Price, Courtney E. Journal of Bacteriology, Vol. 198, Issue 22 https://doi.org/10.1128/JB.00458-16	journal	August 2016
Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering Box, Allison M.; McGuffie, Matthew J.; O'Hara, Brendan J. Journal of Bacteriology, Vol. 198, Issue 3 https://doi.org/10.1128/JB.00747-15	journal	November 2015
The CRISPR/Cas Adaptive Immune System of Pseudomonas aeruginosa Mediates Resistance to Naturally Occurring and Engineered Phages Cady, K. C.; Bondy-Denomy, J.; Heussler, G. E. Journal of Bacteriology, Vol. 194, Issue 21 https://doi.org/10.1128/JB.01184-12	journal	August 2012
Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus Horvath, P.; Romero, D. A.; Coute-Monvoisin, A. -C. Journal of Bacteriology, Vol. 190, Issue 4 https://doi.org/10.1128/JB.01415-07	journal	December 2007
The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation Klug, Aaron Annual Review of Biochemistry, Vol. 79, Issue 1 https://doi.org/10.1146/annurev-biochem-010909-095056	journal	June 2010
DNA Replication in Eukaryotic Cells Bell, Stephen P.; Dutta, Anindya Annual Review of Biochemistry, Vol. 71, Issue 1 https://doi.org/10.1146/annurev.biochem.71.110601.135425	journal	June 2002
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-172	journal	January 2007
CrEdit: CRISPR mediated multi-loci gene integration in Saccharomyces cerevisiae Ronda, Carlotta; Maury, Jérôme; Jakočiu̅nas, Tadas Microbial Cell Factories, Vol. 14, Issue 1 https://doi.org/10.1186/s12934-015-0288-3	journal	July 2015
CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973 Wendt, Kristen E.; Ungerer, Justin; Cobb, Ryan E. Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-016-0514-7	journal	June 2016
CRISPR interference (CRISPRi) for gene regulation and succinate production in cyanobacterium S. elongatus PCC 7942 Huang, Chun-Hung; Shen, Claire R.; Li, Hung Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-016-0595-3	journal	November 2016
CRISPR interference-guided multiplex repression of endogenous competing pathway genes for redirecting metabolic flux in Escherichia coli Kim, Seong Keun; Seong, Wonjae; Han, Gui Hwan Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0802-x	journal	November 2017
Efficient gene editing in Corynebacterium glutamicum using the CRISPR/Cas9 system Peng, Feng; Wang, Xinyue; Sun, Yang Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0814-6	journal	November 2017
Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum Liu, Jiao; Wang, Yu; Lu, Yujiao Microbial Cell Factories, Vol. 16, Issue 1 https://doi.org/10.1186/s12934-017-0815-5	journal	November 2017
Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications Friedland, Ari E.; Baral, Reshica; Singhal, Pankhuri Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0817-8	journal	November 2015
Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements Karvelis, Tautvydas; Gasiunas, Giedrius; Young, Joshua Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0818-7	journal	November 2015
The Cpf1 CRISPR-Cas protein expands genome-editing tools Fagerlund, Robert D.; Staals, Raymond H. J.; Fineran, Peter C. Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0824-9	journal	November 2015
Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design Smith, Justin D.; Suresh, Sundari; Schlecht, Ulrich Genome Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s13059-016-0900-9	journal	March 2016
Genome editing of Clostridium autoethanogenum using CRISPR/Cas9 Nagaraju, Shilpa; Davies, Naomi Kathleen; Walker, David Jeffrey Fraser Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0638-3	journal	October 2016
Type I-E CRISPR-Cas Systems Discriminate Target from Non-Target DNA through Base Pairing-Independent PAM Recognition Westra, Edze R.; Semenova, Ekaterina; Datsenko, Kirill A. PLoS Genetics, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pgen.1003742	journal	September 2013
Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs Gagnon, James A.; Valen, Eivind; Thyme, Summer B. PLoS ONE, Vol. 9, Issue 5 https://doi.org/10.1371/journal.pone.0098186	journal	May 2014
Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium Briner, Alexandra E.; Lugli, Gabriele Andrea; Milani, Christian PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0133661	journal	July 2015
A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT Ding, Pengfei; McFarland, Kirsty A.; Jin, Shujuan PLOS Pathogens, Vol. 11, Issue 6 https://doi.org/10.1371/journal.ppat.1004967	journal	June 2015
Multi‐input CRISPR / C as genetic circuits that interface host regulatory networks Nielsen, Alec AK; Voigt, Christopher A. Molecular Systems Biology, Vol. 10, Issue 11 https://doi.org/10.15252/msb.20145735	journal	November 2014
Genome Engineering With Zinc-Finger Nucleases Carroll, Dana Genetics, Vol. 188, Issue 4 https://doi.org/10.1534/genetics.111.131433	journal	August 2011
High-Throughput Characterization of Cascade type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences Xu Hua Fu, Becky; Wainberg, Michael; Kundaje, Anshul Genetics, Vol. 206, Issue 4 https://doi.org/10.1534/genetics.117.202580	journal	June 2017
RNAi mechanisms and applications Kim, Daniel H.; Rossi, John J. BioTechniques, Vol. 44, Issue 5 https://doi.org/10.2144/000112792	journal	April 2008
Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum Hidalgo-Cantabrana, Claudio; Crawley, Alexandra B.; Sanchez, Borja Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01851	journal	September 2017

Cited By (5)

CRISPR/Cas9-mediated genome editing induces gene knockdown by altering the pre-mRNA splicing in mice Tang, Ji-Xin; Chen, Dafeng; Deng, Shou-Long BMC Biotechnology, Vol. 18, Issue 1 https://doi.org/10.1186/s12896-018-0472-8	journal	October 2018
Challenges and tackles in metabolic engineering for microbial production of carotenoids Wang, Chonglong; Zhao, Shuli; Shao, Xixi Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1105-1	journal	March 2019
Developing a CRISPR/Cas9 System for Genome Editing in the Basidiomycetous Yeast Rhodosporidium toruloides Jiao, Xiang; Zhang, Yue; Liu, Xiangjian Biotechnology Journal, Vol. 14, Issue 7 https://doi.org/10.1002/biot.201900036	journal	May 2019
A CRISPR/Cas9 method to generate heterozygous alleles in Saccharomyces cerevisiae EauClaire, Steven F.; Webb, Christopher J. Yeast, Vol. 36, Issue 10 https://doi.org/10.1002/yea.3432	journal	August 2019
CRISPR system in the yeast Saccharomyces cerevisiae and its application in the bioproduction of useful chemicals Mitsui, Ryosuke; Yamada, Ryosuke; Ogino, Hiroyasu World Journal of Microbiology and Biotechnology, Vol. 35, Issue 7 https://doi.org/10.1007/s11274-019-2688-8	journal	July 2019