Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
Open accessAbstract
Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a method for controlling gene expression based on Cas9, an RNA-guided DNA endonuclease from a type II CRISPR system. We show that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This system, which we call CRISPR interference (CRISPRi), can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects. CRISPRi can be used to repress multiple target genes simultaneously, and its effects are reversible. We also show evidence that the system can be adapted for gene repression in mammalian cells. This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale.
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CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) employ catalytically deactivated forms of Cas9 (dCas9) fused to transcriptional repressors or activators.
“CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) employ catalytically deactivated forms of Cas9 (dCas9) that are fused to transcriptional repressors or activators 29,101 .”
From The promise and challenge of therapeutic genome editing (2020) · cites this paper as [29]
The Summary and the section ‘CRISPRi Efficiently and Selectively Represses Transcription of Target Genes’ describe CRISPRi using catalytically inactive dCas9 and guide RNA to repress transcription. The section ‘CRISPRi as a Platform for Engineering Transcriptional Regulatory Networks’ discusses coupling dCas9 to regulatory domains, including for activation, as a possibility—not as a fusion used in the reported system. Page numbers are not supplied in our copy. (LLM, conf=0.90)
Experimental — accuracy not yet measuredThe use of CRISPR/Cas9 system enables regulation of gene expression and makes epigenetic alterations without introducing DNA double-strand breaks.
“The use of CRISPR/Cas9 system enables regulation of gene expression and make epigenetic alterations without introducing DNA double-strand breaks.428”
From Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential (2023) · cites this paper as [428]
The Introduction and Summary describe CRISPRi using catalytically inactive Cas9 to regulate gene expression without DNA cleavage. In “CRISPRi as a Platform for Engineering Transcriptional Regulatory Networks” (page unavailable), chromatin modification is presented only as a possible future use of dCas9 coupled to regulatory domains; the paper does not report making epigenetic alterations. (LLM, conf=0.90)
Experimental — accuracy not yet measuredCRISPRi and CRISPRa technologies utilize catalytically inactive Cas9 (dCas9) fused to either a transcriptional repressor (e.g., KRAB) or a transcriptional activator (e.g., VPR).
“For example, CRISPRi (interference)23–25 and CRISPRa (activation)26–30 technologies utilize catalytically inactive Cas9 (dCas9) fused to either a transcriptional repressor (e.g., KRAB, Krüppel associated box) or a transcriptional activator (e.g., VPR, VP64-p65-Rta).”
From Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions (2025) · cites this paper as [25]
The Introduction and the section on CRISPRi silencing describe gene repression using catalytically inactive Cas9 and a guide RNA. The section on engineering transcriptional regulatory networks discusses coupling dCas9 to regulatory domains for activation as a possibility, not as a demonstrated system. Our copy does not describe the claimed KRAB or VPR fusions. (LLM, conf=0.89)
Experimental — accuracy not yet measuredAlternatives to DNA cleavage-induced editing include base editing, prime editing, and CRISPRi/CRISPRa.
“Alternatives to DNA cleavage-induced editing include using CRISPR-Cas9 for direct chemical sequence alteration (base editing) 25,26 , providing RNA templates for gene alteration (prime editing) 27,28 , and for transcriptional control (CRISPR interference, CRISPRi; CRISPR activation, CRISPRa) 29,30 (Fig. 3).”
From The promise and challenge of therapeutic genome editing (2020) · cites this paper as [29]
dCas9 can be repurposed as a site-specific DNA-binding domain transporting various functional domains to the target locus.
“dCas9 can be repurposed as a site-specific DNA-binding domain transporting various functional domains to the target locus”
From CRISPR-Cas9: a new and promising player in gene therapy (2015) · cites this paper as [17]
The mutant virus formed in P1 cannot be passed to the P2 virus in equal proportions, which illustrates steric hindrance caused by the association of the Cas9 protein with specific DNA sequences, and the time that elapses during cleavage and repair may affect viral genome packaging.
“Moreover, the mutant virus that is formed in P1 cannot be passed to the P2 virus in equal proportions, which illustrates the steric hindrance caused by the association of the Cas9 protein with specific DNA sequences [34], and the time that elapses during cleavage and repair may affect viral genome packaging.”
From High-efficiency targeted editing of large viral genomes by RNA-guided nucleases (2014) · cites this paper as [34]
CRISPR/Cas9 is a naturally occurring bacterial immune system that protects bacteria from phage infection and has been harnessed for genome-engineering applications.
“Clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 is a naturally occurring bacterial immune system that uses a novel nuclease system to protect bacteria from phage infection (6-9), and it has recently been harnessed for a variety of genome-engineering applications (10)(11)(12)(13)(14)(15)(16)(17).”
From RNA-guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection (2014) · cites this paper as [14]
A Cas9 mutant totally defective in endonuclease activity together with a guide RNA can specifically interfere with gene transcription without inducing any gene mutation (CRISPRi).
“Furthermore, a Cas9 mutant totally defective in endonuclease activity together with a guide RNA can specifically interfere with gene transcription without inducing any gene mutation in a process called CRISPR interference (CRISPRi) [89].”
From Newer Gene Editing Technologies toward HIV Gene Therapy (2013) · cites this paper as [89]
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Cites
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116 · cited 6× · see citing works
“Cell 152, 1173–1183, February 28, 2013 ª2013 Elsevier Inc. 1175 (Jinek et al., 2012), alleviated this lethality, as verified by transformation efficiency and E. coli growth rates (Figures S2A and S2B).”
BackgroundInfluentialSelf-citationMultiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339 · cited 2× · see citing works
“While our paper was under review, several very recent studies reported the use of wild-type Cas9/CRISPR for targeted genome editing in diverse organisms (Mali et al., 2013; Cong et al., 2013; Jinek et al., 2013; Jiang et al., 2013; Hwang et al., 2013; Cho et al., 2013).”
BackgroundMapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696 · cited 1× · see citing works
“To evaluate the specificity of CRISPRi on a genome-wide scale, we performed whole-transcriptome shotgun sequencing (RNAseq) of dCas9-transformed cells with and without sgRNA coexpression (Figure 4A) (Mortazavi et al., 2008).”
MethodRNA-Guided Human Genome Engineering via Cas9
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210 · cited 3× · see citing works
“While our paper was under review, several very recent studies reported the use of wild-type Cas9/CRISPR for targeted genome editing in diverse organisms (Mali et al., 2013; Cong et al., 2013; Jinek et al., 2013; Jiang et al., 2013; Hwang et al., 2013; Cho et al., 2013).”
BackgroundCRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 6,304 · cited 1× · see citing works
“The CRISPR (clustered regularly interspaced short palindromic repeats) system provides a potential platform for targeted gene regulation (Barrangou et al., 2007).”
BackgroundHannon, G. J. (2002) · Nature · doi:10.1038/418244a · Cited by 3,583 · see citing works
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937 · see citing works
Gasiunas, G., Barrangou, R., Horvath, P., & Siksnys, V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208507109 · Cited by 2,769 · cited 2× · see citing works
“…pyogenes: only a single gene encoding the Cas9 protein and two RNAs, a mature CRISPR RNA (crRNA) and a partially complementary trans-acting RNA (tracrRNA), are necessary and sufficient for RNA-guided silencing of foreign DNAs (Figure S1 available online) (Jinek et al., 2012; Gasiunas et al., 2012).”
BackgroundZamore, P. D., Tuschl, T., Sharp, P. A., & Bartel, D. P. (2000) · Cell · doi:10.1016/s0092-8674(00)80620-0 · Cited by 2,667 · cited 1× · see citing works
“This mechanism is distinct from that of RNAi, for which knockdown of gene expression requires the destruction of already transcribed messenger RNAs prior to their translation (Zamore et al., 2000).”
CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III
Deltcheva, E., Chylinski, K., Sharma, C. M., Gonzales, K., Chao, Y., Pirzada, Z. A., Eckert, M. R., Vogel, J., & Charpentier, E. (2011) · Nature · doi:10.1038/nature09886 · Cited by 2,563 · cited 3× · see citing works
“Maturation of crRNA requires tracrRNA and RNase III (Deltcheva et al., 2011).”
MethodInfluentialEvolution and classification of the CRISPR–Cas systems
Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J. J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F. J. M., Wolf, Y. I., Yakunin, A. F., et al. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2577 · Cited by 2,512 · cited 1× · see citing works
“About 40% of bacteria and 90%of archaea possessCRISPR/CRISPR-associated (Cas) systems to confer resistance to foreign DNA elements (Makarova et al., 2011).”
BackgroundRNA-guided editing of bacterial genomes using CRISPR-Cas systems
Jiang, W., Bikard, D., Cox, D., Zhang, F., & Marraffini, L. A. (2013) · Nature Biotechnology · doi:10.1038/nbt.2508 · Cited by 2,429 · cited 3× · see citing works
“While our paper was under review, several very recent studies reported the use of wild-type Cas9/CRISPR for targeted genome editing in diverse organisms (Mali et al., 2013; Cong et al., 2013; Jinek et al., 2013; Jiang et al., 2013; Hwang et al., 2013; Cho et al., 2013).”
BackgroundA monomeric red fluorescent protein
Campbell, R. E., Tour, O., Palmer, A. E., Steinbach, P. A., Baird, G. S., Zacharias, D. A., & Tsien, R. Y. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.082243699 · Cited by 2,346 · cited 2× · see citing works
“We constructed a red fluorescent protein (mRFP)-based reporter system (Campbell et al., 2002) and inserted it into the E. coli MG1655 genome.”
BackgroundMethodEngineering and characterization of a superfolder green fluorescent protein
Pédelacq, J. D., Cabantous, S., Tran, T. H., Terwilliger, T. C., & Waldo, G. S. (2005) · Nature Biotechnology · doi:10.1038/nbt1172 · Cited by 2,295 · cited 2× · see citing works
“The paused RNAP aborts transcription elongation upon encountering the dCas9-sgRNA roadblock. sfGFP (Pédelacq et al., 2006).”
BackgroundRNA-programmed genome editing in human cells
Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., & Doudna, J. (2013) · eLife · doi:10.7554/elife.00471 · Cited by 2,098 · cited 3× · see citing works
“While our paper was under review, several very recent studies reported the use of wild-type Cas9/CRISPR for targeted genome editing in diverse organisms (Mali et al., 2013; Cong et al., 2013; Jinek et al., 2013; Jiang et al., 2013; Hwang et al., 2013; Cho et al., 2013).”
BackgroundTargeted genome engineering in human cells with the Cas9 RNA-guided endonuclease
Cho, S. W., Kim, S., Kim, J. M., & Kim, J.-S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2507 · Cited by 1,863 · cited 2× · see citing works
“While our paper was under review, several very recent studies reported the use of wild-type Cas9/CRISPR for targeted genome editing in diverse organisms (Mali et al., 2013; Cong et al., 2013; Jinek et al., 2013; Jiang et al., 2013; Hwang et al., 2013; Cho et al., 2013).”
BackgroundRNA-guided genetic silencing systems in bacteria and archaea
Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012) · Nature · doi:10.1038/nature10886 · Cited by 1,851 · cited 1× · see citing works
“CRISPR systems use small base-pairing RNAs to target and cleave foreign DNA elements in a sequence-specific manner (Wiedenheft et al., 2012).”
BackgroundSelf-citationLutz, R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.6.1203 · Cited by 1,696 · cited 1× · see citing works
“The genes were PCR amplified and inserted into a vector containing an aTc-inducible promoter PLtetO-1 (Lutz and Bujard, 1997), a chloramphenicol-selectable marker, and a p15A replication origin.”
MethodProgramming cells by multiplex genome engineering and accelerated evolution
Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., & Church, G. M. (2009) · Nature · doi:10.1038/nature08187 · Cited by 1,529 · cited 2× · see citing works
“coli MG1655 strain was transformed with a temperature-sensitive plasmid pKD46 that contained l-Red recombination proteins (Exo, Beta, and Gam) (Wang et al., 2009).”
MethodCRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
Marraffini, L. A., & Sontheimer, E. J. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2749 · Cited by 1,011 · cited 1× · see citing works
“See also Figure S1. determined by both sgRNA-DNA base pairing and a short DNA motif (protospacer adjacent motif [PAM] sequence: NGG) juxtaposed to the DNA complementary region (Marraffini and Sontheimer, 2010).”
BackgroundNascent transcript sequencing visualizes transcription at nucleotide resolution
Churchman, L. S., & Weissman, J. S. (2011) · Nature · doi:10.1038/nature09652 · Cited by 823 · cited 2× · see citing works
“Nascent RNA was purified from the eluate using the miRNeasy kit (QIAGEN) and was converted to DNA using a previously established library generation protocol (Churchman and Weissman, 2011).”
MethodSelf-citationEfficient construction of sequence-specific TAL effectors for modulating mammalian transcription
Zhang, F., Cong, L., Lodato, S., Kosuri, S., Church, G. M., & Arlotta, P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1775 · Cited by 771 · cited 1× · see citing works
“RNA interference (RNAi) and engineered DNA-binding proteins such as zinc finger or transcription-activator-like effector (TALE) proteins, have emerged as powerful technologies for targeted gene regulation (Hannon, 2002; Beerli and Barbas, 2002; Zhang et al., 2011).”
BackgroundThe Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation
Klug, A. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-010909-095056 · Cited by 710 · cited 1× · see citing works
“In addition, custom DNA-binding proteins, such as zinc finger or TALE proteins, remain somewhat difficult and expensive to design, develop, and empirically test in the cellular context (Klug, 2010).”
BackgroundEngineering polydactyl zinc-finger transcription factors
Beerli, R. R., & Barbas, C. F. (2002) · Nature Biotechnology · doi:10.1038/nbt0202-135 · Cited by 495 · cited 1× · see citing works
“RNA interference (RNAi) and engineered DNA-binding proteins such as zinc finger or transcription-activator-like effector (TALE) proteins, have emerged as powerful technologies for targeted gene regulation (Hannon, 2002; Beerli and Barbas, 2002; Zhang et al., 2011).”
BackgroundStructures of the RNA-guided surveillance complex from a bacterial immune system
Wiedenheft, B., Lander, G. C., Zhou, K., Jore, M. M., Brouns, S. J. J., John van der, O. O. S. T., Doudna, J. A., & Nogales, E. (2011) · Nature · doi:10.1038/nature10402 · Cited by 398 · cited 1× · see citing works
“Importantly, any single mutation of the first 7 nt dramatically decreased repression, suggesting that this sequence constitutes a ‘‘seed region’’ for binding, as noted previously for both the type I and type II CRISPR systems (Wiedenheft et al., 2011; Jinek et al., 2012; Gasiunas et al., 2012).”
BackgroundSelf-citationLucks, J. B., Mortimer, S., Trapnell, C., Luo, S. J., Aviran, S., Schroth, G. P., Pachter, L. S., Doudna, J. A., & Arkin, A. P. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1106501108 · Cited by 390 · cited 1× · see citing works
“In the CRISPRi system, it may also be possible to link multiple sgRNAs into transcriptional circuits in which one upstream sgRNA controls the expression of a different downstream sgRNA (Lucks et al., 2011).”
Self-citationLewis, M. (2005) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2005.04.004 · Cited by 260 · cited 1× · see citing works
“We performed b-galactosidase assays to measure LacZ expression from the knockdown strains, with and without isopropyl b-D-1-thiogalactopyranoside (IPTG), a chemical that inhibits the lac repressor (LacI) (Lewis, 2005).”
MethodRNA processing enables predictable programming of gene expression
Qi, L. S., Haurwitz, R. E., Shao, W., Doudna, J. A., & Arkin, A. P. (2012) · Nature Biotechnology · doi:10.1038/nbt.2355 · Cited by 198 · cited 2× · see citing works
“Genetic transformation and verification of transformationwere done as previously described (Qi et al., 2012), using AmpR, CmR, or KanR genes as selectable markers.”
BackgroundMethodSelf-citationDiscontinuous Mechanism of Transcription Elongation
Nudler, E., Goldfarb, A., & Kashlev, M. (1994) · Science · doi:10.1126/science.8047884 · Cited by 144 · cited 1× · see citing works
“The distance between the pause site and the target site is 19 bp, which is in perfect accordance with the previously reported 18 bp distance between the nucleotide incorporation of RNAP and its front edge (Nudler et al., 1994).”
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Genome engineering using the CRISPR-Cas9 system
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133 · see citing works
The new frontier of genome engineering with CRISPR-Cas9
Doudna, J. A., & Charpentier, E. (2014) · Science · doi:10.1126/science.1258096 · Cited by 7,062 · see citing works
Self-citationDevelopment and Applications of CRISPR-Cas9 for Genome Engineering
Hsu, P. D., Lander, E. S., & Zhang, F. (2014) · Cell · doi:10.1016/j.cell.2014.05.010 · Cited by 5,762 · see citing works
Gene regulation by long non-coding RNAs and its biological functions
Statello, L., Guo, C.-J., Chen, L.-L., & Huarte, M. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00315-9 · Cited by 4,991 · see citing works
DNA targeting specificity of RNA-guided Cas9 nucleases
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741 · see citing works
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., et al. (2013) · Cell · doi:10.1016/j.cell.2013.06.044 · Cited by 3,696 · see citing works
Self-citationUnique features of long non-coding RNA biogenesis and function
Quinn, J. J., & Chang, H. Y. (2015) · Nature Reviews Genetics · doi:10.1038/nrg.2015.10 · Cited by 3,653 · see citing works
CRISPR-Cas systems for editing, regulating and targeting genomes
Sander, J. D., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2842 · Cited by 3,153 · see citing works
Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation
Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., Guimaraes, C., Panning, B., Ploegh, H. L., Bassik, M. C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.029 · Cited by 2,728 · see citing works
Self-citationCrystal structure of Cas9 in complex with guide RNA and target DNA
Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306 · see citing works
CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing
Labun, K., Montague, T. G., Krause, M., Cleuren, Y. N. T., Tjeldnes, H., & Valen, E. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz365 · Cited by 2,009 · see citing works
Improving CRISPR-Cas nuclease specificity using truncated guide RNAs
Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2808 · Cited by 1,993 · see citing works
“…to implement with applications involving multiplex 12–14 or genome-wide libraries of gRNAs 15, 16 and, unlike the paired nickase strategy, can also be used to improve the specificities of dCas9 25 or dCas9 fusions to heterologous effector domains such as transcriptional regulatory domains 17–19 .”
MethodDixit, A., Parnas, O., Li, B., Chen, J., Fulco, C. P., Jerby-Arnon, L., Marjanovic, N. D., Dionne, D., Burks, T., Raychowdhury, R., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.038 · Cited by 1,863 · see citing works
Self-citationDynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System
Chen, B., Gilbert, L. A., Cimini, B. A., Schnitzbauer, J., Zhang, W., Li, G., Park, J. S., Blackburn, E. H., Weissman, J. S., Qi, L. S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.12.001 · Cited by 1,931 · see citing works
Self-citationHilton, I. B., D’Ippolito, A. M., Vockley, C. M., Thakore, P. I., Crawford, G. E., Reddy, T. E., & Gersbach, C. A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3199 · Cited by 1,879 · see citing works
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
Sternberg, S. H., Redding, S., Jínek, M., Greene, E. C., & Doudna, J. A. (2014) · Nature · doi:10.1038/nature13011 · Cited by 1,775 · see citing works
Self-citationMali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L., & Church, G. M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2675 · Cited by 1,752 · see citing works
The CRISPR tool kit for genome editing and beyond
Adli, M. (2018) · Nature Communications · doi:10.1038/s41467-018-04252-2 · Cited by 1,642 · see citing works
Highly efficient Cas9-mediated transcriptional programming
Chavez, A., Scheiman, J., Vora, S., Pruitt, B. W., Tuttle, M., P R Iyer, E., Lin, S., Kiani, S., Guzman, C. D., Wiegand, D. J., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3312 · Cited by 1,622 · see citing works
Yang, H., Wang, H., Shivalila, C. S., Cheng, A. W., Shi, L., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.08.022 · Cited by 1,596 · see citing works
RNA virus interference via CRISPR/Cas13a system in plants
Aman, R., Ali, Z., Butt, H., Mahas, A., Aljedaani, F., Khan, M. Z., Ding, S., & Mahfouz, M. (2018) · Genome Biology · doi:10.1186/s13059-017-1381-1 · Cited by 1,497 · see citing works
“However, like dCas9, dCas13a retains its ability to bind specifically to the target RNA and therefore can function as an RNA-guided RNA-binding protein [11, 14].”
BackgroundLi, J., Norville, J. E., Aach, J., McCormack, M., Zhang, D., Bush, J., Church, G. M., & Sheen, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2654 · Cited by 1,499 · see citing works
Zuris, J. A., Thompson, D. B., Shu, Y., Guilinger, J. P., Bessen, J. L., Hu, J. H., Maeder, M. L., Joung, J. K., Chen, Z.-Y., & Liu, D. R. (2015) · Nature Biotechnology · doi:10.1038/nbt.3081 · Cited by 1,460 · see citing works
Pattanayak, V., Lin, S., Guilinger, J. P., Ma, E., Doudna, J. A., & Liu, D. R. (2013) · Nature Biotechnology · doi:10.1038/nbt.2673 · Cited by 1,487 · see citing works
The next generation of CRISPR–Cas technologies and applications
Pickar-Oliver, A., & Gersbach, C. A. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0131-5 · Cited by 1,459 · see citing works
Dunbar, C. E., High, K. A., Joung, J. K., Kohn, D. B., Ozawa, K., & Sadelain, M. (2018) · Science · doi:10.1126/science.aan4672 · Cited by 1,410 · see citing works
“A number of clever strategies that could eventually be applied clinically involve the use of RNA-guided catalytically inactive Cas9 (“dead Cas9” or dCas9) to turn genes on and off by blocking transcriptional machinery or recruiting epigenetic regulators (59, 60).”
Morris, K. V., & Mattick, J. S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3722 · Cited by 1,389 · see citing works
RNA-guided gene activation by CRISPR-Cas9-based transcription factors
Perez-Pinera, P., Kocak, D. D., Vockley, C. M., Adler, A. F., Kabadi, A. M., Polstein, L. R., Thakore, P. I., Glass, K. A., Ousterout, D. G., Leong, K. W., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2600 · Cited by 1,328 · see citing works
Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system
Jiang, Y., Chen, B., Duan, C., Sun, B., Yang, J., & Yang, S. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.04023-14 · Cited by 1,362 · see citing works
“coli (24, 35), which separated cas9 and the sgRNA in pCas and pTarget series, respectively (Fig.”
BackgroundMethodGTP Cyclohydrolase 1/Tetrahydrobiopterin Counteract Ferroptosis through Lipid Remodeling
Kraft, V. A. N., Bezjian, C. T., Pfeiffer, S., Ringelstetter, L., Müller, C., Zandkarimi, F., Merl‐Pham, J., Bao, X., Anastasov, N., Kössl, J., et al. (2019) · ACS Central Science · doi:10.1021/acscentsci.9b01063 · Cited by 1,338 · see citing works
Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease
Anders, C., Niewoehner, O., Duerst, A., & Jínek, M. (2014) · Nature · doi:10.1038/nature13579 · Cited by 1,319 · see citing works
Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening
Joung, J., Konermann, S., Gootenberg, J. S., Abudayyeh, O. O., Platt, R. J., Brigham, M. D., Sanjana, N. E., & Zhang, F. (2017) · Nature Protocols · doi:10.1038/nprot.2017.016 · Cited by 1,243 · see citing works
Off-target Effects in CRISPR/Cas9-mediated Genome Engineering
Zhang, X.-H., Tee, L. Y., Wang, X.-G., Huang, Q.-S., & Yang, S.-H. (2015) · Molecular Therapy - Nucleic Acids · doi:10.1038/mtna.2015.37 · Cited by 1,273 · see citing works
Editing DNA Methylation in the Mammalian Genome
Liu, X. S., Wu, H., Ji, X., Stelzer, Y., Wu, X., Czauderna, S., Shu, J., Dadon, D., Young, R. A., & Jaenisch, R. (2016) · Cell · doi:10.1016/j.cell.2016.08.056 · Cited by 1,224 · see citing works
“…activator/suppressor, chromatin modifier, and green fluorescence protein to regulate gene expression, to modify chromatin, and to image genomic loci respectively (Chen et al., 2013; Gilbert et al., 2013; Hilton et al., 2015; Jinek et al., 2012; Konermann et al., 2015; Qi et al., 2013).”
Li, G., Burkhardt, D. H., Gross, C. A., & Weissman, J. S. (2014) · Cell · doi:10.1016/j.cell.2014.02.033 · Cited by 1,218 · see citing works
Self-citationJiang, W., Zhou, H., Bi, H., Fromm, M., Yang, B., & Weeks, D. P. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt780 · Cited by 1,250 · see citing works
Structures of Cas9 endonucleases reveal RNA-mediated conformational activation
Jinek, M., Jiang, F., Taylor, D. W., Sternberg, S. H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., et al. (2014) · Science · doi:10.1126/science.1247997 · Cited by 1,230 · see citing works
Self-citationHigh-throughput functional genomics using CRISPR-Cas9
Shalem, O., Sanjana, N. E., & Zhang, F. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3899 · Cited by 1,233 · see citing works
CRISPR interference (CRISPRi) for sequence-specific control of gene expression
Larson, M. H., Gilbert, L. A., Wang, X., Lim, W. A., Weissman, J. S., & Qi, L. S. (2013) · Nature Protocols · doi:10.1038/nprot.2013.132 · Cited by 1,193 · see citing works
Self-citationAdamson, B., Norman, T. M., Jost, M., Cho, M. Y., Nuñez, J. K., Chen, Y., Villalta, J. E., Gilbert, L. A., Horlbeck, M. A., Hein, M. Y., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.048 · Cited by 1,193 · see citing works
“coli MG1655-derived strain by lambda Red recombinase-mediated recombineering as described previously (Qi et al., 2013), and moved from the MG1655-derived strain into the dCas9expressing BW25113 strain by P1 transduction and selection on kanamycin following established protocols.”
MethodInfluentialSelf-citationCas9 as a versatile tool for engineering biology
Mali, P., Esvelt, K. M., & Church, G. M. (2013) · Nature Methods · doi:10.1038/nmeth.2649 · Cited by 1,197 · see citing works
The CRISPR/Cas9 system for plant genome editing and beyond
Bortesi, L., & Fischer, R. (2014) · Biotechnology Advances · doi:10.1016/j.biotechadv.2014.12.006 · Cited by 1,234 · see citing works
Delivering CRISPR: a review of the challenges and approaches
Lino, C. A., Harper, J. C., Carney, J. P., & Timlin, J. A. (2018) · Drug Delivery · doi:10.1080/10717544.2018.1474964 · Cited by 1,185 · see citing works
“Qu et al. repurposed CRISPR into an RNA-guided platform for controlling gene expression by developing a catalytically-dead Cas9 enzyme (dCas9) that retained its capability to recognize and bind a target DNA sequence (Qi et al., 2013).”
BackgroundCRISPR RNA–guided activation of endogenous human genes
Maeder, M. L., Linder, S. J., Cascio, V. M., Fu, Y., Ho, Q. H., & Joung, J. K. (2013) · Nature Methods · doi:10.1038/nmeth.2598 · Cited by 1,249 · see citing works
The promise and challenge of therapeutic genome editing
Doudna, J. A. (2020) · Nature · doi:10.1038/s41586-020-1978-5 · Cited by 1,126 · see citing works
Self-citationThe chromatin accessibility landscape of primary human cancers
Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science · doi:10.1126/science.aav1898 · Cited by 1,230 · see citing works
“To verify a regulatory interaction for the predicted peak-to-gene links, we used a CRISPR interference (CRISPRi) (40) strategy using a catalytically dead Cas9 (dCas9) fused to a Kruppelassociated box (KRAB) domain, which mediates focal heterochromatin formation and functional silencing of noncoding DNA regulatory elem…”
MethodCRISPR/Cas9 in Genome Editing and Beyond
Wang, H., Russa, M. F. L., & Qi, L. S. (2016) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060815-014607 · Cited by 1,165 · see citing works
“Although CRISPRi is generally highly efficient in prokaryotes, the dCas9–sgRNA complex alone may not be very efficient at silencing gene expression in mammalian cells (41).”
BackgroundInfluentialSelf-citationBikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., & Marraffini, L. A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt520 · Cited by 1,111 · see citing works
Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities
Sanson, K. R., Hanna, R. E., Hegde, M., Donovan, K. F., Strand, C., Sullender, M. E., Vaimberg, E. W., Goodale, A., Root, D. E., Piccioni, F., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07901-8 · Cited by 1,043 · see citing works
CRISPR technology: A decade of genome editing is only the beginning
Wang, J. Y., & Doudna, J. A. (2023) · Science · doi:10.1126/science.add8643 · Cited by 1,058 · see citing works
“As a result, the first examples of engineered CRISPR-Cas involved transcriptional repression or activation to silence or up-regulate specific genes (8, 9).”
BackgroundSelf-citationGenetic circuit design automation
Nielsen, A. A. K., Der, B. S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E. A., Ross, D., Densmore, D. M., & Voigt, C. A. (2016) · Science · doi:10.1126/science.aac7341 · Cited by 1,032 · see citing works
“Within this paradigm, the regulators performing the gate biochemistry could be transcrip-tionfactors( 21 , 63 ),RNA-basedregulation( 64 – 66 ), protein-protein interactions ( 19 , 67 ), CRISPR/ Cas-based regulation ( 68 – 71 ), or recombinases ( 25 , 26 , 72 ).”
Horlbeck, M. A., Gilbert, L. A., Villalta, J. E., Adamson, B., Pak, R. A., Chen, Y., Fields, A. P., Park, C. Y., Corn, J. E., Kampmann, M., et al. (2016) · eLife · doi:10.7554/elife.19760 · Cited by 894 · see citing works
“…toxicity due to nuclease activity, combined with our previous findings that CRISPRi enables inducible, reversible, and homogenous manipulation of gene expression (Gilbert et al., 2014; Mandegar et al., 2016; Qi et al., 2013), make CRISPRi a state-of-the-art approach for loss-of-function studies.”
BackgroundMethodInfluentialSelf-citationExploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials
Bikard, D., Euler, C. W., Jiang, W., Nussenzweig, P. M., Goldberg, G. W., Duportet, X., Fischetti, V. A., & Marraffini, L. A. (2014) · Nature Biotechnology · doi:10.1038/nbt.3043 · Cited by 986 · see citing works
CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes
Komor, A. C., Badran, A. H., & Liu, D. R. (2016) · Cell · doi:10.1016/j.cell.2016.10.044 · Cited by 1,011 · see citing works
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
Wu, X., Scott, D. A., Kriz, A. J., Chiu, A. C., Hsu, P. D., Dadon, D. B., Cheng, A. W., Trevino, A. E., Konermann, S., Chen, S., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2889 · Cited by 944 · see citing works
Applications of CRISPR technologies in research and beyond
Barrangou, R., & Doudna, J. A. (2016) · Nature Biotechnology · doi:10.1038/nbt.3659 · Cited by 1,005 · see citing works
Self-citationCHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering
Labun, K., Montague, T. G., Gagnon, J. A., Thyme, S. B., & Valen, E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw398 · Cited by 910 · see citing works
Principles of genetic circuit design
Brophy, J. A. N., & Voigt, C. A. (2014) · Nature Methods · doi:10.1038/nmeth.2926 · Cited by 934 · see citing works
A brief history of synthetic biology
Cameron, D. E., Bashor, C. J., & Collins, J. J. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3239 · Cited by 944 · see citing works
Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds
Zalatan, J. G., Lee, M. E., Almeida, R., Gilbert, L. A., Whitehead, E. H., La Russa, M., Tsai, J. C., Weissman, J. S., Dueber, J. E., Qi, L. S., et al. (2015) · Cell · doi:10.1016/j.cell.2014.11.052 · Cited by 938 · see citing works
“The bacterial type II CRISPR (clustered regularly interspaced short palindromic repeats) interference system (CRISPRi) provides an alternative suite of tools for genome regulation (Qi et al., 2013).”
Self-citationCRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity
Barrangou, R., & Marraffini, L. A. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.03.011 · Cited by 907 · see citing works
Nadeem, M. A., Nawaz, M. A., Shahid, M. Q., Doğan, Y., Cömertpay, G., Yıldız, M., Hatipoğlu, R., Ahmad, F., Alsaleh, A., Labhane, N. M., et al. (2017) · Biotechnology & Biotechnological Equipment · doi:10.1080/13102818.2017.1400401 · Cited by 884 · see citing works
Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation
Dominguez, A. A., Lim, W. A., & Qi, L. S. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.2 · Cited by 832 · see citing works
Self-citationGuilinger, J. P., Thompson, D. B., & Liu, D. R. (2014) · Nature Biotechnology · doi:10.1038/nbt.2909 · Cited by 836 · see citing works
Adeno-associated virus as a delivery vector for gene therapy of human diseases
Wang, J.-H., Gessler, D. J., Zhan, W., Gallagher, T. F., & Gao, G. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01780-w · Cited by 895 · see citing works
Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects
Shen, B., Zhang, W., Zhang, J., Zhou, J., Wang, J.-Y., Chen, L., Wang, L., Hodgkins, A., Iyer, V., Huang, X., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2857 · Cited by 827 · see citing works
Principles and Applications of Nucleic Acid Strand Displacement Reactions
Simmel, F. C., Yurke, B., & Singh, H. R. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00580 · Cited by 792 · see citing works
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Kuscu, C., Arslan, S., Singh, R., Thorpe, J., & Adli, M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2916 · Cited by 777 · see citing works
Optical control of mammalian endogenous transcription and epigenetic states
Konermann, S., Brigham, M. D., Trevino, A. E., Hsu, P. D., Heidenreich, M., Cong, L., Platt, R. J., Scott, D. A., Church, G. M., & Zhang, F. (2013) · Nature · doi:10.1038/nature12466 · Cited by 803 · see citing works
Orthogonal Cas9 proteins for RNA-guided gene regulation and editing
Esvelt, K. M., Mali, P., Braff, J. L., Moosburner, M., Yaung, S. J., & Church, G. M. (2013) · Nature Methods · doi:10.1038/nmeth.2681 · Cited by 786 · see citing works
Repurposing the CRISPR-Cas9 system for targeted DNA methylation
Vojta, A., Dobrinić, P., Tadić, V., Bočkor, L., Korać, P., Jülg, B. D., Klasić, M., & Zoldoš, V. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw159 · Cited by 772 · see citing works
“Even when lower transcript levels were confidently detected after using the inactive construct, they could be explained by CRISPR interference (16), where inactive Cas9 competes with transcription factors for binding to the promoter region.”
BackgroundIn vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9
Swiech, L., Heidenreich, M., Banerjee, A., Habib, N., Li, Y., Trombetta, J., Sur, M., & Zhang, F. (2015) · Nature Biotechnology · doi:10.1038/nbt.3055 · Cited by 772 · see citing works
Cheng, A. W., Wang, H., Yang, H., Shi, L., Yarden Katz, A., Theunissen, T. W., Rangarajan, S., Shivalila, C., Dadon, D. B., & Jaenisch, R. (2013) · Cell Research · doi:10.1038/cr.2013.122 · Cited by 743 · see citing works
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells
Liu, S. J., Horlbeck, M. A., Cho, S. W., Birk, H. S., Malatesta, M., He, D. X., Attenello, F. J., Villalta, J. E., Cho, M. Y., Chen, Y., et al. (2016) · Science · doi:10.1126/science.aah7111 · Cited by 734 · see citing works
Self-citationCRISPR/Cas9 therapeutics: progress and prospects
Li, T., Yang, Y., Qi, H., Cui, W., Zhang, L., Fu, X., He, X., Liu, M., Li, P., & Yu, T. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01309-7 · Cited by 770 · see citing works
A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing
Mok, B. Y., de Moraes, M. H., Zeng, J., Bosch, D. E., Kotrys, A. V., Raguram, A., Hsu, F., Radey, M. C., Peterson, S. B., Mootha, V. K., et al. (2020) · Nature · doi:10.1038/s41586-020-2477-4 · Cited by 733 · see citing works
Unravelling the structural and mechanistic basis of CRISPR–Cas systems
John van der, O. O. S. T., Westra, E. R., Jackson, R. N., & Wiedenheft, B. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3279 · Cited by 715 · see citing works
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria
Peters, J. M., Colavin, A., Shi, H., Czarny, T. L., Larson, M. H., Wong, S. S., Hawkins, J. S., Lu, C. H. S., Koo, B., Marta, E., et al. (2016) · Cell · doi:10.1016/j.cell.2016.05.003 · Cited by 716 · see citing works
Self-citationDeterminants of enhancer and promoter activities of regulatory elements
Andersson, R., & Sandelin, A. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0173-8 · Cited by 713 · see citing works
Mitochondrial stress is relayed to the cytosol by an OMA1–DELE1–HRI pathway
Guo, X., Aviles, G., Liu, Y., Tian, R., Unger, B. A., Lin, Y.-H. T., Wiita, A. P., Xu, K., Correia, M. A., & Kampmann, M. (2020) · Nature · doi:10.1038/s41586-020-2078-2 · Cited by 674 · see citing works
A split-Cas9 architecture for inducible genome editing and transcription modulation
Zetsche, B., Volz, S. E., & Zhang, F. (2015) · Nature Biotechnology · doi:10.1038/nbt.3149 · Cited by 704 · see citing works
RNA-guided DNA insertion with CRISPR-associated transposases
Strecker, J. G., Ladha, A., Gardner, Z., Schmid-Burgk, J. L., Makarova, K. S., Koonin, E. V., & Zhang, F. (2019) · Science · doi:10.1126/science.aax9181 · Cited by 696 · see citing works
“Mali P et al., RNA-Guided Human Genome Engineering via Cas9.”
BackgroundInfluentialA CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation
Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., Voytas, D. F., Hsieh, T.-F., Zhang, Y., & Qi, Y. (2015) · Plant Physiology · doi:10.1104/pp.15.00636 · Cited by 707 · see citing works
“…to successfully target endogenous plant genes, creatingmutations, gene replacements, deletions, or inversions in Arabidopsis (Arabidopsis thaliana), tobacco (Nicotiana benthamiana), and soybean (Glycine max; Townsend et al., 2009; Zhang et al., 2010; Curtin et al., 2011; Qi et al., 2013b, 2014).”
BackgroundMethodInfluentialHow do lncRNAs regulate transcription?
Long, Y., Wang, X., Youmans, D. T., & Cech, T. R. (2017) · Science Advances · doi:10.1126/sciadv.aao2110 · Cited by 688 · see citing works
“Inserting multiple polyadenylation sequences downstream from a lncRNA promoter and interfering with lncRNA transcription using CRISPR interference (159) are more surgically incisive, but negative results must be interpreted with caution because these techniques truncate rather than eliminate lncRNA transcription.”
BackgroundCRISPR/Cas9 for genome editing: progress, implications and challenges
Zhang, F., Wen, Y., & Guo, X. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu125 · Cited by 694 · see citing works
Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems
Mohanraju, P., Makarova, K. S., Zetsche, B., Zhang, F., Koonin, E. V., & John van der, O. O. S. T. (2016) · Science · doi:10.1126/science.aad5147 · Cited by 668 · see citing works
“The dCas9 has been used for transcriptional activation and repression [134-137], for localizing fluorescent protein labels [138], and for recruiting histone modifying enzymes [139, 140].”
MethodSynthetic lethality and cancer
O’Neil, N. J., Bailey, M. L., & Hieter, P. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.47 · Cited by 658 · see citing works
A light-inducible CRISPR-Cas9 system for control of endogenous gene activation
Polstein, L. R., & Gersbach, C. A. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1753 · Cited by 630 · see citing works
Sequence determinants of improved CRISPR sgRNA design
Xu, H., Xiao, T., Chen, C.-H., Li, W., Meyer, C. A., Wu, Q., Wu, D., Cong, L., Zhang, F., Liu, J. S., et al. (2015) · Genome Research · doi:10.1101/gr.191452.115 · Cited by 625 · see citing works
“Alternatively, in the CRISPRi/a systems, catalytically inactive Cas9 (dCas9) proteins guided by sgRNAs enable the localization of effector domains to repress or activate gene transcription without modifying DNA (Gilbert et al. 2013; Qi et al. 2013).”
Harnessing genomics to fast-track genetic improvement in aquaculture
Houston, R. D., Bean, T. P., Macqueen, D. J., Gundappa, M. K., Jin, Y. H., Jenkins, T. L., Selly, S.-L. C., Martín, S., Stevens, J. R., Santos, E. M., et al. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0227-y · Cited by 633 · see citing works
Exosome–Liposome Hybrid Nanoparticles Deliver CRISPR/Cas9 System in MSCs
Lin, Y., Wu, J., Gu, W., Huang, Y., Tong, Z., Huang, L., & Tan, J. (2018) · Advanced Science · doi:10.1002/advs.201700611 · Cited by 625 · see citing works
Photoactivatable CRISPR-Cas9 for optogenetic genome editing
Nihongaki, Y., Kawano, F., Nakajima, T., & Sato, M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3245 · Cited by 609 · see citing works
Rock, J. M., Hopkins, F. F., Chavez, A., Diallo, M., Chase, M. R., Gerrick, E. R., Pritchard, J. R., Church, G. M., Rubin, E. J., Sassetti, C. M., et al. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.274 · Cited by 538 · see citing works
“4 and Supplementary Table 1); (3) a Tet repressor; (4) a single-copy L5-integrating backbone44; (5) a pBR322-derived E.”
Past, present, and future of CRISPR genome editing technologies
Pacesa, M., Pelea, O., & Jinek, M. (2024) · Cell · doi:10.1016/j.cell.2024.01.042 · Cited by 609 · see citing works
“196 To suppress gene expression in eukaryotic cells, nuclease-inactive Cas9 can be fused to various transcriptional and epigenetic modulators, for example, the KRAB transcriptional repressor domain, 197,198 and targeted to promoter regions of actively transcribed genes.”
BackgroundCano-Gamez, E., & Trynka, G. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00424 · Cited by 608 · see citing works
Bock, C., Datlinger, P., Chardon, F. M., Coelho, M. A., Dong, M. B., Lawson, K. A., Lu, T., Maroc, L., Norman, T. M., Song, B., et al. (2022) · Nature Reviews Methods Primers · doi:10.1038/s43586-021-00093-4 · Cited by 591 · see citing works
Self-citationA Call for Systematic Research on Solute Carriers
César‐Razquin, A., Snijder, B., Frappier‐Brinton, T., Isserlin, R., Gyimesi, G., Bai, X., Reithmeier, R. A., Hepworth, D., Hediger, M. A., Edwards, A. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.022 · Cited by 578 · see citing works
Liu, Q., Gao, R., Li, J., Lin, L., Zhao, J., Sun, W., & Tian, C. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-016-0693-9 · Cited by 577 · see citing works
Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function
Shifrut, E., Carnevale, J., Tobin, V., Roth, T. L., Woo, J. M., Bui, C. T., Li, P. J., Diolaiti, M. E., Ashworth, A., & Marson, A. (2018) · Cell · doi:10.1016/j.cell.2018.10.024 · Cited by 573 · see citing works
The CRISPR-Cas immune system: Biology, mechanisms and applications
Rath, D., Amlinger, L., Rath, A., & Lundgren, M. (2015) · Biochimie · doi:10.1016/j.biochi.2015.03.025 · Cited by 565 · see citing works
- Authors
- Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A.
- Affiliations
- QB3 (US)
- Corresponding author
- Qi, Lei S.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-02
- Volume
- 152
- Issue
- 5
- Pages
- 1173-1183
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3664290
- OpenAlex
- W2160051211
- Cited by
- 5,016
- References
- 30
- Citations by year
- 2026: 291 · 2025: 375 · 2024: 418 · 2023: 403 · 2022: 497 · 2021: 465 · 2020: 499 · 2019: 444 · 2018: 417 · 2017: 382 · 2016: 315 · 2015: 229 · 2014: 189 · 2013: 87
- FWCI
- 121.73
- Type
- journal article
- Language
- en
- Update notices
- erratum (2021-02-04)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Cancer Institute (U01CA168370)
- National Institute of General Medical Sciences (P50GM081879, F32GM100611)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- CRISPR interference, Cas9, transcriptional repression, dCas9, guide RNA, RNA polymerase binding, transcription factor binding, Escherichia coli, mammalian cells, off-target effects
- MeSH terms
- Endodeoxyribonucleases, Escherichia coli, Streptococcus pyogenes, Gene Expression, RNA Interference, Gene Knockdown Techniques, RNA, Small Untranslated, Transcription Initiation, Genetic, Transcription Elongation, Genetic
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