The DOI matches its Crossref record; 29 of the 30 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“Due to its catalytically inactive nature, modifications of gene expression caused by dCas9 are transient, since the genomic DNA is not altered [61,77].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [77]
The cited source says what the claim attributes to it.
In the citing paper
“When both RuvC and HNH catalytic domains of Cas9 are modified through two silencing mutations, the system loses its DNA cleaving capabilities but retains the ability to bind to targeted sequences [61,77].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [77]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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×
“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×
“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×
“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×
“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 5,947 · cited 1×
“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 3,651
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
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×
“…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 2,751 · cited 1×
“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×
“Maturation of crRNA requires tracrRNA and RNase III (Deltcheva et al., 2011).”
MethodInfluential
Cited by
Sorted by citations
Items 901–1,000 of 1,026
Genetic circuit characterization and debugging using RNA‐seq
Gorochowski, T. E., Borujeni, A. E., Park, Y., Nielsen, A. A. K., Zhang, J., Der, B. S., Gordon, D. B., & Voigt, C. A. (2017) · Molecular Systems Biology · doi:10.15252/msb.20167461 · Cited by 78
“…(e.g., DNA-binding proteins (Moon et al , 2012; Stanton et al , 2014), recombinases (Bonnet et al , 2013; Siuti et al , 2013; Fernandez-Rodriguez et al , 2015), and CRISPRi (Gilbert et al , 2013; Larson et al , 2013; Qi et al , 2013; Kiani et al , 2014; Nielsen & Voigt, 2014; Gander et al , 2017)).”
CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases
Koo, B., Kim, J., Kweon, J., Jin, C. E., Kim, S., Kim, Y., & Shin, Y. M. (2018) · Sensors and Actuators B Chemical · doi:10.1016/j.snb.2018.06.069 · Cited by 78
“Cas9 is guided by the sgRNA that specifically bind to and cleave double-stranded DNA in a site-specific manner [18] [19] [20] [21] .”
BackgroundNewer Gene Editing Technologies toward HIV Gene Therapy
Manjunath, N., Yi, G., Dang, Y., & Shankar, P. (2013) · Viruses · doi:10.3390/v5112748 · Cited by 77
Next stop for the CRISPR revolution: RNA‐guided epigenetic regulators
Vora, S., Tuttle, M. L., Cheng, J. Y., & Church, G. M. (2016) · FEBS Journal · doi:10.1111/febs.13768 · Cited by 75
Targeted Transcriptional Repression in Bacteria Using CRISPR Interference (CRISPRi)
Hawkins, J. S., Wong, S., Peters, J. M., Almeida, R., & Qi, L. S. (2015) · Methods in Molecular Biology · doi:10.1007/978-1-4939-2687-9_23 · Cited by 61
Self-citationDetermination of local chromatin composition by CasID
Schmidtmann, E., Anton, T., Rombaut, P., Herzog, F., & Leonhardt, H. (2016) · Nucleus · doi:10.1080/19491034.2016.1239000 · Cited by 75
Xu, X., Duan, D., & Chen, S. (2017) · Scientific Reports · doi:10.1038/s41598-017-00180-1 · Cited by 79
A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells
Fonseca, J. P., Bonny, A. R., Kumar, G. R., Ng, A. H., Town, J. P., Wu, Q. C., Aslankoohi, E., Chen, S. Y., Dods, G., Harrigan, P., et al. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00322 · Cited by 78
Broadening the GMO risk assessment in the EU for genome editing technologies in agriculture
Kawall, K., Cotter-Howells, J. D., & Then, C. (2020) · Environmental Sciences Europe · doi:10.1186/s12302-020-00361-2 · Cited by 84
CRISPR/Cas: From Tumor Gene Editing to T Cell-Based Immunotherapy of Cancer
Azangou‐Khyavy, M., Ghasemi, M., Khanali, J., Boroomand-Saboor, M., Jamalkhah, M., Soleimani, M., & Kiani, J. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.02062 · Cited by 80
“Through binding different effector parts to dCas9, it can be used as a transcription inhibitor or activator or even epigenetic modulator (16).”
BackgroundCRISPR/Cas-Based Modifications for Therapeutic Applications: A Review
Bharathkumar, N., Abraham, S., Meera, P., Aksah, S., Muthu, K., Saravanan, K. M., & Anand, T. (2021) · Molecular Biotechnology · doi:10.1007/s12033-021-00422-8 · Cited by 80
Enhancement of specialized metabolites using CRISPR/Cas gene editing technology in medicinal plants
Das, S., Kwon, M., & Kim, J. (2024) · Frontiers in Plant Science · doi:10.3389/fpls.2024.1279738 · Cited by 82
Transposons As Tools for Functional Genomics in Vertebrate Models
Kawakami, K., Largaespada, D. A., & Ivics, Z. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.07.006 · Cited by 77
Programmable DNA looping using engineered bivalent dCas9 complexes
Hao, N., Shearwin, K. E., & Dodd, I. B. (2017) · Nature Communications · doi:10.1038/s41467-017-01873-x · Cited by 80
Transcription of Bacterial Chromatin
Shen, B. A., & Landick, R. C. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.05.041 · Cited by 79
In vivo locus-specific editing of the neuroepigenome
Yim, Y. Y., Teague, C. D., & Nestler, E. J. (2020) · Nature Reviews Neuroscience · doi:10.1038/s41583-020-0334-y · Cited by 76
Synthetic Biology: A Unifying View and Review Using Analog Circuits
Teo, J. J. Y., Woo, S. S., & Sarpeshkar, R. (2015) · IEEE Transactions on Biomedical Circuits and Systems · doi:10.1109/tbcas.2015.2461446 · Cited by 77
“do not benefit from editing the genome, but desire specific regulation, a mutated Cas9 (dCas9), with a DNA binding domain but no nuclease activity can efficiently implement steric blocking of transcription: A CRISPR interference system (CRISPRi) that uses dCas9 and sgRNA was able to repress transcription efficiency by…”
Stachler, A.-E., & Marchfelder, A. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.724062 · Cited by 76
“This is in contrast to the CRISPR-Cas9 CRISPRi tool used in eukarya and bacteria and the type I-E CRISPRi system in bacteria, where the targeting efficiency in the promoter region is independent of the nature of the strand (14, 19, 20).”
BackgroundMethodResultInfluentialApplications of CRISPR Genome Engineering in Cell Biology
Wang, F., & Qi, L. S. (2016) · Trends in Cell Biology · doi:10.1016/j.tcb.2016.08.004 · Cited by 79
“In bacteria, the dCas9 protein was sufficient to induce strong sequence-specific gene repression, simply by sterically hindering the transcriptional activity of RNA polymerase [55, 56].”
Self-citationRepurposing a Two-Component System-Based Biosensor for the Killing of Vibrio cholerae
Jayaraman, P., Holowko, M. B., Yeoh, J. W., Lim, S., & Poh, C. L. (2017) · ACS Synthetic Biology · doi:10.1021/acssynbio.7b00058 · Cited by 76
Hupfeld, M., Trasanidou, D., Ramazzini, L., Klumpp, J., Loessner, M. J., & Kilcher, S. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky544 · Cited by 77
Martínez, O. F., Rigueiras, P. O., Pires, Á. D. S., Porto, W. F., Silva, O. N., de la Fuente‐Núñez, C., & Franco, O. L. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2018.00444 · Cited by 76
“This system is based on the use of a Cas-9 DNA endonuclease that is not catalytically active (dCas-9) but can be directed toward the target gene by a small guide RNA and repress the expression of the target gene via interfering with the transcriptional process (Qi et al., 2013).”
MethodMultiplexed CRISPR-Cas9-Based Genome Editing of Rhodosporidium toruloides
Otoupal, P. B., Ito, M., Arkin, A. P., Magnuson, J. K., Gladden, J. M., & Skerker, J. M. (2019) · mSphere · doi:10.1128/msphere.00099-19 · Cited by 79
“as using two (37) or three (38) NLSs in tandem has previously been shown to increase editing efficiency due to improved nuclear localization (39).”
BackgroundSelf-citationPenicillium chrysogenum, a Vintage Model with a Cutting-Edge Profile in Biotechnology
Fierro, F., Vaca, I., Castillo, N. I., García-Rico, R. O., & Chávez, R. (2022) · Microorganisms · doi:10.3390/microorganisms10030573 · Cited by 79
“dCas9 refers to defective versions of the Cas9 protein that cannot cut target DNA but still can bind to it, so they can be used for transcriptional regulation [358].”
BackgroundMolecular tools for gene manipulation in filamentous fungi
Wang, S., Chen, H., Tang, X., Zhang, H., Chen, W., & Chen, Y. Q. (2017) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-017-8486-z · Cited by 82
“Other applications of the CRISPR/Cas9 systems used in bacteria, such as CRISPR interference (Cleto et al. 2016; Qi et al. 2013) and activation (Cheng et al.”
BackgroundCRISPR–Cas9 a boon or bane: the bumpy road ahead to cancer therapeutics
Ghosh, D., Venkataramani, P., Nandi, S., & Bhattacharjee, S. (2019) · Cancer Cell International · doi:10.1186/s12935-019-0726-0 · Cited by 83
Choi, S. Y., & Woo, H. M. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00091 · Cited by 75
Evaluation of sgRNA Target Sites for CRISPR-Mediated Repression of TP53
Lawhorn, I. E. B., Ferreira, J. P., & Wang, C. L. (2014) · PLoS ONE · doi:10.1371/journal.pone.0113232 · Cited by 75
Direct observation of TALE protein dynamics reveals a two-state search mechanism
Cuculis, L., Abil, Z., Zhao, H., & Schroeder, C. M. (2015) · Nature Communications · doi:10.1038/ncomms8277 · Cited by 75
“Error in localizing single-TALE proteins arises from two main sources as follows: (1) uncertainty due to the finite number of photons collected within each frame during image acquisition, which amounts to localization precision and (2) thermal fluctuations in the DNA template parallel to the direction of TALE diffusio…”
BackgroundYan, M., Li, S., Ding, X.-Y., Guo, X.-P., Jin, Q., & Sun, Y. (2020) · mBio · doi:10.1128/mbio.02364-19 · Cited by 75
“Genomewide screens with CRISPRi technology have been widely used in many organisms, including prokaryotes and eukaryotes (55–57), whereas CRISPR KO screening has only been used in eukaryotes due to the low efficiency of NHEJ-mediated genome editing in prokaryotes.”
Development and Application of CRISPR/Cas in Microbial Biotechnology
Ding, W., Zhang, Y., & Shi, S. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00711 · Cited by 81
“Especially, the CRISPR interference (CRISPRi) (Qi et al., 2013) and the CRISPR activation (CRISPRa) (Tanenbaum et al., 2014) that allow programmed controlling of gene expression without altering the genome, are effective tools for metabolic engineering, and are highlighted here.”
BackgroundMethodInfluentialStrategies to target long non-coding RNAs in cancer treatment: progress and challenges
Dizaji, B. F. (2020) · Egyptian Journal of Medical Human Genetics · doi:10.1186/s43042-020-00074-4 · Cited by 78
O’Geen, H., Tomková, M., Combs, J. A., Tilley, E., & Segal, D. J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac123 · Cited by 81
“As the name implies, CRISPR interference (CRISPRi) functions by interfering with transcription by blocking polymerase binding (21,22,46).”
BackgroundGenome engineering and gene expression control for bacterial strain development
Song, C. W., Lee, J., & Lee, S. Y. (2014) · Biotechnology Journal · doi:10.1002/biot.201400057 · Cited by 77
“This modified and simplified CRISPRdCas9-mediated transcription repression system was successfully used for gene expression regulation [101, 102].”
BackgroundMethodGenome Editing and Its Applications in Model Organisms
Ma, D., & Liu, F. (2015) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.12.001 · Cited by 81
“In addition to genome editing, a modified form of Cas9 that lacks the endonuclease activity, dead Cas9 (dCas9), was first shown to regulate endogenous gene expression in Escherichia coli and mammalian cells [67].”
BackgroundGolden Gate Assembly of CRISPR gRNA expression array for simultaneously targeting multiple genes
Vad‐Nielsen, J., Lin, L., Bolund, L., Nielsen, A. L., & Luo, Y. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2271-5 · Cited by 72
“Targeted inhibition/activation of genes by CRISPRi/ CRISPRa frequently required manipulating multiple genes simultaneously [5, 6, 13].”
BackgroundMetabolic engineering of Escherichia coli for the production of isoprenoids
Ward, V. C. A., Chatzivasileiou, A. O., & Stephanopoulos, G. N. (2018) · FEMS Microbiology Letters · doi:10.1093/femsle/fny079 · Cited by 79
Krause, M. D., Huang, R., Wu, D., Shentu, T., Harrison, D. L., Whalen, M. B., Stolze, L. K., Rienzo, A. D., Moskowitz, I. P. G., Civelek, M., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810568115 · Cited by 77
“Our studies demonstrate that the latest human genetics approaches, such as caQTL mapping (22), AI assay (23), CRISPRi (20), and CRISPR-based assays (19), are powerful tools to investigate possible genetic contributions to cellular mechanotransduction.”
BackgroundEngineered Transcriptional Systems for Cyanobacterial Biotechnology
Camsund, D., & Lindblad, P. (2014) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2014.00040 · Cited by 70
CRISPR-based genome editing in wheat: a comprehensive review and future prospects
Kumar, R., Kaur, A., Pandey, A., Mamrutha, H. M., & Singh, G. P. (2019) · Molecular Biology Reports · doi:10.1007/s11033-019-04761-3 · Cited by 70
Huang, J., Shen, Z., Mao, Q.-L., Zhang, X.-M., Zhang, B., Wu, J.-S., Liu, Z., & Zheng, Y. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00249 · Cited by 74
Functional methylome analysis of human diabetic kidney disease
Park, J., Guan, Y., Sheng, X., Gluck, C. A., Seasock, M. J., Hakimi, A. A., Qiu, C., Pullman, J. M., Verma, A. K., Li, H., et al. (2019) · JCI Insight · doi:10.1172/jci.insight.128886 · Cited by 74
Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium
Lee, M., Lindner, S. E., Lopez-Rubio, J.-J., & Llinás, M. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz012 · Cited by 78
“By disabling the nuclease activity of Cas9, the resulting ‘dead’ Cas9 (or dCas9), when bound to the target gene, can interfere with RNA polymerase-mediated transcription [48].”
BackgroundHow genetic errors in GPCRs affect their function: Possible therapeutic strategies
Stoy, H., & Gurevich, V. V. (2015) · Genes & Diseases · doi:10.1016/j.gendis.2015.02.005 · Cited by 77
Gene targeting and editing in crop plants: a new era of precision opportunities
Rinaldo, A., & Ayliffe, M. (2015) · Molecular Breeding · doi:10.1007/s11032-015-0210-z · Cited by 74
Efficient genome engineering in eukaryotes using Cas9 from Streptococcus thermophilus
Xu, K., Ren, C., Liu, Z., Zhang, T., Zhang, T., Li, D., Wang, L., Yan, Q., Guo, L., Shen, J., et al. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1679-z · Cited by 78
Genome-Scale CRISPR Screens Identify Human Pluripotency-Specific Genes
Ihry, R. J., Salick, M. R., Ho, D. J., Sondey, M., Kommineni, S., Paula, S., Raymond, J., Henry, B., Frias, E., Wang, Q., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.043 · Cited by 73
“To independently validate these results, we used CRISPR-mediated interference (CRISPRi) to knock down the expression of PAWR mRNA without causing DNA damage or genetic mutations (Data S1) (Qi et al., 2013).”
Functional genomics to uncover drug mechanism of action
Nijman, S. M. B. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1963 · Cited by 75
Müh, U., Pannullo, A. G., Weiss, D. S., & Ellermeier, C. D. (2019) · Journal of Bacteriology · doi:10.1128/jb.00711-18 · Cited by 73
“pyogenes that was amplified from pdCas9_bacteria (20).”
Manivannan, P., Siddiqui, M. A., & Malathi, K. (2020) · Journal of Virology · doi:10.1128/jvi.00205-20 · Cited by 71
“RNase L-cleaved small RNAs and control small RNAs were prepared as previously described (46, 80) and transfected (2 g/ml) using Polyjet reagent (SignaGen Laboratories) according to the manufacturer’s protocol.”
MethodNguyen, C. T., Dhakal, D., Pham, V. T. T., Nguyen, H. T., & Sohng, J. K. (2020) · Microorganisms · doi:10.3390/microorganisms8040616 · Cited by 80
“The application of CRISPR interference (CRISPRi) [102] and CRISPR activation (CRISPRa) [103] in addition to gene deletions in multiplexed fashion, can bring forth rational metabolic engineering approaches for activating cryptic BGCs mediated by multi-repurposing of precursor pathways, regulators, and biosynthetic enzy…”
BackgroundApplications of CRISPR-Cas systems in lactic acid bacteria
Roberts, A., & Barrangou, R. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa016 · Cited by 74
Gene Editing by Extracellular Vesicles
Kostyushev, D. S., Kostyusheva, A., Brezgin, S., Vv, S., Volchkova, E. V., Lukashev, A. N., & Chulanov, V. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21197362 · Cited by 75
“Alternatively, nuclease-null Cas9 (or dead Cas9; dCas) proteins may serve as carriers to bring enzymes or functionally active factors to certain locations in the genome [6,7].”
BackgroundSynthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals
Jin, S., Bae, J., Song, Y., Pearcy, N., Shin, J., Kang, S., Minton, N. P., Soucaille, P., & Cho, B. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21207639 · Cited by 73
“CRISPR interference (CRISPRi) replaces Cas9 with dCas9, which binds to a target site without cleaving the DNA, which consequently abolishes transcription [18,136].”
BackgroundReuter, A., Hilpert, C., Berne-Dedieu, A., Lematre, S., Gueguen, E., Launay, G., Bigot, S., & Lesterlin, C. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab126 · Cited by 78
Cámara, E., Lisbeth Olsson, A., Zrimec, J., Zelezniak, A., Geijer, C., & Nygård, Y. (2022) · Biotechnology Advances · doi:10.1016/j.biotechadv.2022.107947 · Cited by 73
Inducible expression of large gRNA arrays for multiplexed CRISPRai applications
Shaw, W. M., Studená, L., Roy, K., Hapeta, P., McCarty, N. S., Graham, A. E., Ellis, T., & Ledesma‐Amaro, R. (2022) · Nature Communications · doi:10.1038/s41467-022-32603-7 · Cited by 73
Synthetic lethal strategies for the development of cancer therapeutics
Ngoi, N. Y. L., Gallo, D., Torrado, C., Nardo, M., Durocher, D., & Yap, T. A. (2024) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-024-00966-z · Cited by 81
“Examples of effector proteins include transcriptional activators (CRISPRa) 77–79 or repressors (CRISPRi) 80–82 , epigenetic regulators 83–90 , and systems capable of directly modifying DNA such as base editors 91,92 or prime editors 93–95 .”
A molecular toolbox for genetic manipulation of zebrafish
Köster, R. W., & Sassen, W. A. (2015) · Advances in Genomics and Genetics · doi:10.2147/agg.s57585 · Cited by 83
“92,93 However, all novel techniques have their drawbacks.”
Metabolic engineering to enhance the value of plants as green factories
Yuan, L., & Grotewold, E. (2014) · Metabolic Engineering · doi:10.1016/j.ymben.2014.11.005 · Cited by 73
Horizontal gene transfer from Agrobacterium to plants
Matveeva, T. V., & Lutova, L. A. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00326 · Cited by 73
de la Fuente‐Núñez, C., & Lu, T. K. (2016) · Integrative Biology · doi:10.1039/c6ib00140h · Cited by 75
tCRISPRi: tunable and reversible, one-step control of gene expression
Li, X., Jun, Y., Erickstad, M. J., Brown, S. D., Parks, A. R., Court, D. L., & Jun, S. (2016) · Scientific Reports · doi:10.1038/srep39076 · Cited by 77
Epigenetic Targeting of Granulin in Hepatoma Cells by Synthetic CRISPR dCas9 Epi-suppressors
Wang, H., Guo, R., Du, Z., Bai, L., Li, L., Cui, J., Li, W., Hoffman, A. R., & Hu, J. (2018) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2018.01.002 · Cited by 73
“CRISPR interference has been reported to prevent transcription by steric blockage of the RNA polymerase complex.(18,25) We also observed significant inhibition of the CMV promoter activity by dCas9-gRNAs without epi-suppressors.”
BackgroundSynthetic epigenetics—towards intelligent control of epigenetic states and cell identity
Jurkowski, T. P., Ravichandran, M., & Stepper, P. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0044-x · Cited by 73
“For targeting epigenetic modification, a catalytically inactive Cas9 variant has to be used, which still can recognize and bind the target sequence, but cannot cleave it [78-80].”
BackgroundExploiting CRISPR–Cas immune systems for genome editing in bacteria
Barrangou, R., & van Pijkeren, J. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2015.10.003 · Cited by 75
“In particular, variants of Cas9 in which both domains have been inactivated, generated a deactivated Cas9 (dCas9), constitute DNA binding proteins that can be used as transcriptional effectors when targeting promoter regions, either as repressors that block RNA polymerases, or fused to activators that enhance transcri…”
BackgroundFunctional Genomics for Cancer Drug Target Discovery
Haley, B., & Roudnicky, F. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.04.006 · Cited by 75
CRISPR-Based Epigenome Editing: Mechanisms and Applications
Fadul, S. M., Arshad, A., & Mehmood, R. (2023) · Epigenomics · doi:10.2217/epi-2023-0281 · Cited by 86
Targeted Gene Manipulation in Plants Using the CRISPR/Cas Technology
Zhang, D., Li, Z., & Li, J.-F. (2016) · Journal of Genetics and Genomics · doi:10.1016/j.jgg.2016.03.001 · Cited by 67
“Interestingly, although no cytotoxicity of SpCas9 has so far been reported in mammalian or plant cells, it often exhibits toxicity to E. coli (Qi et al., 2013; Johnson et al., 2015) and the single-cell alga Chlamydomonas reinhardtii even if its nuclease activities were disarmed (Jiang et al.,…”
BackgroundBruder, M. R., Pyne, M. E., Moo‐Young, M., Chung, D. A., & Chou, C.-H. P. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.02128-16 · Cited by 78
“The strategy of using a nuclease-deficient Cas9 (dCas9), which can nonetheless be guided to target a gene locus for interfering with various proteins involved in transcription, such as RNA polymerase and transcription factors, is known as CRISPR interference (CRISPRi) (42).”
BackgroundMethodInfluentialZhao, H., Sun, Y., Peters, J. M., Gross, C. A., Garner, E. C., & Helmann, J. D. (2016) · Journal of Bacteriology · doi:10.1128/jb.00507-16 · Cited by 71
“interference is thought to be most effective in bacteria (28, 30).”
BackgroundMethodModulating the expression of long non‐coding RNAs for functional studies
Liu, S. J., & Lim, D. A. (2018) · EMBO Reports · doi:10.15252/embr.201846955 · Cited by 74
“Engineered Cas9 variants, in particular dCas9 fused to transcriptional activators or repressors, are highly effective for modulating the expression of lncRNAs without alterations to the underlying genomic DNA sequence [90 – 96].”
A CRISPR Interference Platform for Efficient Genetic Repression in Candida albicans
Wensing, L. F., Sharma, J., Uthayakumar, D., Proteau, Y., Chavez, A., & Shapiro, R. S. (2019) · mSphere · doi:10.1128/msphere.00002-19 · Cited by 71
“coli (47, 69), and CRISPRi was subsequently applied to numerous other bacterial species.”
BackgroundInfluentialRecent advances in gene therapy for neurodevelopmental disorders with epilepsy
Turner, T. J., Zourray, C., Schorge, S., & Lignani, G. (2021) · Journal of Neurochemistry · doi:10.1111/jnc.15168 · Cited by 71
Tóth, E., Czene, B. C., Kulcsár, P. I., Krausz, S. L., Tálas, A., Nyeste, A., Varga, É., Huszár, K., Weinhardt, N., Ligeti, Z., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky815 · Cited by 74
Genome Engineering of Eubacterium limosum Using Expanded Genetic Tools and the CRISPR-Cas9 System
Shin, J., Kang, S., Song, Y., Jin, S., Lee, J. S., Lee, J.-K., Kim, D. R., Kim, S. C., Cho, S., & Cho, B. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00150 · Cited by 69
CRISPR-based metabolic pathway engineering
Zhao, D., Zhu, X., Zhou, H., Sun, N., Wang, T., Bi, C., & Zhang, X. (2020) · Metabolic Engineering · doi:10.1016/j.ymben.2020.10.004 · Cited by 70
Optogenetic characterization methods overcome key challenges in synthetic and systems biology
Olson, E. J., & Tabor, J. J. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1559 · Cited by 71
Long, L., Guo, H., Yao, D., Xiong, K., Li, Y., Liu, P., Zhu, Z., & Liu, D. (2015) · Cell Research · doi:10.1038/cr.2015.35 · Cited by 71
Genome scale engineering techniques for metabolic engineering
Liu, R., Bassalo, M. C., Zeitoun, R. I., & Gill, R. T. (2015) · Metabolic Engineering · doi:10.1016/j.ymben.2015.09.013 · Cited by 71
“…genome editing with easy target reprogramming capabilities Off-target effects Mali et al., 2013 Cong et al., 2013 Jinek et al., 2012 Kuscu et al., 2014 RuvC1 and HNH nuclease domains was used to provide an easily programmable and broadly applicable gene regulation platform (Qi et al., 2013).”
MethodCRISPR/Cas9-Based Genome Editing in Mice by Single Plasmid Injection
Fujihara, Y., & Ikawa, M. (2014) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-801185-0.00015-5 · Cited by 70
Efficient Screening of CRISPR/Cas9-Induced Events in Drosophila Using a Co-CRISPR Strategy
Kane, N. S., Vora, M., Varre, K. J., & Padgett, R. W. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.036723 · Cited by 71
“Originally discovered as part of the immune system of bacteria and archaea, Cas9 endonuclease cleaves highly specific DNA targets, determined by the guide RNA (gRNA) sequence (Cong et al. 2013; Jinek et al. 2012; Mali et al. 2013; Qi et al. 2013).”
BackgroundDifferent Methods of Delivering CRISPR/Cas9 Into Cells
Chandrasekaran, A. P., Song, M., Kim, K.-S., & Ramakrishna, S. (2018) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2018.05.001 · Cited by 73
Jing, X., Xie, B., Chen, L., Zhang, N., Jiang, Y., Qin, H., Wang, H., Hao, P., Yang, S., & Li, X. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky433 · Cited by 71
“Similar to the mutant Cas9 variant (dCas9) that is capable of binding target DNA but inactive in DNA cleavage (22,23), the LshCas13a R1278A mutant (referred to as dCas13a) bound target RNA more strongly (KD ∼ 7 nM) than the wild-type (KD ∼ 46 nM), although it was catalytically inactive (7).”
BackgroundBasak, J., & Nithin, C. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.01001 · Cited by 72
“Another way of promoter targeting can be done by using a catalytically inactive Cas9 in combination with sgRNA (CRISPRi) for precise interference of the transcriptional machinery (Qi et al., 2013).”
BackgroundNew Plant Breeding Techniques in Citrus for the Improvement of Important Agronomic Traits. A Review
Salonia, F., Ciacciulli, A., Poles, L., Pappalardo, H. D., Malfa, S. G. L., & Licciardello, C. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.01234 · Cited by 84
“recognizes target DNA without inducing double (or single) strand breaks (Qi et al., 2013).”
BackgroundApplying multi‐omics toward tumor microbiome research
Zhang, N., Kandalai, S., Zhou, X., Hossain, F., & Zheng, Q. (2023) · iMeta · doi:10.1002/imt2.73 · Cited by 70
“…as dead Cas9 or dCas9) is a mutant form of Cas9, that can no longer act as an endonuclease, due to point mutations in its endonuclease domains [107]. dCas9, which serves as a gene location guide, is now widely used in the genome editing of different biological systems through the fusion…”
BackgroundCurrent Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects
Naeem, M., & Alkhnbashi, O. S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076261 · Cited by 70
Cas9-Based Tools for Targeted Genome Editing and Transcriptional Control
Xu, T., Li, Y., Nostrand, J. D. V., He, Z., & Zhou, J. Z. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.03786-13 · Cited by 71
Heo, M.-J., Jung, H.-M., Um, J., Lee, S., & Oh, M. (2016) · ACS Synthetic Biology · doi:10.1021/acssynbio.6b00134 · Cited by 70
Zhang, W., Tong, H., Zhang, Z., Shao, S., Liu, D., Li, S., & Yan, Y. (2017) · Journal of Cellular Physiology · doi:10.1002/jcp.25883 · Cited by 70
“Four sgRNAs targeting different sites in the EGR1 (NCBI Gene ID: 407125) promoter (from −354 to +263) were designed following the methods described by Larson et al. (2013) and Qi et al. (2013).”
MethodMultiplexed DNA Identification Using Site Specific dCas9 Barcodes and Nanopore Sensing
Weckman, N. E., Ermann, N., Gutierrez, R., Chen, K., Graham, J. E., Tivony, R., Heron, A., & Keyser, U. F. (2019) · ACS Sensors · doi:10.1021/acssensors.9b00686 · Cited by 69
High-throughput PRIME-editing screens identify functional DNA variants in the human genome
Ren, X., Yang, H., Nierenberg, J. L., Sun, Y., Chen, J., Beaman, C., Pham, T., Nobuhara, M., Takagi, M. A., Narayan, V., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.11.021 · Cited by 70
NgAgo-based fabp11a gene knockdown causes eye developmental defects in zebrafish
Qi, J., Dong, Z., Shi, Y., Wang, X., Qin, Y., Wang, Y., & Liu, D. (2016) · Cell Research · doi:10.1038/cr.2016.134 · Cited by 69
CRISPR-Cas System: History and Prospects as a Genome Editing Tool in Microorganisms
Javed, M. R., Sadaf, M., Ahmed, T., Jamil, A., Nawaz, M., Abbas, H., & Ijaz, A. (2018) · Current Microbiology · doi:10.1007/s00284-018-1547-4 · Cited by 78
Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories
Fernández‐Cabezón, L., Cros, A., & Nikel, P. I. (2019) · Biotechnology Journal · doi:10.1002/biot.201800439 · Cited by 70
CRISPR/Cas9 gene-editing strategies in cardiovascular cells
Vermersch, E., Jouve, C., & Hulot, J. (2019) · Cardiovascular Research · doi:10.1093/cvr/cvz250 · Cited by 74
Genome editing technology and application in soybean improvement
Bao, A., Zhang, C., Huang, Y., Chen, H., Zhou, X., & Cao, D. (2020) · Oil Crop Science · doi:10.1016/j.ocsci.2020.03.001 · Cited by 68
Ni, C., Dinh, C. V., & Prather, K. L. J. (2021) · Annual Review of Chemical and Biomolecular Engineering · doi:10.1146/annurev-chembioeng-091720-125738 · Cited by 70
Next-Generation Diagnostic with CRISPR/Cas: Beyond Nucleic Acid Detection
Bhardwaj, P., Kant, R., Behera, S. P., Dwivedi, G. R., & Singh, R. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23116052 · Cited by 74
Metadata
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
