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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) 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]
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“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]
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“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]
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Citations
Cites
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MethodRNA-Guided Human Genome Engineering via Cas9
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Items 501–600 of 1,026
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“Recently, nuclease-defi- cient derivatives (dCas9) were used to modify gene expression in many model organisms, including plants (Qi et al., 2013; Piatek et al., 2015).”
BackgroundNanomedicine-mediated cancer stem cell therapy
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Self-citationRepurposing CRISPR/Cas9 for in situ functional assaysPreprint
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CRISPR-based screening of genomic island excision events in bacteria
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“CRISPR-Cas technology has applications in strain typing and detection (8–10), exploitation of natural/engineered immunity against mobile genetic elements (11), programmable genome editing in diverse backgrounds (12), transcriptional control (13, 14), and manipulation of microbial populations in defined consortia (15).”
BackgroundCRISPR/Cas9 mediated genome engineering in Drosophila
Bassett, A. R., & Liu, J. (2014) · Methods · doi:10.1016/j.ymeth.2014.02.019 · Cited by 131
Removal of Integrated Hepatitis B Virus DNA Using CRISPR-Cas9
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“…can be more easily reprogrammed and delivered both in vitro and in vivo to cleave virtually any DNA sequence by simply redesigning the guide RNAs (gRNAs), which is predicated to be a promising genome-editing tool with broad applications (Qi et al., 2013; Ran et al., 2013; Zhang et al., 2014).”
BackgroundMethodSpecificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
Stojic, L., Lun, A. T. L., Mangei, J., Mascalchi, P., Quarantotti, V., Barr, A. R., Bakal, C., Marioni, J. C., Gergely, F. V., & Odom, D. T. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky437 · Cited by 132
“Deactivated Cas9 (dCas9) fused to a Krüppel-associated box (KRAB) repression domain can be directed to a specific genomic locus to prevent transcription, an approach known as CRISPR interference (CRISPRi) (6-9).”
BackgroundCRISPR/Cas-based genome engineering in natural product discovery
Tong, Y., Weber, T., & Lee, S. Y. (2018) · Natural Product Reports · doi:10.1039/c8np00089a · Cited by 131
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Impeding Transcription of Expanded Microsatellite Repeats by Deactivated Cas9
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Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage
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RNA Strand Displacement Responsive CRISPR/Cas9 System for mRNA Sensing
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“coli (Qi et al., 2013) using rfp targeted by variants of a single sgRNA.”
BackgroundMethodResultInfluentialSelf-citationThe impact of genetic diversity on gene essentiality within the Escherichia coli species
Rousset, F., Cabezas-Caballero, J., Piastra-Facon, F., Fernández-Rodríguez, J., Clermont, O., Denamur, É., Rocha, E. P. C., & Bikard, D. (2021) · Nature Microbiology · doi:10.1038/s41564-020-00839-y · Cited by 140
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“Without ABA, sg1-Cdh1 had minimal effects, whereas sg2-Cdh1 reduced Ecadherin to 20% of controls (Figures S5D–S5F), likely due to direct transcriptional blockade (Qi et al., 2013).”
Multiplexed Gene Editing and Protein Overexpression Using a Tobacco mosaic virus Viral Vector
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“These indels cause localized DNA disruption and have been used for sequence-specific disruption of downstream gene products, such as proteins and long noncoding RNAs (Schiml et al., 2014; Ran et al., 2013).”
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Editing the microbiome the CRISPR way
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Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria
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An engineered ScCas9 with broad PAM range and high specificity and activity
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“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].”
BackgroundNext Generation Prokaryotic Engineering: The CRISPR-Cas Toolkit
Mougiakos, I., Bosma, E. F., de Vos, W. M., van Kranenburg, R., & John van der, O. O. S. T. (2016) · Trends in biotechnology · doi:10.1016/j.tibtech.2016.02.004 · Cited by 137
“Induction When using an inducible promoter for dCas9, Cascade, or guide RNA expression, in most cases the amount of repression was shown to increase with increasing inducer concentration or time [41,49].”
BackgroundMethodInfluentialStabilization of Foxp3 expression by CRISPR-dCas9-based epigenome editing in mouse primary T cells
Okada, M., Kanamori, M., Someya, K., Nakatsukasa, H., & Yoshimura, A. (2017) · Epigenetics & Chromatin · doi:10.1186/s13072-017-0129-1 · Cited by 129
“As dCas9 itself is reported to inhibit transcription, and it is utilized in CRISPR interference technology [55].”
Synthetic genetic circuits for programmable biological functionalities
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Modeling Alzheimer's disease with human induced pluripotent stem (iPS) cells
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“(2015), http://dx.doi.org/10.1016/j.mcn.2015.11.010 or repressors also allow us to examine the consequences of enhanced or suppressed expression of specific genes without alterations to the genome itself (Qi et al., 2013).”
BackgroundInfluentialEngineering Synthetic Gene Circuits in Living Cells with CRISPR Technology
Jusiak, B., Cleto, S., Pérez‐Piñera, P., & Lu, T. K. (2016) · Trends in biotechnology · doi:10.1016/j.tibtech.2015.12.014 · Cited by 132
“Active Cas9 endonuclease is used for genome editing [25,26] while dCas9 (a deactivated point-mutant protein) acts as a TF by recruiting transcriptional activators or repressors to its target gene [30–36].”
BackgroundInfluentialIn Silico Meets In Vivo : Towards Computational CRISPR-Based sgRNA Design
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Dead Cas Systems: Types, Principles, and Applications
Brezgin, S., Kostyusheva, A., Kostyushev, D. S., & Chulanov, V. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20236041 · Cited by 135
“Introducing point mutations into each domain (D10A and H840A, correspondingly) blocks nucleolytic activity of Cas9 but does not impact its binding to its target [2].”
BackgroundKhoshandam, M., Soltaninejad, H., Mousazadeh, M., Hamidieh, A. A., & Hosseinkhani, S. (2023) · Genes & Diseases · doi:10.1016/j.gendis.2023.02.027 · Cited by 136
Biotechnological production of omega-3 fatty acids: current status and future perspectives
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“…et al. 2013b), and a catalytically inactive form of Cas9 (dCas9) can be fused to regulatory domains for targeted gene regulation (Cheng et al. 2013; Farzadfard et al. 2013; Gilbert et al. 2013; Maeder et al. 2013b; Perez-Pinera et al. 2013a; Qi et al. 2013; Hilton et al. 2015; Kearns et al. 2015).”
BackgroundMultigene disruption in undomesticated Bacillus subtilis ATCC 6051a using the CRISPR/Cas9 system
Zhang, K., Duan, X., & Wu, J. (2016) · Scientific Reports · doi:10.1038/srep27943 · Cited by 127
CRISPR/Cas9‐mediated genome editing: From basic research to translational medicine
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CRISPR/dCas-mediated transcriptional and epigenetic regulation in plants
Pan, C., Sretenovic, S., & Qi, Y. (2021) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2020.101980 · Cited by 127
Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies
Jensen, E. D., Ferreira, R., Jakočiūnas, T., Arsovska, D., Zhang, J., Ding, L., Smith, J., David, F., Nielsen, J., Jensen, M. K., et al. (2017) · Microbial Cell Factories · doi:10.1186/s12934-017-0664-2 · Cited by 125
“In recent years, the use of endonuclease-deficient, yet RNA-binding, Cas9 variants (dCas9) has shown tunable and orthogonal control of gene expression by blocking transcription elongation [18, 19].”
InfluentialExpanding the CRISPR Toolbox in Zebrafish for Studying Development and Disease
Liu, K., Petree, C., Requena, T., Varshney, P., & Varshney, G. K. (2019) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00013 · Cited by 139
CRISPR/Cas9: Principle, Applications, and Delivery through Extracellular Vesicles
Horodecka, K., & Düchler, M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22116072 · Cited by 121
“RNA polymerase movement and hinders transcription, thus silencing gene expression through CRISPR interference (CRISPRi) [31].”
BackgroundZhou, J., Shen, B., Zhang, W., Wang, J., Yang, J., Chen, L., Zhang, N., Zhu, K., Xu, J., Hu, B., et al. (2013) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2013.10.010 · Cited by 124
Cut Site Selection by the Two Nuclease Domains of the Cas9 RNA-guided Endonuclease
Chen, H., Choi, J., & Bailey, S. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.539726 · Cited by 131
Recent progress in genome engineering techniques in the silkworm, B ombyx mori
Daimon, T., Kiuchi, T., & Takasu, Y. (2013) · Development Growth & Differentiation · doi:10.1111/dgd.12096 · Cited by 124
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Self-citationEngineering cell signaling using tunable CRISPR–Cpf1-based transcription factors
Liu, Y., Han, J., Chen, Z., Wu, H., Dong, H., & Nie, G. (2017) · Nature Communications · doi:10.1038/s41467-017-02265-x · Cited by 126
CRISPR artificial splicing factors
Du, M., Jillette, N., Zhu, J. J., Li, S., & Cheng, A. W. (2020) · Nature Communications · doi:10.1038/s41467-020-16806-4 · Cited by 127
Genome editing for plant research and crop improvement
Zhan, X., Lu, Y., Zhu, J., & Botella, J. R. (2020) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13063 · Cited by 121
RNA therapeutics: updates and future potential
Zhang, C., & Zhang, B. (2022) · Science China Life Sciences · doi:10.1007/s11427-022-2171-2 · Cited by 125
“break and forming a ribonucleoprotein complex by binding with the guide RNA (Qi et al., 2013).”
BackgroundTuning plant phenotypes by precise, graded downregulation of gene expression
Xue, C., Qiu, F., Wang, Y., Li, B., Zhao, K. T., Chen, K., & Gao, C. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01707-w · Cited by 122
“Widely used genetic tools, such as CRISPR–Cas 3 , CRISPR interference (CRISPRi) 4 and RNA interference (RNAi) 5 , generally result in a unique change of gene expression level that ranges from a given level of downregulation to complete absence 6 .”
MethodAdeno-associated Virus Vectors in Gene Therapy
Mary, B., Khan, N., Arumugam, S., Saxena, H., Kumar, M., Manimaran, P., Chattopadhyay, S., & Jayandharan, G. R. (2018) · Springer eBooks · doi:10.1007/978-981-13-0481-1_2 · Cited by 126
Single-Nucleotide-Resolution Computing and Memory in Living Cells
Farzadfard, F., Gharaei, N., Higashikuni, Y., Jung, G., Cao, J., & Lu, T. K. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.011 · Cited by 122
From Genomics to Gene Therapy: Induced Pluripotent Stem Cells Meet Genome Editing
Hotta, A., & Yamanaka, S. (2015) · Annual Review of Genetics · doi:10.1146/annurev-genet-112414-054926 · Cited by 124
The functional proteome landscape of Escherichia coli
Mateus, A., Hevler, J. F., Bobonis, J., Kurzawa, N., Shah, M., Mitosch, K., Goemans, C., Helm, D., Stein, F., Typas, A., et al. (2020) · Nature · doi:10.1038/s41586-020-3002-5 · Cited by 113
CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences
Karlson, C. K. S., Noor, S. N. M., Nolte, N., & Tan, B. C. (2021) · Plants · doi:10.3390/plants10102055 · Cited by 139
“[89] found that the expression of the mRFP gene was repressed up to 1000-fold.”
BackgroundMethodInfluentialBottcher, R., Hollmann, M., Merk, K., Nitschko, V., Obermaier, C. D., Philippou‐Massier, J., Wieland, I., Gaul, U., & Förstemann, K. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku289 · Cited by 126
Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription
Lenstra, T. L., Coulon, A., Chow, C. C., & Larson, D. R. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.09.028 · Cited by 116
“coli, CRISPRi can interfere with recruitment of polymerase and transcription factors when targeted to a DNA sequence in the gene promoter, or it can strand-specifically repress transcriptional elongation when targeted to the non-template (NT) strand of the gene body (Qi et al., 2013).”
DeBiasse, M. B., & Kelly, M. W. (2015) · Journal of Heredity · doi:10.1093/jhered/esv073 · Cited by 131
Gene Expression Knockdown by Modulating Synthetic Small RNA Expression in Escherichia coli
Noh, M., Yoo, S. M., Kim, W. J., & Lee, S. Y. (2017) · Cell Systems · doi:10.1016/j.cels.2017.08.016 · Cited by 121
“To overcome these limitations of conventional gene manipulation strategies, researchers have developed trans-acting RNAbased knockdown tools, such as antisense RNA and CRISPRi (Qi et al., 2013).”
BackgroundDynamic pathway regulation: recent advances and methods of construction
Tan, S. Z., & Prather, K. L. J. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2017.10.004 · Cited by 121
“the CRISPR interference (CRISPRi) system has been characterized to provide up to 100-fold repression of RFP fluorescence that is expressed from the genome[32].”
MethodUnderstanding Biological Regulation Through Synthetic Biology
Bashor, C. J., & Collins, J. J. (2018) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-070816-033903 · Cited by 121
“In recent years, one notable addition to the circuit engineering toolkit is CRISPR-Cas9, which has been used as tool to recruit transcriptional machinery to specific genomic loci (20, 48, 86), and to construct multi-node circuitry (57, 62).”
MethodApplications of CRISPR-Cas Enzymes in Cancer Therapeutics and Detection
Huang, C., Lee, K.-C., & Doudna, J. A. (2018) · Trends in cancer · doi:10.1016/j.trecan.2018.05.006 · Cited by 119
“A catalytically deactivated Cas9 (dCas9) has been repurposed for targeted gene repression (CRISPRi) [12, 13] and activation (CRISPRa) in a genome-wide fashion (Figure 1A) [14– 16].”
BackgroundSelf-citationDetection of CRISPR-dCas9 on DNA with Solid-State Nanopores
Yang, W., Restrepo-Pérez, L., Bengtson, M., Heerema, S. J., Birnie, A., van der Torre, J., & Dekker, C. (2018) · Nano Letters · doi:10.1021/acs.nanolett.8b02968 · Cited by 120
Multiplexed activation of endogenous genes by CRISPRa elicits potent antitumor immunity
Wang, G., Chow, R. D.-W., Bai, Z., Zhu, L., Errami, Y., Dai, X., Dong, M. B., Ye, L., Zhang, X., Renauer, P. A., et al. (2019) · Nature Immunology · doi:10.1038/s41590-019-0500-4 · Cited by 120
Chemistry of Class 1 CRISPR-Cas effectors: Binding, editing, and regulation
Liu, T. Y., & Doudna, J. A. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.rev120.007034 · Cited by 125
“Transcriptional inhibition is strongest when guide RNAs target the promoter rather than the open reading frame, similar to dCas9, a cleavage-deficient mutant of Cas9 engineered to repress transcription in cells (125, 126).”
BackgroundSelf-citationKumar, D., Yadav, A., Ahmad, R., Dwivedi, U. N., & Yadav, K. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.932859 · Cited by 139
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Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation
Mahas, A., Neal Stewart, C., & Mahfouz, M. M. (2018) · Biotechnology Advances · doi:10.1016/j.biotechadv.2017.11.008 · Cited by 110
“Consequently, binding of dCas9 would interfere with transcription factor or RNA polymerase binding, thus hindering transcriptional initiation and/or elongation and leading to the repression of gene expression (Qi et al., 2013).”
BackgroundMultiplex genome editing of microorganisms using CRISPR-Cas
Adiego-Pérez, B., Randazzo, P., Daran, J.-M. G., Verwaal, R., Roubos, J. A., Daran-Lapujade, P. A. S., & John van der, O. O. S. T. (2019) · FEMS Microbiology Letters · doi:10.1093/femsle/fnz086 · Cited by 116
“This CRISPR interference (CRISPRi) technique has initially been established in Escherichia coli, resulting in significant transcriptional repression when targeting either the promoter or the non-template DNA strand of an open reading frame (Bikard et al. 2013; Qi et al. 2013).”
MethodProduction of itaconic acid from alkali pretreated lignin by dynamic two stage bioconversion
Elmore, J. R., Dexter, G. N., Salvachúa, D., Martinez-Baird, J., Hatmaker, E. A., Huenemann, J. D., Klingeman, D. M., Peabody, G. L., V, Peterson, D. J., Singer, C. A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22556-8 · Cited by 120
Epigenome editing technologies for discovery and medicine
McCutcheon, S. R., Rohm, D., Iglesias, N., & Gersbach, C. A. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02320-1 · Cited by 130
“Notably, the inactivation of one or both nuclease domains of Cas9 to create Cas9 nickase (nCas9) 6 or ‘dead’ Cas9 (dCas9) 5,8 has expanded the CRISPR–Cas9 DNA-targeting platform to include base editors, prime editors and epigenome editors, each suited for specific applications (Fig.”
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CRISPR/Cas9-mediated noncoding RNA editing in human cancers
Yang, J., Meng, X., Pan, J., Jiang, N., Zhou, C., Wu, Z., & Gong, Z. (2017) · RNA Biology · doi:10.1080/15476286.2017.1391443 · Cited by 122
“Interestingly, the off-target effects, which are commonly found when using CRISPR KI and CRISPR KO, are rarely detected.(25)”
BackgroundChow, R. D.-W., & Chen, S. (2018) · Trends in cancer · doi:10.1016/j.trecan.2018.03.002 · Cited by 122
“In addition to its canonical use for targeted gene knockouts [5,6], CRISPR has been reengineered for a variety of purposes including transcriptional activation [7,8], transcriptional repression [9], histone modification [10], base editing [11,12], DNA methylation [13–15], and genome architecture manipulation [16].”
BackgroundAdvanced CRISPR/Cas-based genome editing tools for microbial biofuels production: A review
Shanmugam, S., Ngo, H. H., & Wu, Y. (2019) · Renewable Energy · doi:10.1016/j.renene.2019.10.107 · Cited by 120
Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems
Li, M., Gong, L., Cheng, F., Yu, H., Zhao, D., Wang, R., Wang, T., Zhang, S., Zhou, J. B., Shmakov, S., et al. (2021) · Science · doi:10.1126/science.abe5601 · Cited by 114
“By disrupting their nucleolytic activity, DNA-cleaving CRISPR effectors have been engineered to develop versatile gene regulators (6, 7).”
BackgroundA new age in functional genomics using CRISPR/Cas9 in arrayed library screening
Agrotis, A., & Ketteler, R. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00300 · Cited by 116
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sgRNA Sequence Motifs Blocking Efficient CRISPR/Cas9-Mediated Gene Editing
Graf, R., Li, X., Chu, V. T., & Rajewsky, K. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.024 · Cited by 118
“Furthermore, while our study did not include experiments involving dCas9, the in vitro data suggest that the motifs may also reduce target gene regulation inCRISPRi (interference) and CRISPRa (activation) experiments, as they do not interfere at the level of DNA cutting (Gilbert et al., 2013; Qi et al., 2013).”
Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron
Taketani, M., Zhang, J., Zhang, S., Triassi, A. J., Huang, Y.-J., Griffith, L. G., & Voigt, C. A. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0468-5 · Cited by 117
CRISPR Modeling and Correction of Cardiovascular Disease
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Nested epistasis enhancer networks for robust genome regulation
Lin, X., Liu, Y., Liu, S., Zhu, X., Wu, L., Zhu, Y., Zhao, D., Xu, X., Chemparathy, A., Wang, H., et al. (2022) · Science · doi:10.1126/science.abk3512 · Cited by 112
Self-citationMolecular mechanisms of CRISPR-mediated microbial immunity
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Pol III Promoters to Express Small RNAs: Delineation of Transcription Initiation
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Efficient, Complete Deletion of Synaptic Proteins using CRISPR
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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
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