The DOI matches its Crossref record; 90 of the 91 references it cites were found in a registry or an index.
Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation
Open accessAbstract
The bacterial CRISPR-Cas9 system has emerged as a multifunctional platform for sequence-specific regulation of gene expression. This Review describes the development of technologies based on nuclease-deactivated Cas9, termed dCas9, for RNA-guided genomic transcription regulation, both by repression through CRISPR interference (CRISPRi) and by activation through CRISPR activation (CRISPRa). We highlight different uses in diverse organisms, including bacterial and eukaryotic cells, and summarize current applications of harnessing CRISPR-dCas9 for multiplexed, inducible gene regulation, genome-wide screens and cell fate engineering. We also provide a perspective on future developments of the technology and its applications in biomedical research and clinical studies.
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 cited source says what the claim attributes to it.
In the citing paper
“Novel strategies of Cas9-based transcription modulators rapidly appeared prompted by the fusion of dCas9 or gRNA to different activator or repressor elements, with multiple degrees of modulation and specificity, and enabling single or multiplexed transcriptional control [74,75,76].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [76]
The cited source says what the claim attributes to it.
In the citing paper
“Therefore, catalytically inactive dCas-9 can be used to activate (CRISPRa) or silence (CRISPRi) the expression of a specific gene of interest.50”
From Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing (2021) · cites this paper as [50]
In the citing paper
“One general challenge for these CRISPR methods involves the specificity and efficiency of gRNAs (reviewed in [94]).”
From Mapping gene regulatory networks from single-cell omics data (2018) · cites this paper as [94]
In the citing paper
“As all four methods are based on CRISPR/CAS9, in principle, any CRISPR-based perturbations could be used, including knockouts and transcriptional- or epigenetic-based repression or activation (e.g. CRISPRi, CRISPRa [94]).”
From Mapping gene regulatory networks from single-cell omics data (2018) · cites this paper as [94]
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
Multiplex 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
RNA-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
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
CRISPR 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
Development 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
Genome-scale CRISPR-Cas9 knockout screening in human cells
Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X., Scott, D. A., Mikkelsen, T. S., Heckl, D., Ebert, B. L., Root, D. E., Doench, J. G., et al. (2014) · Science · doi:10.1126/science.1247005 · Cited by 5,234
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016
Self-citationCpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., van der Oost, J., Regev, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.038 · Cited by 4,761
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
Cited by
Sorted by citations
Cellular uptake of nanoparticles: Journey inside the cell
Behzadi, S., Serpooshan, V., Tao, W., Hamaly, M. A., Alkawareek, M. Y., Dreaden, E. C., Brown, D., Alkilany, A. M., Farokhzad, O. C., & Mahmoudi, M. (2017) · Chemical Society Reviews · doi:10.1039/c6cs00636a · Cited by 2,859
Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors
Anzalone, A. V., Koblan, L. W., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0561-9 · Cited by 2,237
CRISPR–Cas9 Structures and Mechanisms
Jiang, F., & Doudna, J. A. (2017) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-062215-010822 · Cited by 2,029
CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture
Chen, K., Wang, Y., Zhang, R., Zhang, H., & Gao, C. (2019) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-050718-100049 · Cited by 1,696
“, VP64, p65AD, and VPR) can be used for gene regulation (26) (Figure 2c).”
BackgroundInduced pluripotent stem cell technology: a decade of progress.
Shi, Y., Inoue, H., Wu, J. C., & Yamanaka, S. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.245 · Cited by 1,525
CRISPR/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 1,213
Self-citationThe Post-GWAS Era: From Association to Function
Gallagher, M. D., & Chen-Plotkin, A. S. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.04.002 · Cited by 822
“Thus, genome editing technologies can also be used to validate potential CREs by altering epigenetic state, rather than the underlying DNA sequence.(66,67) A more recent study used CRISPR/Cas9 gene editing to investigate candidate causal variants at the SNCA locus,(68) which is associated with risk for Parkinson’s dis…”
BackgroundCRISPR/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 824
“In addition, unlike CRISPR/ Cas9 gene editing, because the genome has not been modified, CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) are reversible, which greatly reduces the unknown problems caused by off-target effects.(143) Since the base sequence of DNA is not directly changed, the efficiency of…”
BackgroundDirected Evolution: Methodologies and Applications
Wang, Y., Xue, P., Cao, M., Yu, T., Lane, S., & Zhao, H. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00260 · Cited by 745
Regulation of gene expression by cis-acting long non-coding RNAs
Gil, N., & Ulitsky, I. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0184-5 · Cited by 736
Kleinstiver, B. P., Sousa, A. A., Walton, R. T., Tak, Y. E., Hsu, J. Y., Clement, K., Welch, M. M., Horng, J. E., Malagon-Lopez, J., Scarfò, I., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0011-0 · Cited by 698
Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally
Huang, H., Weng, H., Zhou, K., Wu, T., Zhao, B. S., Sun, M., Chen, Z., Deng, X., Xiao, G., Auer, F., et al. (2019) · Nature · doi:10.1038/s41586-019-1016-7 · Cited by 677
Epigenetics and epigenomics in diabetic kidney disease and metabolic memory
Kato, M. V., & Natarajan, R. D. (2019) · Nature Reviews Nephrology · doi:10.1038/s41581-019-0135-6 · Cited by 615
The interplay of epigenetic marks during stem cell differentiation and development
Atlasi, Y., & Stunnenberg, H. G. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.57 · Cited by 583
CRISPR/Cas system: recent advances and future prospects for genome editing
Manghwar, H., Lindsey, K., Zhang, X., & Jin, S. (2019) · Trends in Plant Science · doi:10.1016/j.tplants.2019.09.006 · Cited by 529
“The histone demethylase Lys-specific histone demethylase 1 (LSD1) fused to Neisseria meningitidis dCas9 has been used for experimentally controlling gene repression [92].”
BackgroundComparison of Cas9 activators in multiple species
Chavez, A., Tuttle, M. L., Pruitt, B. W., Ewen‐Campen, B., Chari, R., Ter‐Ovanesyan, D., Haque, S. J., Cecchi, R. J., Kowal, E. J. K., Buchthal, J., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3871 · Cited by 521
Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing
Yin, H., Song, C.-Q., Suresh, S., Wu, Q., Walsh, S., Rhym, L. H., Mintzer, E., Bolukbasi, M. F., Zhu, L. J., Kauffman, K., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.4005 · Cited by 499
Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing
Mengstie, M. A., & Wondimu, B. Z. (2021) · Biologics: Targets and Therapy · doi:10.2147/btt.s326422 · Cited by 478
Shifting paradigms in restoration of the world's coral reefs
van Oppen, M. J. H., Gates, R. D., Blackall, L. L., Cantin, N. E., Chakravarti, L. J., Chan, W. Y., Cormick, C., Crean, A. J., Damjanovic, K., Epstein, H. E., et al. (2017) · Global Change Biology · doi:10.1111/gcb.13647 · Cited by 460
Anti-CRISPR: discovery, mechanism and function
Pawluk, A., Davidson, A. R., & Maxwell, K. L. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.120 · Cited by 398
Xu, Y., & Li, Z. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.08.031 · Cited by 457
“Then, by fusing transcriptional activators or repressors to dCas9, the CRISPRdCas9 system can be used to activate (CRISPRa) or inhibit (CRISPRi) transcription of target genes [37,38].”
MethodNaturally Occurring Off-Switches for CRISPR-Cas9
Pawluk, A., Amrani, N., Zhang, Y., García, B., Hidalgo-Reyes, Y., Lee, J., Edraki, A., Shah, M. K., Sontheimer, E. J., Maxwell, K. L., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.017 · Cited by 392
Gene Editing and Crop Improvement Using CRISPR-Cas9 System
Arora, L., & Narula, A. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.01932 · Cited by 412
“…catalytic domains, HNH and RuvC) that fuses with general transcription factors to its C-termini (Figure 7). dCas9 has the ability to bind to specific target DNA guided by sgRNA and allows direct imaging and manipulation of transcription without altering the DNA sequence (Dominguez et al., 2016).”
BackgroundInfluentialAmino acids production focusing on fermentation technologies – A review
D’Este, M., Alvarado-Morales, M., & Angelidaki, İ. (2017) · Biotechnology Advances · doi:10.1016/j.biotechadv.2017.09.001 · Cited by 360
Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells
Dong, M. B., Wang, G., Chow, R. D., Ye, L., Zhu, L., Dai, X., Park, J. J., Kim, H. R., Errami, Y., Guzman, C. D., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.044 · Cited by 330
“Other CRISPR technologies, such as CRISPR activation, CRISPR repression, and orthogonal genetic manipulation will further empower the study of cancer immunotherapy with available and evolving toolkits (Dominguez et al., 2016; Esvelt et al., 2013; Gilbert et al., 2013; Thakore et al., 2016).”
Nguyen, D. N., Roth, T. L., Li, P. J., Chen, P. A., Apathy, R., Mamedov, M. R., Vo, L. T., Tobin, V. R., Goodman, D. B., Shifrut, E., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0325-6 · Cited by 320
“CRISPR-Cas9 interacts specifically with both genomic and non-genomic dsDNA 8 , and nuclease-inactive dCas9 has been used in many applications to localize protein and RNA effectors to specific DNA sequences without cleaving the target sequence 9 .”
Paixão, J. F. R., Gillet, F., Ribeiro, T. P., Bournaud, C., Lourenço‐Tessutti, I. T., Vasquez, D. D. N., de Melo, B. P., Engler, J. D. A., & Grossi‐de‐Sá, M. F. (2019) · Scientific Reports · doi:10.1038/s41598-019-44571-y · Cited by 318
From profiles to function in epigenomics
Stricker, S. H., Köferle, A., & Beck, S. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.138 · Cited by 300
Designing cell function: assembly of synthetic gene circuits for cell biology applications
Xie, M., & Fussenegger, M. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0024-z · Cited by 304
A compact, high-accuracy Cas9 with a dinucleotide PAM for in vivo genome editing
Edraki, A., Mir, A., Ibraheim, R., Gainetdinov, I., Yoon, Y., Song, C.-Q., Cao, Y., Gallant, J., Xue, W., Rivera-Pérez, J. A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.12.003 · Cited by 265
“The availability of a catalytically dead version of Nme2Cas9 (dNme2Cas9) also promises to expand the scope of applications such as CRISPRi, CRISPRa, base editing, and related approaches (Dominguez et al., 2016; Komor et al., 2017).”
BackgroundMapping gene regulatory networks from single-cell omics data
Fiers, M. W. E. J., Minnoye, L., Aibar, S., Bravo González-Blas, C., Kalender Atak, Z., & Aerts, S. (2018) · Briefings in Functional Genomics · doi:10.1093/bfgp/elx046 · Cited by 235
Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing
Li, K., Liu, Y., Cao, H., Zhang, Y., Gu, Z., Liu, X., Yu, A., Kaphle, P., Dickerson, K. E., Ni, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14362-5 · Cited by 257
Jost, M., Chen, Y., Gilbert, L. A., Horlbeck, M. A., Krenning, L., Menchon, G., Rai, A., Cho, M. Y., Stern, J. J., Prota, A. E., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.012 · Cited by 244
Cas9 versus Cas12a/Cpf1: Structure–function comparisons and implications for genome editing
Swarts, D. C., & Jinek, M. (2018) · WIREs RNA · doi:10.1002/wrna.1481 · Cited by 267
Targeted mRNA demethylation using an engineered dCas13b-ALKBH5 fusion protein
Li, J., Chen, Z., Chen, F., Xie, G., Ling, Y., Peng, Y., Yu, L., Luo, N., Chiang, C., & Wang, H. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa269 · Cited by 236
Colasante, G., Lignani, G., Brusco, S., Berardino, C. D., Carpenter, J. C., Giannelli, S. G., Valassina, N., Bido, S., Ricci, R., Castoldi, V., et al. (2019) · Molecular Therapy · doi:10.1016/j.ymthe.2019.08.018 · Cited by 246
Averesch, N. J. H., & Krömer, J. O. (2018) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2018.00032 · Cited by 232
Kramer, N. J., Haney, M. S., Morgens, D. W., Jovičić, A., Couthouis, J., Li, A., Ousey, J., Ma, R., Bieri, G., Tsui, C. K., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0070-7 · Cited by 226
Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors
Zabidi, M. A., & Stark, A. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.10.003 · Cited by 228
Zou, Y., Sun, X., Yang, Q., Zheng, M., Shimoni, O., Ruan, W., Wang, Y., Zhang, D., Yin, J., Huang, X., et al. (2022) · Science Advances · doi:10.1126/sciadv.abm8011 · Cited by 227
Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria
Dong, C., Fontana, J. T., Patel, A., Carothers, J. M., & Zalatan, J. G. (2018) · Nature Communications · doi:10.1038/s41467-018-04901-6 · Cited by 221
Manan, S., Ullah, M. W., Ul‐Islam, M., Shi, Z., Gauthier, M., & Yang, G. (2022) · Progress in Materials Science · doi:10.1016/j.pmatsci.2022.100972 · Cited by 224
Esposito, R., Bosch, N., Lanzós, A., Polidori, T., Pulido-Quetglas, C., & Johnson, R. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.01.019 · Cited by 223
The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes
Shmakov, S., Sitnik, V., Makarova, K. S., Wolf, Y. I., Severinov, K., & Koonin, E. V. (2017) · mBio · doi:10.1128/mbio.01397-17 · Cited by 217
“…success of the Cas9 and later Cas12a (Cpf1) endonucleases as two of the new generation of genome editing, regulation, and interrogation tools (5–9), comparative genomics, structures, biochemical activities, and biological functions of CRISPR-Cas systems have been recently explored in…”
Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein
Lei, Y., Zhang, X., Su, J., Jeong, M., Gundry, M. C., Huang, Y.-H., Zhou, Y., Li, W., & Goodell, M. A. (2017) · Nature Communications · doi:10.1038/ncomms16026 · Cited by 218
Marshall, R., Maxwell, C. S., Collins, S. P., Jacobsen, T., Luo, M. L., Begemann, M. B., Gray, B. N., January, E., Singer, A., He, Y., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2017.12.007 · Cited by 209
Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors
Tak, Y. E., Kleinstiver, B. P., Nuñez, J. K., Hsu, J. Y., Horng, J. E., Gong, J., Weissman, J. S., & Joung, J. K. (2017) · Nature Methods · doi:10.1038/nmeth.4483 · Cited by 208
The functions of long noncoding RNAs in development and stem cells
Perry, R. B., & Ulitsky, I. (2016) · Development · doi:10.1242/dev.140962 · Cited by 216
“…catalytically inactive CRISPR/Cas9 system (dCas9) have the potential of harnessing the targeting specificity of CRISPR without altering the genome (Dominguez et al., 2016), but they still may have lncRNAunrelated effects on chromatin, in particular when the dCas9 is coupled with a…”
BackgroundEngineering biological systems using automated biofoundries
Chao, R., Mishra, S., Si, T., & Zhao, H. (2017) · Metabolic Engineering · doi:10.1016/j.ymben.2017.06.003 · Cited by 209
CRISPR Cpf1 proteins: structure, function and implications for genome editing
Safari, F., Zare, K., Negahdaripour, M., Barekati‐Mowahed, M., & Ghasemi, Y. (2019) · Cell & Bioscience · doi:10.1186/s13578-019-0298-7 · Cited by 208
“Modulation of endogenous genes by ddCpf1‐mediated technology In addition to the usage of CRISPR system for genome editing, this technology can be used as a sequence-specific, non-mutagenic gene regulation strategy [73].”
MethodGene editing and CRISPR in the clinic: current and future perspectives
Hirakawa, M. P., Krishnakumar, R., Timlin, J. A., Carney, J. P., & Butler, K. S. (2020) · Bioscience Reports · doi:10.1042/bsr20200127 · Cited by 207
A CRISPR toolbox to study virus–host interactions
Puschnik, A. S., Majzoub, K., Ooi, Y. S., & Carette, J. E. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.29 · Cited by 185
High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli
Cho, S., Choe, D., Lee, E., Kim, S. C., Palsson, B. Ø., & Cho, B. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.7b00462 · Cited by 195
Spatiotemporal control of CRISPR/Cas9 gene editing
Zhuo, C., Zhang, J., Lee, J., Jiao, J., Cheng, D., Liu, L., Kim, H., Tao, Y., & Li, M. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00645-w · Cited by 196
“GENETIC REGULATION CRISPR/Cas9 technology provides a diversified sequence-specific gene regulation “tool kit” by using catalytically impaired Cas9 (dCas9), which does not cleave DNA but can precisely and specifically bind DNA under the guidance of specific sgRNA.(36) Therefore, dCas9 can be designed to recruit differe…”
BackgroundMethodRecent progress in genetically modified microalgae for enhanced carbon dioxide sequestration
Barati, B., Zeng, K., Baeyens, J., Wang, S., Addy, M., Gan, S. Y., & Abomohra, A. (2020) · Biomass and Bioenergy · doi:10.1016/j.biombioe.2020.105927 · Cited by 189
Human pluripotent reprogramming with CRISPR activators
Weltner, J., Balboa, D., Katayama, S., Bespalov, M., Krjutškov, K., Jouhilahti, E.-M., Trokovic, R., Kere, J., & Otonkoski, T. (2018) · Nature Communications · doi:10.1038/s41467-018-05067-x · Cited by 181
Precision genome editing in the CRISPR era
Salsman, J., & Dellaire, G. (2016) · Biochemistry and Cell Biology · doi:10.1139/bcb-2016-0137 · Cited by 193
Epigenetics of Alzheimer’s Disease
Perković, M. N., Paska, A. V., Konjevod, M., Kouter, K., Štrac, D. Š., Erjavec, G. N., & Pivac, N. (2021) · Biomolecules · doi:10.3390/biom11020195 · Cited by 192
“The mutant form of the Cas9, called dead Cas9 (dCas9), advanced the CRISPR/Cas9 gene editing tool and resulted in CRISPR interference (CRISPRi) technology, when dCas9 is fused or interacts with transcriptional repressors, and in CRISPR activation (CRISPRa) technology, when dCas9 is fused or interacts with transcriptio…”
BackgroundMultidimensional chemical control of CRISPR–Cas9
Maji, B., Moore, C. L., Zetsche, B., Volz, S. E., Zhang, F., Shoulders, M. D., & Choudhary, A. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2224 · Cited by 180
Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9
Yang, H., & Patel, D. J. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.05.024 · Cited by 177
“Besides, a catalytically dead mutant, SpyCas9 (dSpyCas9, D10A/H840A) hasservedasaneffective andspecificRNA-guided genome-binding platform (Dominguez et al., 2016; Qi et al., 2013; Wang et al., 2016a).”
RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors
Thakore, P. I., Kwon, J. B., Nelson, C. E., Rouse, D. C., Gemberling, M. P., Oliver, M. L., & Gersbach, C. A. (2018) · Nature Communications · doi:10.1038/s41467-018-04048-4 · Cited by 181
CRISPR–Cas9-based photoactivatable transcription systems to induce neuronal differentiation
Nihongaki, Y., Furuhata, Y., Otabe, T., Hasegawa, S., Yoshimoto, K., & Sato, M. (2017) · Nature Methods · doi:10.1038/nmeth.4430 · Cited by 175
Duchenne muscular dystrophy: disease mechanism and therapeutic strategies
Angulski, A. B. B., Hosny, N., Cohen, H., Martin, A. A., Hahn, D., Bauer, J., & Metzger, J. M. (2023) · Frontiers in Physiology · doi:10.3389/fphys.2023.1183101 · Cited by 205
“This approach enables single-base transitions or transversions, as well as site-specific genomic insertions and deletions, without introducing DSBs or the need for an exogenous donor DNA as a template for HDR repair.”
BackgroundInfluentialHuang, C.-H., Shen, C. R., Li, H., Sung, L.-Y., Wu, M.-Y., & Hu, Y.-C. (2016) · Microbial Cell Factories · doi:10.1186/s12934-016-0595-3 · Cited by 164
“This new technology, termed CRISPR interference (CRISPRi), was recently repurposed to repress sequence-specific genes in diverse eucaryotic and procaryotic cells, for rewiring metabolic networks [23, 24] and high-throughput interrogation of genome-wide gene functions [25, 26].”
MethodRaschmanová, H., Weninger, A., Glieder, A., Kovar, K., & Vogl, T. J. (2018) · Biotechnology Advances · doi:10.1016/j.biotechadv.2018.01.006 · Cited by 167
Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs
Jost, M., Santos, D. A., Saunders, R. A., Horlbeck, M. A., Hawkins, J. S., Scaria, S. M., Norman, T. M., Hussmann, J. A., Liem, C. R., Gross, C. A., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0387-5 · Cited by 164
Sanborn, A. L., Yeh, B. T., Feigerle, J. T., Hao, C. V., Townshend, R. J. L., Aiden, E. L., Dror, R. O., & Kornberg, R. D. (2021) · eLife · doi:10.7554/elife.68068 · Cited by 168
Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays
Reis, A. C., Halper, S. M., Vezeau, G. E., Cetnar, D. P., Hossain, A., Clauer, P. R., & Salis, H. M. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0286-9 · Cited by 160
Exploring the potential of genome editing CRISPR-Cas9 technology
Singh, V., Braddick, D., & Dhar, P. K. (2016) · Gene · doi:10.1016/j.gene.2016.11.008 · Cited by 172
“The primary disadvantage of this system is that it may repress downstream genes within an operon instead of an isolated targeted gene (Dominguez et al., 2016).”
BackgroundInfluentialAdvances in Engineering the Fly Genome with the CRISPR-Cas System
Bier, E., Harrison, M. M., O’Connor-Giles, K. M., & Wildonger, J. (2018) · Genetics · doi:10.1534/genetics.117.1113 · Cited by 155
CRISPR interference-based specific and efficient gene inactivation in the brain
Zheng, Y., Shen, W., Zhang, J., Yang, B., Liu, Y., Qi, H., Yu, X., Lu, S., Chen, Y., Xu, Y., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0077-5 · Cited by 162
C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9–APEX2
Gao, X. D., Tu, L., Mir, A., Rodríguez, T., Ding, Y., Leszyk, J., Dekker, J., Shaffer, S. A., Zhu, L. J., Wolfe, S. A., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0006-2 · Cited by 160
Shao, J., Wang, M., Yu, G., Zhu, S., Yu, Y., Heng, B. C., Wu, J., & Ye, H. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1802448115 · Cited by 154
CRISPR-Cas9/Cas12a biotechnology and application in bacteria
Yao, R., Liu, D., Jia, X., Zheng, Y., Liu, W. Y., & Xiao, Y. (2018) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2018.09.004 · Cited by 165
The Caenorhabditis elegans Transgenic Toolbox
Nance, J., & Frøkjær‐Jensen, C. (2019) · Genetics · doi:10.1534/genetics.119.301506 · Cited by 142
CRISPR technologies for bacterial systems: Current achievements and future directions
Choi, K. R., & Lee, S. Y. (2016) · Biotechnology Advances · doi:10.1016/j.biotechadv.2016.08.002 · Cited by 151
Immunity to CRISPR Cas9 and Cas12a therapeutics
Chew, W. L. (2017) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1408 · Cited by 150
Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells
Nakamura, M., Srinivasan, P., Chavez, M., Carter, M., Dominguez, A. A., Russa, M. F. L., Lau, M. B., Abbott, T. R., Xu, X., Zhao, D., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08158-x · Cited by 147
Self-citationOpportunities and challenges in modeling human brain disorders in transgenic primates
Jennings, C. G. B., Landman, R., Zhou, Y., Sharma, J., Hyman, J. B., Movshon, J. A., Qiu, Z., Roberts, A., Roe, A. W., Wang, X., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4362 · Cited by 145
A CRISPR Activation Screen Identifies a Pan-avian Influenza Virus Inhibitory Host Factor
Heaton, B. E., Kennedy, E. M., Dumm, R. E., Harding, A. T., Sacco, M. T., Sachs, D. M., & Heaton, N. S. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.07.060 · Cited by 138
“This is likely due to poor gene induction with only one of the guide RNAs in an individual cell; previous work has shown that multiple sgRNAs per gene are more efficient at inducing expression (Dominguez et al., 2016).”
BackgroundEngineering Nanoparticles for Targeted Delivery of Nucleic Acid Therapeutics in Tumor
Xiao, Y., Shi, K. Y., Qu, Y., Chu, B., & Qian, Z. (2018) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2018.09.002 · Cited by 144
CRISPR-Cas in Streptococcus pyogenes
Rhun, A. L., Escalera-Maurer, A., Bratovič, M., & Charpentier, E. (2019) · RNA Biology · doi:10.1080/15476286.2019.1582974 · Cited by 143
In vivo CRISPRa decreases seizures and rescues cognitive deficits in a rodent model of epilepsy
Colasante, G., Qiu, Y., Massimino, L., Berardino, C. D., Cornford, J. H., Snowball, A., Weston, M., Jones, S. P., Giannelli, S. G., Lieb, A., et al. (2020) · Brain · doi:10.1093/brain/awaa045 · Cited by 141
“In addition to permanently altering endogenous gene sequences, CRISPR/Cas9 can regulate the activity of genes through promoter modulation, an approach known as CRISPR activation (CRISPRa) (Dominguez et al., 2016; Liao et al., 2017; Matharu et al., 2019).”
BackgroundCebrian-Serrano, A., & Davies, B. (2017) · Mammalian Genome · doi:10.1007/s00335-017-9697-4 · Cited by 143
Lyu, Y., He, S., Li, J., Jiang, Y., Sun, H., Miao, Y., & Pu, K. (2019) · Angewandte Chemie International Edition · doi:10.1002/anie.201909264 · Cited by 134
Specificity 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
“These poor overlaps may reflect the potential dependency of CRISPRi off-target effects on the cell type, the epigenetic landscape, or other factors (56).”
BackgroundRNA Strand Displacement Responsive CRISPR/Cas9 System for mRNA Sensing
Li, Y., Teng, X., Zhang, K., Deng, R., & Li, J. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.8b05238 · Cited by 128
Computational Tools and Resources for CRISPR/Cas Genome Editing
Li, C., Chu, W., Gill, R. A., Sang, S., Shi, Y., Hu, X., Yang, Y., Zaman, Q. U., & Zhang, B. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.02.006 · Cited by 134
Loureiro, A., & da Silva, G. J. (2019) · Antibiotics · doi:10.3390/antibiotics8010018 · Cited by 129
Synthetic genetic circuits for programmable biological functionalities
Xia, P., Ling, H., Foo, J. L., & Chang, M. W. (2019) · Biotechnology Advances · doi:10.1016/j.biotechadv.2019.04.015 · Cited by 129
CRISPR/Cas9 systems: Delivery technologies and biomedical applications
Du, Y., Liu, Y., Hu, J., Peng, X., & Liu, Z. (2023) · Asian Journal of Pharmaceutical Sciences · doi:10.1016/j.ajps.2023.100854 · Cited by 140
“CRISPR interference (CRISPRi) is a technique that employs a Cas9 enzyme without nuclease activity, combined with transcriptional repressors, to modulate the expression levels of endogenous genes [155] .”
BackgroundThe NIH Somatic Cell Genome Editing program
Saha, K., Sontheimer, E. J., Brooks, P. J., Dwinell, M. R., Gersbach, C. A., Liu, D. R., Murray, S. A., Tsai, S. Q., Wilson, R. C., Anderson, D. G., et al. (2021) · Nature · doi:10.1038/s41586-021-03191-1 · Cited by 127
NmeCas9 is an intrinsically high-fidelity genome-editing platform
Amrani, N., Gao, X. D., Liu, P., Edraki, A., Mir, A., Ibraheim, R., Gupta, A., Sasaki, K. E., Wu, T., Donohoue, P. D., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1591-1 · Cited by 128
“In addition to genome editing, 101 catalytically inactivated Cas9 (“dead” Cas9, dCas9) retains its sgRNA-guided DNA binding function, 102 enabling fused or tethered functionalities to be delivered to precise genomic loci [25, 26].”
BackgroundCharacterization of noncoding regulatory DNA in the human genome
Elkon, R., & Agami, R. (2017) · Nature Biotechnology · doi:10.1038/nbt.3863 · Cited by 132
CRISPR/Cas9 for Cancer Therapy: Hopes and Challenges
Martínez-Lage, M., Puig-Serra, P., Menéndez, P. R., Torres-Ruiz, R., & Rodríguez, S. (2018) · Biomedicines · doi:10.3390/biomedicines6040105 · Cited by 128
“Another important advantage of CRISPR/Cas9 is its flexibility: modifications and customizations of CRISPR/Cas9 components and interactors have not only improved the specificity and efficiency of the system but have also extended the scope of its applications beyond editing [25].”
BackgroundEngineering 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
Engineering disease resistant plants through CRISPR-Cas9 technology
Tyagi, S., Kumar, R., Kumar, V., Won, S. Y., & Shukla, P. (2020) · GM crops & food · doi:10.1080/21645698.2020.1831729 · Cited by 129
“GE, which is a biotechnological approach, can create stable, permanent, and heritable changes to the genetic code and can achieve specific potential goals, has several advantages over conventional breeding methods.(8) For example, modification of plant traits such as yield, growth improvement, and to develop resistanc…”
BackgroundKumar, D., Yadav, A., Ahmad, R., Dwivedi, U. N., & Yadav, K. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.932859 · Cited by 139
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
“Unlike ZFs and TALE-based transcriptional regulators, fusing dCas9 to effector domains such as transcriptional activators (CRISPRa) or repressors (CRISPRi) has enabled the repurposing of the system for scalable and robust transcriptome manipulation (Dominguez et al., 2016).”
BackgroundPrecision Control of CRISPR-Cas9 Using Small Molecules and Light
Gangopadhyay, S. A., Cox, K. J., Manna, D., Lim, D., Maji, B., Zhou, Q., & Choudhary, A. (2019) · Biochemistry · doi:10.1021/acs.biochem.8b01202 · Cited by 119
Metadata
- Authors
- Dominguez, A. A., Lim, W. A., & Qi, L. S.
- Affiliations
- Stanford University (US)
- QB3 (US)
- Corresponding author
- Lim, Wendell A.
- Qi, Lei S.
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2015-12-16
- Volume
- 17
- Issue
- 1
- Pages
- 5-15
- ISSN
- 1471-0072 (ISSN-L)
- 1471-0080
- PMC
- PMC4922510
- OpenAlex
- W2204875887
- Cited by
- 832
- References
- 91
- Citations by year
- 2026: 39 · 2025: 41 · 2024: 58 · 2023: 65 · 2022: 78 · 2021: 81 · 2020: 95 · 2019: 105 · 2018: 106 · 2017: 96 · 2016: 63 · 2015: 2
- FWCI
- 8.63
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Molecular Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (DP5OD017887)
- National Institute on Drug Abuse (R01DA036858)
- 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 regulation and disease
- Keywords
- CRISPR/Cas9, dCas9, CRISPR interference, CRISPR activation, gene expression inhibition, gene activation, genome-wide screen
- MeSH terms
- Animals, Humans, Models, Genetic, Transcription, Genetic, Genome, RNA Editing, Genomics, CRISPR-Cas Systems
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
