The DOI matches its Crossref record; 52 of the 52 references it cites were found in a registry or an index.
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
Open accessAbstract
Systematic interrogation of gene function requires the ability to perturb gene expression in a robust and generalizable manner. Here we describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. We used these engineered Cas9 activation complexes to investigate single-guide RNA (sgRNA) targeting rules for effective transcriptional activation, to demonstrate multiplexed activation of ten genes simultaneously, and to upregulate long intergenic non-coding RNA (lincRNA) transcripts. We also synthesized a library consisting of 70,290 guides targeting all human RefSeq coding isoforms to screen for genes that, upon activation, confer resistance to a BRAF inhibitor. The top hits included genes previously shown to be able to confer resistance, and novel candidates were validated using individual sgRNA and complementary DNA overexpression. A gene expression signature based on the top screening hits correlated with markers of BRAF inhibitor resistance in cell lines and patient-derived samples. These results collectively demonstrate the potential of Cas9-based activators as a powerful genetic perturbation technology.
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 doesn’t support the claim as written.
In the citing paper
“Because of the relatively large size of 4277 bp of dCas9-VPR cDNA, the authors used a dual rAAV system to express the dCas9-VPR and gRNA expression cassettes [223,224].”
From Recombinant Adeno-Associated Viral Vectors (rAAV)-Vector Elements in Ocular Gene Therapy Clinical Trials and Transgene Expression and Bioactivity Assays (2020) · cites this paper as [224]
Checked by a reasoning model — may be wrong.
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 [30]
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
“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 [74]
Experimental — accuracy not yet measuredIn the citing paper
“This dCas9-effector strategy has already been applied in genome wide screening study in which gain-of-function mutations in melanoma cells that confer drug resistance were identified.46”
From CRISPR-Cas9: a new and promising player in gene therapy (2015) · cites this paper as [46]
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
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Li, B., & Dewey, C. N. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-323 · Cited by 22,179
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
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D., et al. (2012) · Nature · doi:10.1038/nature11003 · Cited by 7,950
Molecular signatures database (MSigDB) 3.0
Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr260 · Cited by 7,111
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
Self-citationGenome-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
Self-citationDNA 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
Self-citationSystematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1
Barbie, D. A., Tamayo, P., Boehm, J. S., Kim, S. Y., Moody, S. E., Dunn, I. F., Schinzel, A. C., Sandy, P., Meylan, E., Scholl, C., et al. (2009) · Nature · doi:10.1038/nature08460 · Cited by 3,922
Integrins in cancer: biological implications and therapeutic opportunities
Desgrosellier, J. S., & Cheresh, D. A. (2009) · Nature reviews. Cancer · doi:10.1038/nrc2748 · Cited by 3,815
Flagged first, then by citations
Cited by
Sorted by citations
Items 401–500 of 1,005
Different Effects of sgRNA Length on CRISPR-mediated Gene Knockout Efficiency
Zhang, J., Li, X., Neises, A., Chen, W., Hu, L., Ji, G., Yu, J.-Y., Xu, J., Yuan, W., Cheng, T., et al. (2016) · Scientific Reports · doi:10.1038/srep28566 · Cited by 104
Silencing of LINE-1 retrotransposons is a selective dependency of myeloid leukemia
Gu, Z., Liu, Y., Zhang, Y., Cao, H., Lyu, J., Wang, X., Wylie, A., Newkirk, S. J., Jones, A. E., Lee, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00829-8 · Cited by 111
Bi, G., Liang, J., Zhao, M., Zhang, H., Jin, X. Y., Lu, T., Zheng, Y., Bian, Y., Chen, Z., Huang, Y., et al. (2022) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2022.03.020 · Cited by 105
Carrier strategies boost the application of CRISPR/Cas system in gene therapy
Xu, Z., Wang, Q., Zhong, H., Jiang, Y., Shi, X., Yuan, B., Yu, N., Zhang, S., Yuan, X., Guo, S., et al. (2022) · Exploration · doi:10.1002/exp.20210081 · Cited by 105
CRISPR screens in plants: approaches, guidelines, and future prospects
Gaillochet, C., Develtere, W., & Jacobs, T. B. (2021) · The Plant Cell · doi:10.1093/plcell/koab099 · Cited by 102
Ultrasound-Controlled CRISPR/Cas9 System Augments Sonodynamic Therapy of Hepatocellular Carcinoma
Yin, H., Sun, L., Pu, Y., Yu, J., Feng, W., Dong, C., Zhou, B., Du, D., Zhang, Y., Chen, Y., et al. (2021) · ACS Central Science · doi:10.1021/acscentsci.1c01143 · Cited by 102
Buck, T., & Wijnholds, J. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21124197 · Cited by 92
“Because of the relatively large size of 4277 bp of dCas9-VPR cDNA, the authors used a dual rAAV system to express the dCas9-VPR and gRNA expression cassettes [223,224].”
BackgroundVersatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation
Braun, C. J., Bruno, P. M., Horlbeck, M. A., Gilbert, L. A., Weissman, J. S., & Hemann, M. T. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600582113 · Cited by 104
Transforming plant biology and breeding with CRISPR /Cas9, Cas12 and Cas13
Schindele, P., Wolter, F., & Puchta, H. (2018) · FEBS Letters · doi:10.1002/1873-3468.13073 · Cited by 110
A neuroscientist’s guide to transgenic mice and other genetic tools
Navabpour, S., Kwapis, J. L., & Jarome, T. J. (2019) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.12.013 · Cited by 108
Human myotube formation is determined by MyoD–Myomixer/Myomaker axis
Zhang, H., Wen, J., Bigot, A., Chen, J., Shang, R., Mouly, V., & Bi, P. (2020) · Science Advances · doi:10.1126/sciadv.abc4062 · Cited by 102
“We then used a CRISPR tool to interrogate gene regulatory networks as previously reported ( 50 – 52 ).”
MethodHimeda, C. L., Jones, T. I., & Jones, P. L. (2015) · Molecular Therapy · doi:10.1038/mt.2015.200 · Cited by 102
Hu, L., Yu, Y., Huang, H., Fan, H., Hu, L., Yin, C., Li, K., Fulton, D. J. R., & Chen, F. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2016.00696 · Cited by 100
“With the ability to robustly activate coding and non-coding elements (lincRNA), CRISPR-ON could be used to regulate gene expression epigenetically (37).”
BackgroundVázquez‐Vilar, M., Quijano‐Rubio, A., Fernández‐del‐Carmen, A., Sarrion‐Perdigones, A., Ochoa‐Fernandez, R., Ziarsolo, P., Blanca, J., Granell, A., & Orzáez, D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1326 · Cited by 99
“It has been also shown before using Cas9 genome-wide activation that the arrangement of different ADs in close proximity has a cooperative effect (42).”
BackgroundAdvancing chimeric antigen receptor T cell therapy with CRISPR/Cas9
Ren, J., & Zhao, Y. (2017) · Protein & Cell · doi:10.1007/s13238-017-0410-x · Cited by 103
“These discoveries paved the way and opened the era for the use of CRISPR/Cas9 in genome engineering, including gene editing and gene expression regulation, epigenetic modification, and genome imaging (Cheng et al., 2013; DiCarlo et al., 2013; Gilbert et al., 2013; Hwang et al., 2013; Li et al., 2013; Maeder et al., 20…”
BackgroundNiu, X., Pu, S., Ling, C., Xu, J., Wang, J., Sun, S., Yao, Y., & Zhang, Z. (2020) · Cell Proliferation · doi:10.1111/cpr.12818 · Cited by 98
Challenges in delivery systems for CRISPR-based genome editing and opportunities of nanomedicine
Sioson, V. A., Kim, M., & Joo, J. (2021) · Biomedical Engineering Letters · doi:10.1007/s13534-021-00199-4 · Cited by 120
An RNA-aptamer-based two-color CRISPR labeling system
Wang, S. S., Su, J.-H., Zhang, F., & Zhuang, X. (2016) · Scientific Reports · doi:10.1038/srep26857 · Cited by 98
Self-citationFunctional Genomics via CRISPR–Cas
Ford, K. M., McDonald, D., & Mali, P. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.06.034 · Cited by 103
Corre, S., Tardif, N., Mouchet, N., Leclair, H. M., Boussemart, L., Gautron, A., Bachelot, L., Perrot, A., Soshilov, A. A., Rogiers, A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06951-2 · Cited by 102
A split CRISPR–Cpf1 platform for inducible genome editing and gene activation
Nihongaki, Y., Otabe, T., Ueda, Y., & Sato, M. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0338-y · Cited by 98
Xu, L., Zhao, L., Gao, Y., Xu, J., & Han, R. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1048 · Cited by 91
“The modified gene activation systems can robustly activate the gene expression with gRNA targeted to within 200 bp upstream of the transcription start site (13).”
BackgroundTian, C., Huang, Y., Clauser, K. R., Rickelt, S., Lau, A. N., Carr, S. A., Heiden, M. G. V., & Hynes, R. O. (2021) · Nature Communications · doi:10.1038/s41467-021-22490-9 · Cited by 100
CRISPR/Cas System and Factors Affecting Its Precision and Efficiency
Javaid, N., & Choi, S. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.761709 · Cited by 106
“This system has been applied for large-scale genome screening because of its increased efficiency (Konermann et al., 2015).”
BackgroundMethodInfluentialGenetic screens and functional genomics using CRISPR /Cas9 technology
Hartenian, E., & Doench, J. G. (2015) · FEBS Journal · doi:10.1111/febs.13248 · Cited by 100
Silverman, A. M., Qiao, K., Xu, P., & Stephanopoulos, G. N. (2016) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-016-7376-0 · Cited by 93
“…when comparing several genes overexpressed in the same manner in other organisms, through ectopic inductions of transcription factors in M. tuberculosis (Rustad et al. 2014) and through transcriptional activator-bound Cas9-mediated upregulation of genes in human 293FT cells (Konermann et al. 2014).”
BackgroundGuide RNA modification as a way to improve CRISPR/Cas9-based genome-editing systems
Filippova, J. A., Matveeva, A. M., Zhuravlev, E. S., & Stepanov, G. A. (2019) · Biochimie · doi:10.1016/j.biochi.2019.09.003 · Cited by 98
Xiong, F., Wang, R., Lee, J.-H., Li, S., Chen, S.-F., Liao, Z., Hasani, L. A., Nguyen, P. T.-M., Zhu, X., Krakowiak, J., et al. (2021) · Cell Research · doi:10.1038/s41422-021-00515-8 · Cited by 107
Gogleva, A. A., Polychronopoulos, D., Pfeifer, M., Poroshin, V., Ughetto, M., Martin, M. J., Thorpe, H., Bornot, A., Smith, P. D., Sidders, B. S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29292-7 · Cited by 95
CRISPR-Cas9 therapeutics in cancer: promising strategies and present challenges
Yi, L., & Li, J. (2016) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2016.09.002 · Cited by 96
“25 appending a minimal hairpin aptamer of MS2-binding stem-loops to the tetra loop and stem loop 2 of sgRNAs can enhance target specificity without sacrificing on-target efficiency [100, 112, 113].”
Tadić, V., Josipović, G., Zoldoš, V., & Vojta, A. (2019) · Methods · doi:10.1016/j.ymeth.2019.05.003 · Cited by 99
Zhang, S., Guo, F., Yan, W., Dai, Z., Dong, W., Zhou, J., Zhang, W., Xin, F., & Jiang, M. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00459 · Cited by 95
Liu, Y., Zhang, P., Wu, Q., Fang, H., Wang, Y., Xiao, Y., Cong, M., Wang, T., He, Y., Ma, C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25552-0 · Cited by 97
Hit and go CAS9 delivered through a lentiviral based self-limiting circuit
Petris, G., Casini, A., Montagna, C., Lorenzin, F., Prandi, D., Romanel, A., Zasso, J., Conti, L., Demichelis, F., & Cereseto, A. (2017) · Nature Communications · doi:10.1038/ncomms15334 · Cited by 98
PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens
Lenoir, W. F., Lim, T. L., & Hart, T. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx993 · Cited by 94
“The most commonly used CRISPR-associated endonuclease, SpCas9, has been modified to disable its endonuclease activity, facilitating protein fusion with domains for transcriptional activation (13,14), transcriptional repression (13,15), and chromatin modification (16).”
MethodSchwartz, C., Curtis, N. C., Löbs, A., & Wheeldon, I. R. (2018) · Biotechnology Journal · doi:10.1002/biot.201700584 · Cited by 94
Multiple Input Sensing and Signal Integration Using a Split Cas12a System
Kempton, H. R., Goudy, L., Love, K. S., & Qi, L. S. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.01.016 · Cited by 94
“Using a nuclease-dead dCas protein fused to effector domains in combination with a guide RNA generates an artificial transcription factor for themodulation of endogenous genes (Gilbert et al., 2013; Chavez et al., 2015; Konermann et al., 2015; Perez-Pinera et al., 2013).”
Epigenome engineering: new technologies for precision medicine
Sgro, A., & Blancafort, P. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1000 · Cited by 96
“were able to recruit multiple distinct EDs with a single gRNA (46) (Figure 3A-VII).”
BackgroundCRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing
Noman, A., Aqeel, M. A., & He, S. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.01740 · Cited by 97
“These approaches have been successfully used for genomic regulatory programming (Konermann et al., 2015; Zalatan et al., 2015).”
MethodRational design of inducible CRISPR guide RNAs for de novo assembly of transcriptional programs
Ferry, Q. R. V., Lyutova, R., & Fulga, T. A. (2017) · Nature Communications · doi:10.1038/ncomms14633 · Cited by 93
PRMT3-mediated arginine methylation of IGF2BP1 promotes oxaliplatin resistance in liver cancer
Shi, Y., Niu, Y., Yuan, Y., Li, K., Zhong, C., Qiu, Z., Li, K., Zhu, L., Yang, Z., Zuo, D., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37542-5 · Cited by 98
Guide RNAs with embedded barcodes boost CRISPR-pooled screens
Zhu, S., Cao, Z., Liu, Z., He, Y. M., Wang, Y., Yuan, P., Li, W., Tian, F., Bao, Y., & Wei, W. (2019) · Genome biology · doi:10.1186/s13059-019-1628-0 · Cited by 89
Zhu, H., & Liang, C. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty1061 · Cited by 88
Targeted attenuation of elevated histone marks at SNCA alleviates α‐synuclein in Parkinson's disease
Guhathakurta, S., Kim, J.-I., Adams, L., Basu, S., Song, M. K., Adler, E. R., Je, G., Fiadeiro, M. B., & Kim, Y. (2021) · EMBO Molecular Medicine · doi:10.15252/emmm.202012188 · Cited by 95
“…a combination of all three), and synergistic activation mediator (SAM; MS2-p65-HSF1)-based systems to activate gene expression by modulating local chromatin structure (CRISPR activator; Gilbert et al , 2013; Tanenbaum et al , 2014; Chavez et al , 2015; Konermann et al , 2015; Chavez et al , 2016).”
Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox
Koonin, E. V., Gootenberg, J. S., & Abudayyeh, O. O. (2023) · Biochemistry · doi:10.1021/acs.biochem.3c00159 · Cited by 95
Self-citationCell type-specific delivery by modular envelope design
Strebinger, D., Frangieh, C. J., Friedrich, M., Faure, G., Macrae, R. K., & Zhang, F. (2023) · Nature Communications · doi:10.1038/s41467-023-40788-8 · Cited by 95
Self-citationCRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
Heigwer, F., Zhan, T., Breinig, M., Winter, J., Brügemann, D., Leible, S., & Boutros, M. (2016) · Genome biology · doi:10.1186/s13059-016-0915-2 · Cited by 92
“, coding regions, target length, exon targeting, start and stop codon targeting), which enable the design of libraries against protein-coding and non-coding genes or transcription start sites for CRISPRi and CRISPRa applications [4, 26] (see also Additional file 3: Figure S1).”
BackgroundWaking up dormant tumor suppressor genes with zinc fingers, TALEs and the CRISPR/dCas9 system
García‐Bloj, B., Moses, C., Sgro, A., Plani-Lam, J. H. C., Arooj, M., Duffy, C., Thiruvengadam, S., Sorolla, A., Rashwan, R., Mancera, R. L., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.11142 · Cited by 92
“In addition, a modified gRNA, that incorporates two MS2 RNA aptamers into exposed loops of the scaffold structure of the guide, resulted in the generation of the Synergistic Activation Mediator (SAM) complex, which improved the potency of the transactivation by binding p65 and HSF1 in an activation helper protein [41].”
BackgroundMethodInfluentialAlda-Catalinas, C., Bredikhin, D., Hernando-Herraez, I., Santos, F., Kubinyecz, O., Eckersley-Maslin, M. A., Stegle, O., & Reik, W. (2020) · Cell Systems · doi:10.1016/j.cels.2020.06.004 · Cited by 88
Programmable CRISPR‐Cas transcriptional activation in bacteria
Ho, H., Fang, J. R., Cheung, J., & Wang, H. H. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199427 · Cited by 91
“CRISPRa is a powerful approach to elucidate the cellular and genetic basis of various biological phenomena in bacteria and higher organisms (Konermann et al , 2015; Liu et al , 2018).”
Design of a self-driven probiotic-CRISPR/Cas9 nanosystem for sono-immunometabolic cancer therapy
Yu, J., Zhou, B., Zhang, S., Yin, H., Sun, L., Pu, Y., Zhou, B., Sun, Y., Li, X., Fang, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35580-z · Cited by 98
CRISPR/Cas9 Landscape: Current State and Future Perspectives
Tyumentsev, A. I., Tyumentsev, A. I., & Акимкин, В. Г. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242216077 · Cited by 98
“In order to increase the degree of activation, a system of synergistic activation mediators (SAM) was developed [110].”
BackgroundGEPIA3: Enhanced drug sensitivity and interaction network analysis for cancer research
Kang, Y.-J., Pan, L., Liu, Y., Rong, Z., Liu, J., & Liu, F. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf423 · Cited by 112
“Furthermore, CRISPR screening was a powerful tool for identifying gene-drug interactions to uncover genetic vulnerabilities with agents, such as novel resistance genes with BRAF inhibitor [ 29 , 30 ].”
Transcriptional regulation with CRISPR-Cas9: principles, advances, and applications
Didovyk, A., Borek, B., Tsimring, L., & Hasty, J. (2016) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2016.06.003 · Cited by 90
“A gain of function screen with dCas9-VP64 identified genes that modulate resistance to inhibition of BRAF, a human proto-oncogene [36].”
Gene therapy clinical trials worldwide to 2023—an update
Ginn, S. L., Mandwie, M., Alexander, I. E., Edelstein, M. L., & Abedi, M. R. (2024) · The Journal of Gene Medicine · doi:10.1002/jgm.3721 · Cited by 100
“23,24 Alternatively, gene repression effector domains have been demonstrated using the fusion of a novel KRAB – MeCP2 bipartite repressor domain to a catalytically inactive Cas9 (dCas9).”
Novel Epigenetic Techniques Provided by the CRISPR/Cas9 System
Xie, N., Zhou, Y., Sun, Q., & Tang, B. (2018) · Stem Cells International · doi:10.1155/2018/7834175 · Cited by 90
“RNA aptamers are added onto the two loops to recruit more activation domains [35].”
Hazafa, A., Mumtaz, M., Farooq, M. F., Bilal, S., Chaudhry, S. N., Firdous, M., Naeem, H., Ullah, M. O., Yameen, M., Mukhtiar, M., et al. (2020) · Life Sciences · doi:10.1016/j.lfs.2020.118525 · Cited by 98
CRISPR-Cas9 library screening approach for anti-cancer drug discovery: overview and perspectives
Chan, Y.-T., Lu, Y., Wu, J., Zhang, C., Tan, H., Bian, Z., Wang, N., & Feng, Y. (2022) · Theranostics · doi:10.7150/thno.71144 · Cited by 93
“The dCas9 protein and a suppression or activation domain could readily modulate gene expression, including the lncRNA level [88].”
BackgroundCRISPR Approaches to Small Molecule Target Identification
Jost, M., & Weissman, J. S. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.7b00965 · Cited by 88
ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin
Hu, H., Ji, Q., Song, M., Ren, J., Liu, Z., Wang, Z., Liu, X., Yan, K., Hu, J., Jing, Y., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa425 · Cited by 89
“Furthermore, we induced the endogenous expression of ZKSCAN3 in RS-hMSCs by using CRISPR-dCas9 transcriptional activation system (Supplementary Figure S7A-C) (61,62).”
MethodRevolutionizing DNA repair research and cancer therapy with CRISPR–Cas screens
Awwad, S. W., Serrano-Benítez, A., Thomas, J. C., Gupta, V., & Jackson, S. P. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00571-x · Cited by 93
Chromatin context-dependent regulation and epigenetic manipulation of prime editing
Li, X., Chen, W., Martin, B., Calderon, D., Lee, C., Choi, J., Chardon, F. M., McDiarmid, T. A., Daza, R. M., Kim, H., et al. (2024) · Cell · doi:10.1016/j.cell.2024.03.020 · Cited by 95
“59 For these experiments, we sought to enhance prime editing of the endogenous genome, rather than synHEK3 reporters.”
Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer
Shukla, S. K., Zhang, X., Niknafs, Y. S., Xiao, L., Mehra, R., Cieslik, M. P., Ross, A. E., Schaeffer, E. M., Malik, B., Guo, S., et al. (2016) · Neoplasia · doi:10.1016/j.neo.2016.07.001 · Cited by 86
“CRISPR Based Overexpression of PCAT14 Stable cell lines overexpressing PCAT14 endogenously were made using previously published protocol [18].”
CRISPR/Cas9: Transcending the Reality of Genome Editing
Chira, S., Gulei, D., Hajitou, A., Zimța, A., Cordelier, P., & Berindan‐Neagoe, I. (2017) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2017.04.001 · Cited by 89
“transcriptional activator by fusing the VP64 transcription activation domain to a catalytically inactive Cas9 and linking a MS2-p65HSF1 activation complex to sgRNA via a hairpin aptamer.(45) Rendering sgRNA from 20 bp to 11–15 bp, an RNA-guided transcriptional activation complex, Cas9-MS2-p65-HSF1, was obtained with a…”
MethodBeyond Native Cas9: Manipulating Genomic Information and Function
Mitsunobu, H., Teramoto, J., Nishida, K., & Kondo, A. (2017) · Trends in biotechnology · doi:10.1016/j.tibtech.2017.06.004 · Cited by 87
CRISPR-Cas based antiviral strategies against HIV-1
Wang, G., Zhao, N., Berkhout, B., & Das, A. T. (2017) · Virus Research · doi:10.1016/j.virusres.2017.07.020 · Cited by 86
Application of the CRISPR/Cas9 System to Drug Resistance in Breast Cancer
Chen, Y., & Zhang, Y. (2018) · Advanced Science · doi:10.1002/advs.201700964 · Cited by 91
Cai, Y., Cheng, T., Yao, Y., Li, X., Ma, Y., Li, L., Zhao, H., Bao, J., Zhang, M., Qiu, Z., et al. (2019) · Science Advances · doi:10.1126/sciadv.aav3335 · Cited by 87
Mapping human cell phenotypes to genotypes with single-cell genomics
Camp, J. G., Platt, R. J., & Treutlein, B. (2019) · Science · doi:10.1126/science.aax6648 · Cited by 85
STING-Mediated IFI16 Degradation Negatively Controls Type I Interferon Production
Li, D., Wu, R., Guo, W., Xie, L., Qiao, Z., Chen, S., Zhu, J., Huang, C., Huang, J. A., Chen, B., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.09.069 · Cited by 87
Sapozhnikov, D. M., & Szyf, M. (2021) · Nature Communications · doi:10.1038/s41467-021-25991-9 · Cited by 83
Puchta, H. (2015) · The Plant Journal · doi:10.1111/tpj.13100 · Cited by 87
Chemically Modified Cpf1-CRISPR RNAs Mediate Efficient Genome Editing in Mammalian Cells
McMahon, M. A., Prakash, T. P., Cleveland, D. W., Bennett, C. F., & Rahdar, M. (2018) · Molecular Therapy · doi:10.1016/j.ymthe.2018.02.031 · Cited by 87
Guide RNA engineering for versatile Cas9 functionality
Nowak, C. M., Lawson, S., Zerez, M., & Bleris, L. G. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw908 · Cited by 83
“MS2 loops have been added to the 3′ end of the sgRNA (Figure 4A), as well as engineered into the tetraloop and 1st hairpin with successful transactivation of target genes (84,90,91) (Figure 4B).”
BackgroundTargeted HIV-1 Latency Reversal Using CRISPR/Cas9-Derived Transcriptional Activator Systems
Bialek, J. K., Dunay, G. A., Voges, M., Schäfer, C., Spohn, M., Stucka, R., Hauber, J., & Lange, U. C. (2016) · PLoS ONE · doi:10.1371/journal.pone.0158294 · Cited by 85
“We explored two systems: the SunTag and synergistic activation mediator (SAM) systems [25,26].”
BackgroundMethodHo, S., Hartley, B. J., Flaherty, E. K., Rajarajan, P., Abdelaal, R., Obiorah, I., Barretto, N., Muhammad, H., Phatnani, H. P., Akbarian, S., et al. (2017) · Stem Cell Reports · doi:10.1016/j.stemcr.2017.06.012 · Cited by 82
“Several groups have successfully applied the CRISPRdCas9 system to modulate gene expression levels for large-scale genome-wide screens (Carlson-Stevermer et al., 2016; Gilbert et al., 2014; Horlbeck et al., 2016a; Konermann et al., 2015).”
MethodGenomes in Focus: Development and Applications of CRISPR‐Cas9 Imaging Technologies
Knight, S. C., Tjian, R., & Doudna, J. A. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201709201 · Cited by 86
Hallmarks of cancer: The CRISPR generation
Moses, C., García‐Bloj, B., Harvey, A. R., & Blancafort, P. (2018) · European Journal of Cancer · doi:10.1016/j.ejca.2018.01.002 · Cited by 90
CRISPR/Cas9 screening using unique molecular identifiers
Schmierer, B., Botla, S. K., Zhang, J., Turunen, M. M., Kivioja, T., & Taipale, J. (2017) · Molecular Systems Biology · doi:10.15252/msb.20177834 · Cited by 79
“The RSL strategy is not limited to CRISPR knockout screening, but can be applied in other screening methods such as CRISPR-dependent inhibition or activation screens (Gilbert et al , 2014; Konermann et al , 2015).”
Ritter, N. J., Ali, T., Kopitchinski, N., Schuster, P., Beisaw, A., Hendrix, D. A., Schulz, M. H., Müller-McNicoll, M., Dimmeler, S., & Grote, P. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.07.013 · Cited by 85
Li, J., Mahata, B., Escobar, M., Goell, J., Wang, K., Khemka, P., & Hilton, I. B. (2021) · Nature Communications · doi:10.1038/s41467-021-21188-2 · Cited by 85
The therapeutic application of CRISPR/Cas9 technologies for HIV
Saayman, S. M., Ali, S. A., Morris, K. V., & Weinberg, M. S. (2015) · Expert Opinion on Biological Therapy · doi:10.1517/14712598.2015.1036736 · Cited by 91
Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments
Canver, M. C., Haeussler, M., Bauer, D. E., Orkin, S. H., Sanjana, N. E., Shalem, O., Yuan, G., Zhang, F., Concordet, J., & Pinello, L. (2018) · Nature Protocols · doi:10.1038/nprot.2018.005 · Cited by 91
Self-citationBacterial CRISPR: accomplishments and prospects
Peters, J. M., Silvis, M. R., Zhao, D., Hawkins, J. S., Gross, C. A., & Qi, L. S. (2015) · Current Opinion in Microbiology · doi:10.1016/j.mib.2015.08.007 · Cited by 88
“Second, CRISPRi is scalable; thousands of sgRNAs can be constructed using pooled cloning strategies with complex oligo libraries [37,38,39 ,40].”
CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects
Paul, J. W., & Qi, Y. (2016) · Plant Cell Reports · doi:10.1007/s00299-016-1985-z · Cited by 90
“0) to recruit MS2 coat protein fused to additional activators (Konermann et al. 2015; Zalatan et al. 2015).”
InfluentialGenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens
Rauscher, B., Heigwer, F., Breinig, M., Winter, J., & Boutros, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw997 · Cited by 84
“fitness) is observed (8,17,15) and positive selection screens, where gain of phenotypes is measured (such as resistance to a drug) (18,19).”
BackgroundWangensteen, K. J., Wang, Y. J., Dou, Z., Wang, A. W., Mosleh‐Shirazi, E., Horlbeck, M. A., Gilbert, L. A., Weissman, J. S., Berger, S. L., & Kaestner, K. H. (2017) · Hepatology · doi:10.1002/hep.29626 · Cited by 84
“CRISPRa systems are now capable of producing several log-fold gene activation by (1) linking multiple different types of transcriptional activator domains to dCas9(19, 22), or (2) by fusing dCas9 to a repeating peptide array known as the ‘SunTag’ domain(20, 21).”
Chiarella, A. M., Butler, K. V., Gryder, B. E., Lu, D., Wang, T. A., Yu, X., Pomella, S., Khan, J. I., Jin, J. J., & Hathaway, N. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0296-7 · Cited by 85
“The ms2-gRNAs have a modified stem-loop, capable of recruiting both a dCas9-fusion as well as a bacteriophage MS2 coat protein (MCP)- fusion 7,21 .”
Gaglia, G., Burger, M. L., Ritch, C. C., Rammos, D., Dai, Y., Crossland, G. E., Tavana, S. Z., Warchol, S., Jaeger, A. M., Naranjo, S., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.03.015 · Cited by 84
RNA Interference in the Age of CRISPR: Will CRISPR Interfere with RNAi?
Unniyampurath, U., Pilankatta, R., & Krishnan, M. N. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17030291 · Cited by 88
“Alternatively, dCas9 fused to a transcription activator protein by various means (e.g., VP64 protein) could be targeted to any gene of interest using appropriate gRNA, to drive gene expression at an enhanced level transiently (called CRISPR activation, CRISPRa) [35,60,61].”
BackgroundInfluentialcis–trans Engineering: Advances and Perspectives on Customized Transcriptional Regulation in Plants
Shrestha, A., Khan, A., & Dey, N. (2018) · Molecular Plant · doi:10.1016/j.molp.2018.05.008 · Cited by 86
Testing thousands of nanoparticles in vivo using DNA barcodes
Lokugamage, M. P., Sago, C. D., & Dahlman, J. E. (2018) · Current Opinion in Biomedical Engineering · doi:10.1016/j.cobme.2018.08.001 · Cited by 84
Wang, J., Jiang, X., Zhao, L., Zuo, S., Chen, X., Zhang, L., Lin, Z., Zhao, X., Qin, Y., Zhou, X., et al. (2019) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2019.09.003 · Cited by 83
PTENα and PTENβ promote carcinogenesis through WDR5 and H3K4 trimethylation
Shen, S.-M., Zhang, C., Ge, M.-K., Dong, S.-S., Li, X., He, P., Zhang, N., Ji, Y., Yang, S., Yu, Y., et al. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0409-z · Cited by 82
Chen, P., Zhou, J., Wan, Y., Liu, H., Li, Y., Liu, Z., Wang, H., Lei, J., Zhao, K., Zhang, Y., et al. (2020) · Genome biology · doi:10.1186/s13059-020-01989-2 · Cited by 86
He, Y., Jiang, S., Mao, C., Zheng, H., Cao, B., Zhang, Z., Zhao, J., Zeng, Y., & Mao, X. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101088 · Cited by 84
“The sgRNA sequences were cloned into lentiCRISPRv2 as reported previously (35).”
MethodMS4A15 drives ferroptosis resistance through calcium-restricted lipid remodeling
Shan, X., Mueller, C., Pfeiffer, S., Kraft, V. A. N., Merl‐Pham, J., Bao, X., Feederle, R., Jin, X., Hauck, S. M., Schmitt‐Kopplin, P., et al. (2021) · Cell Death and Differentiation · doi:10.1038/s41418-021-00883-z · Cited by 83
Parkinson's disease motor symptoms rescue by CRISPRa‐reprogramming astrocytes into GABAergic neurons
Giehrl‐Schwab, J., Giesert, F., Rauser, B., Lao, C. L., Hembach, S., Lefort, S., Ibarra, I. L., Koupourtidou, C., Luecken, M. D., Truong, D. J., et al. (2022) · EMBO Molecular Medicine · doi:10.15252/emmm.202114797 · Cited by 84
Law, C., Wei, L., Tsang, F. H., Chan, C. Y., Xu, M., Lai, R. K., Ho, D. W., Lee, J. M., Wong, C. C., Ng, I. O., et al. (2018) · Hepatology · doi:10.1002/hep.30414 · Cited by 82
“The HELLS overexpressing system was established by CRISPR/dCas9 synergistic activation mediator (SAM) system.(19) Lenti dCas-VP64_Blast and Leni MS2-p65-Hsf1_Hygo were sequentially infected into Hep3B cells.”
MethodHighly multiplexed genome engineering using CRISPR/Cas9 gRNA arrays
Kurata, M., Wolf, N. K., Lahr, W. S., Weg, M. T., Kluesner, M. G., Lee, S. A., Hui, K., Shiraiwa, M., Webber, B. R., & Moriarity, B. S. (2018) · PLoS ONE · doi:10.1371/journal.pone.0198714 · Cited by 89
Metadata
- Authors
- Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., Nureki, O., & Zhang, F.
- Affiliations
- Broad Institute (US)
- The University of Tokyo (JP)
- Corresponding author
- Zhang, Feng
- ORCID
- Venue
- Nature
- Published
- 2014-12-10
- Volume
- 517
- Issue
- 7536
- Pages
- 583-588
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4420636
- OpenAlex
- W2127862779
- Cited by
- 2,825
- References
- 52
- Citations by year
- 2026: 154 · 2025: 204 · 2024: 266 · 2023: 236 · 2022: 279 · 2021: 281 · 2020: 301 · 2019: 270 · 2018: 261 · 2017: 229 · 2016: 214 · 2015: 122 · 2014: 3
- FWCI
- 77.58
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- PMC
- Funders
- Japan Society for the Promotion of Science (26291010)
- National Institute of Mental Health (DP1MH100706)
- National Institute of Neurological Disorders and Stroke (R01NS062849, R01NS073124)
- National Center for Chronic Disease Prevention and Health Promotion (DP1‑MH100706)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- CRISPR/Cas9, transcriptional activation, long intergenic non-coding RNA, gain-of-function screen, BRAF inhibitor resistance, melanoma, drug resistance, gene expression signatures, gene perturbation
- MeSH terms
- Genetic Engineering, Genetic Testing, Humans, Indoles, Melanoma, Sulfonamides, Reproducibility of Results, Transcriptional Activation, Gene Library, Up-Regulation, Genome, Human, Gene Expression Regulation, Neoplastic, DNA, Complementary, Drug Resistance, Neoplasm, RNA, Untranslated, Cell Line, Tumor, Proto-Oncogene Proteins B-raf, Genetic Loci, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems, CRISPR-Associated Proteins
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
