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 901–1,000 of 1,005
Jo, D., Kaczmarek, S., Shin, O., Wang, L., Cowan, J., McComb, S., & Lee, S.-H. (2023) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2023.03.006 · Cited by 39
Mahato, R. K., Bhattacharya, S., Khullar, N., Sidhu, I. S., Reddy, P. H., Bhatti, G. K., & Bhatti, J. S. (2023) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2023.12.003 · Cited by 40
Long-range regulation of transcription scales with genomic distance in a gene-specific manner
Jensen, C. L., Chen, L.-F., Swigut, T., Crocker, O. J., Yao, D., Bassik, M. C., Ferrell, J. E., Boettiger, A. N., & Wysocka, J. (2025) · Molecular Cell · doi:10.1016/j.molcel.2024.10.021 · Cited by 39
A Toolkit of CRISPR-Based Genome Editing Systems in Drosophila
Jiang, X., Ren, X., Sun, J., Wang, X., Qiao, H., Xu, B., Liu, L., & Ni, J. (2015) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2015.02.007 · Cited by 39
Carbonic anhydrase III protects osteocytes from oxidative stress
Shi, C., Uda, Y., Dedic, C., Azab, E., Sun, N., Hussein, A. I., Petty, C. A., Fulzele, K. S., Mitterberger, M. C., Zwerschke, W., et al. (2017) · The FASEB Journal · doi:10.1096/fj.201700485rr · Cited by 39
“LentisgRNA(MS2) zeo backbone, lenti-dCAS-VP64_Blast, and lenti-MS2-P65-HSF1_Hygro were all obtained from Addgene (Cambridge, MA, USA) and were gifts from F. Zhang [Massachusetts Institute of Technology, Cambridge, MA, USA (29)].”
BackgroundChen, Y.-C., Farzadfard, F., Gharaei, N., Chen, W. C. W., Cao, J., & Lu, T. K. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.014 · Cited by 39
“Thus, randomized gRNA screening with PRISM is complementary to targeted screening strategies that have been used with CRISPR-Cas nucleases, crisprTFs, and RNA interference (Blancafort et al., 2005; Demir and Boutros, 2012; Gilbert et al., 2014; Konermann et al., 2015; Moffat et al., 2006; Park et al., 2003; Parnas et…”
InfluentialCRISPR History: Discovery, Characterization, and Prosperity
Han, W., & She, Q. (2017) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2017.10.001 · Cited by 43
CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries
Hardigan, A. A., Roberts, B. S., Moore, D. E., Ramaker, R. C., Jones, A. L., & Myers, R. M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz425 · Cited by 37
CRISPR-Sunspot: Imaging of endogenous low-abundance RNA at the single-molecule level in live cells
Sun, N., Chen, D., Ye, L.-P., Sheng, G., Gong, J.-J., Chen, B., Lu, Y., & Han, F. (2020) · Theranostics · doi:10.7150/thno.43094 · Cited by 39
“Reprogramming of CRISPR systems through the recruitment of artificial activators or repressors can be used to achieve gene activation (CRISPRa) or gene interference (CRISPRi), respectively [39,40].”
BackgroundChen, X., Zhao, Q., Zhao, Y., Chai, G., Cheng, W., Zhao, Z., Wang, J., Luo, G., & Cao, N. (2021) · Advanced Science · doi:10.1002/advs.202003902 · Cited by 37
Alternative splicing is a developmental switch for hTERT expression
Penev, A., Bazley, A., Shen, M. J., Boeke, J. D., Savage, S. A., & Sfeir, A. J. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.033 · Cited by 43
Lu, H., Zhang, Q., He, S., Liu, S., Xie, Z., Li, X., & Huang, Y. (2021) · Small · doi:10.1002/smll.202102494 · Cited by 40
Rittiner, J. E., Cumaran, M., Malhotra, S., & Kantor, B. (2022) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2022.1035543 · Cited by 42
Myoediting: Toward Prevention of Muscular Dystrophy by Therapeutic Genome Editing
Zhang, Y., Long, C., Bassel‐Duby, R., & Olson, E. N. (2018) · Physiological Reviews · doi:10.1152/physrev.00046.2017 · Cited by 42
“ity and can be fused with different effectors, including cytidine deaminase, transcriptional activators/repressors, and epigenetic modifiers for different purposes, such as nucleotide conversion as well as genome and epigenome regulation (66, 126, 142, 179, 194, 196, 228, 274, 294).”
BackgroundReprogramming the anti-tumor immune response via CRISPR genetic and epigenetic editing
Alves, E., Taifour, S., Dolcetti, R., Chee, J., Nowak, A. K., Gaudieri, S., & Blancafort, P. (2021) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2021.04.009 · Cited by 40
“Notably, aptameric motifs engineered in combination with the gRNA scaffold (such as two copies of an RNA hairpin from the MS2 bacteriophage) were first described in the context of gene activation with the synergistic activation mediator (SAM) system.(58) This approach has been exploited to combine multiple activator d…”
BackgroundWerder, R. B., Liu, T., Abo, K. M., Lindstrom-Vautrin, J., Villacorta-Martín, C., Huang, J., Hinds, A., Boyer, N., Bullitt, E., Liesa, M., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo6566 · Cited by 42
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding
Pan, C., & Qi, Y. (2023) · Nature Protocols · doi:10.1038/s41596-023-00823-w · Cited by 41
Efficient gene activation in plants by the MoonTag programmable transcriptional activator
Casas-Mollano, J. A., Zinselmeier, M. H., Sychla, A., & Smanski, M. J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad458 · Cited by 38
Huang, X., Li, A., Xu, P., Yu, Y., Li, S., Hu, L., & Feng, S. (2023) · Journal of Nanobiotechnology · doi:10.1186/s12951-023-01952-w · Cited by 43
“At the cellular level, particles of different sizes elicit unique uptake mechanisms; that is, particles smaller than 100 nm can be taken up via clathrin- or caveolae-mediated endocytosis, whereas larger complexes may require macropinocytosis [4, 5].”
BackgroundMethodAn inducible CRISPR activation tool for accelerating plant regeneration
Zhang, C., Tang, Y., Tang, S., Chen, L., Li, T., Yuan, H., Xu, Y., Zhou, Y., Zhang, S., Wang, J., et al. (2024) · Plant Communications · doi:10.1016/j.xplc.2024.100823 · Cited by 38
“…and CRISPR-Combo, has significantly expanded the versatility of CRISPR techniques for gene regulation and functional studies (Gilbert et al., 2014; Konermann et al., 2014; Tanenbaum et al., 2014; Chavez et al., 2015; Li et al., 2017; Lowder et al., 2018; Papikian et al., 2019; Selma et al., 2019;…”
Kantor, B., O’Donovan, B., Rittiner, J. E., Hodgson, D., Lindner, N., Guerrero, S., Dong, W., Zhang, A., & Chiba‐Falek, O. (2024) · Nature Communications · doi:10.1038/s41467-024-50515-6 · Cited by 48
“The samples were collected at day 7, 14, and 21 post-trans-duction, followed by BCA normalization and a Luciferase assay, as above (Fig.”
Efficient mRNA delivery to resting T cells to reverse HIV latency
Cevaal, P. M., Kan, S., Fisher, B. M., Moso, M. A., Tan, A., Liu, H., Ali, A., Tanaka, K., Shepherd, R. A., Kim, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-60001-2 · Cited by 38
“The recruitment of multiple copies of the MS2-p65-HSF1 fusion protein, whichsynergisewith dCas9-VP64,greatly enhances the potency of CRISPRa 39 , but can result in non-speci fi c promoter activation if present in excess.”
InfluentialIncreased Expression of Laminin Subunit Alpha 1 Chain by dCas9-VP160
Perrin, A., Rousseau, J., & Tremblay, J. P. (2016) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2016.11.004 · Cited by 39
Wang, Y., Gudikote, J. P., Giri, U. P., Yan, J., Deng, W., Ye, R., Jiang, W., Li, N., Hobbs, B. P., Wang, J., et al. (2017) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-1455 · Cited by 38
“Endogenous RAD50 upregulation by dCas9 To upregulate the endogenous expression of RAD50 in the radiosensitive lung cancer cell lineH23,we used theCRISPR/Cas9 Synergistic Activation Mediator (SAM) system developed by Konermann and colleagues (13).”
BackgroundMethodMusunuru, K. (2017) · Journal of the American College of Cardiology · doi:10.1016/j.jacc.2017.10.002 · Cited by 38
Deaner, M., Holzman, A., & Alper, H. S. (2018) · Biotechnology Journal · doi:10.1002/biot.201700582 · Cited by 38
Contribution of allelic imbalance to colorectal cancer
Palin, K., Pitkänen, E., Turunen, M. M., Sahu, B., Pihlajamaa, P., Kivioja, T., Kaasinen, E., Välimäki, N., Hänninen, U. A., Cajuso, T., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06132-1 · Cited by 38
CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system
Lee, J., Lim, H., Jang, H. S., Hwang, B., Lee, J. H., Cho, J., Lee, J. H., & Bang, D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky820 · Cited by 39
“Guided nuclease (20), transcriptional regulation (21,22), epigenetic modification (23,24), and targetbase editing (25,26) are well-known examples of in vivo applications of the CRISPR system.”
BackgroundLiu, L. D., Huang, M., Dai, P., Liu, T., Fan, S., Cheng, X., Zhao, Y., Yeap, L.-S., & Meng, F. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.09.090 · Cited by 37
Heat-Triggered Remote Control of CRISPR-dCas9 for Tunable Transcriptional Modulation
Gamboa, L., Phung, E. V., Li, H., Meyers, J. P., Hart, A. C., Miller, I. C., & Kwong, G. A. (2020) · ACS Chemical Biology · doi:10.1021/acschembio.9b01005 · Cited by 36
CRISPR/Cas9 Technology: Applications and Human Disease Modeling
Martínez-Lage, M., Torres-Ruiz, R., & Rodríguez, S. (2017) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2017.09.002 · Cited by 40
Lian, Z., Du, W., Zhang, Y., Fu, Y., Liu, T., Wang, A., Cai, T., Zhu, J., Zeng, Y., Liu, Z., et al. (2020) · Thoracic Cancer · doi:10.1111/1759-7714.13485 · Cited by 38
Synthetic immunomodulation with a CRISPR super-repressor in vivo
Moghadam, F., LeGraw, R., Velazquez, J. J., Yeo, N. C., Xu, C., Park, J. H., Chavez, A., Ebrahimkhani, M. R., & Kiani, S. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0563-3 · Cited by 38
An optimized genome-wide, virus-free CRISPR screen for mammalian cells
Xiong, K., Karottki, K. J. L. C., Hefzi, H., Li, S., Grav, L. M., Li, S., Spahn, P. N., Lee, J. S., Ventiņa, I., Lee, G. M., et al. (2021) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100062 · Cited by 38
“…by the percentage of gRNA with at least 1 read in the library and skew ratio analysis was calculated by the ratio of reads at cumulative percentage 90% to 10%, following suggestions in former CRISPR GeCKO library screens protocol from Feng Zhang’s lab (Konermann et al., 2015; Joung et al., 2017).”
InfluentialLo, Y.-H., Horn, H. T., Huang, M.-F., Yu, W.-C., Young, C.-M., Liu, Q., Tomaske, M., Towers, M., Dominguez, A., Bassik, M. C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-62818-3 · Cited by 37
“For example, CRISPRi (interference) 23 – 25 and CRISPRa (activation) 26 – 30 technologiesutilizecatalyticallyinactiveCas9(dCas9)fusedtoeithera transcriptional repressor (e.g., KRAB, Krüppel associated box) or a transcriptional activator (e.g., VPR, VP64-p65-Rta).”
Wu, Q., Wu, J., Karim, M. K. A., Chen, X., Wang, T., Iwama, S., Carobbio, S., Keen, P., Vidal‐Puig, A., Kotter, M., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.02.011 · Cited by 37
Guo, Y., Shen, M., Dong, Q., Méndez-Albelo, N. M., Huang, S. X., Sirois, C. L., Le, J., Li, M., Jarzembowski, E. D., Schoeller, K. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39337-0 · Cited by 42
CRISPR-Cas Technology as a Revolutionary Genome Editing tool: Mechanisms and Biomedical Applications
Ebrahimi, S., Khosravi, M. A., Raz, A., Karimipoor, M., & Parvizi, P. (2023) · ̒Ulūm va funūn-i bastah/bandī · doi:10.61186/ibj.27.5.219 · Cited by 40
Applications of CRISPR-Cas9 mediated genome engineering
Yang, X. P. (2015) · Military Medical Research · doi:10.1186/s40779-015-0038-1 · Cited by 38
“hibitor through a genome-wide dCas9-based transcription activation screening in a melanoma model [65].”
Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression
Agrawal, D. K., Tang, X., Westbrook, A. M., Marshall, R., Maxwell, C. S., Lucks, J. B., Noireaux, V., Beisel, C. L., Dunlop, M. J., & Franco, E. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00040 · Cited by 37
Metabolic Signaling Cascades Prompted by Glutaminolysis in Cancer
Shah, R., & Chen, S. (2020) · Cancers · doi:10.3390/cancers12092624 · Cited by 36
“Additionally, two large omics studies have highlighted the role of glutamate-mediated activation of G-protein coupled receptors (GPCRs) in conferring BRAF inhibitor resistance in melanoma cells [40,41].”
BackgroundSahlén, P., Spalinskas, R., Asad, S., Mahapatra, K. D., Höjer, P., Anil, A., Eisfeldt, J., Srivastava, A., Nikamo, P., Mukherjee, A., et al. (2020) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2020.09.035 · Cited by 38
The GB4.0 Platform, an All-In-One Tool for CRISPR/Cas-Based Multiplex Genome Engineering in Plants
Vázquez‐Vilar, M., García‐Carpintero, V., Selma, S., Bernabé‐Orts, J. M., Sánchez-Vicente, J., Salazar‐Sarasua, B., Ressa, A., de Paola, C., Ajenjo-Bauza, M., Quintela, J. C., et al. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.689937 · Cited by 39
“A more elaborated regulatory strategy consists in introducing modified gRNAs that incorporate RNA aptamers attached to different positions of the gRNA scaffold [SAM and scRNA strategies (Konermann et al., 2015)].”
BackgroundWang, Q., Dou, S., Zhang, B., Jiang, H., Qi, X., Duan, H., Wang, X., Dong, C., Zhang, B. N., Xie, L., et al. (2022) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2022.01.005 · Cited by 39
Genome‐wide meta‐analysis identifies susceptibility loci for autoimmune hepatitis type 1
Li, Y., Sun, Y., Liu, Y., Wang, B., Li, J., Wang, H., Zhang, H., Wang, X., Han, X., Lin, Q., et al. (2022) · Hepatology · doi:10.1002/hep.32417 · Cited by 37
“Zhang.[26] Singleguide RNA (sgRNAs) for CRISPR activation were designed using CHOPCHOP (http://chopc hop.”
Closely related type II-C Cas9 orthologs recognize diverse PAMs
Wei, J., Hou, L., Liu, J., Wang, Z., Gao, S., Qi, T., Gao, S., Sun, S., & Wang, Y. (2022) · eLife · doi:10.7554/elife.77825 · Cited by 38
A synthetic transcription platform for programmable gene expression in mammalian cells
Chen, W. C. W., Gaidukov, L., Lai, Y., Wu, M.-R., Cao, J., Gutbrod, M. J., Choi, G. C. G., Utomo, R. P., Chen, Y.-C., Wróblewska, L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33287-9 · Cited by 36
EpiCas-DL : Predicting sgRNA activity for CRISPR-mediated epigenome editing by deep learning
Yang, Q., Wu, L., Meng, J., Ma, L., Zuo, E., & Sun, Y. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.11.034 · Cited by 37
“The cutoff of label categorization foreach dataset wasdefinedaccordingto the criteriareportedinthe respective experiment [7,12,20].”
MethodThe type V effectors for CRISPR/Cas-mediated genome engineering in plants
Zhang, R., Chai, N., Liu, T., Zheng, Z., Lin, Q., Xie, X., Wen, J., Yang, Z. F., Liu, Y., & Zhu, Q. (2024) · Biotechnology Advances · doi:10.1016/j.biotechadv.2024.108382 · Cited by 36
Ultrasound Control of Genomic Regulatory Toolboxes for Cancer Immunotherapy
Wu, Y., Huang, Z., Liu, Y., He, P., Wang, Y., Yan, L., Wang, X., Gao, S., Zhou, X., Yoon, C. W., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54477-7 · Cited by 47
“We constructed an all-in-one piggyBac plasmid containing Hsp-RGR targeting the human IL1B (hIL1B) gene, which is a common target of CRISPRa 46 , together with the constitutive dCas9-SAM (Supplementary Fig.”
High-Throughput Silencing Using the CRISPR-Cas9 System: A Review of the Benefits and Challenges
Wade, M. R. (2015) · SLAS DISCOVERY · doi:10.1177/1087057115587916 · Cited by 39
“98 Several lncRNAs were suppressed using CRISPRi,13 whereas others were transcriptionally up-regulated using SAM.11 Going beyond this, CRISPR/Cas9 could also be used to probe the functional significance of even nontranscribed regions.”
BackgroundJo, Y.-I., Suresh, B., Kim, S., & Ramakrishna, S. (2015) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2015.09.003 · Cited by 36
The expanding footprint of CRISPR/Cas9 in the plant sciences
Schaeffer, S. M., & Nakata, P. A. (2016) · Plant Cell Reports · doi:10.1007/s00299-016-1987-x · Cited by 37
CRISPR ‐Cas9 technology and its application in haematological disorders
Zhang, H., & McCarty, N. (2016) · British Journal of Haematology · doi:10.1111/bjh.14297 · Cited by 37
“…the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated protein 9 (Cas9) technique, has initiated a new era of genome editing by overcoming the limitations of these earlier methods (Cong et al, 2013; Hsu et al, 2014; Niu et al, 2014; Konermann et al, 2015).”
MethodGene editing tools: state-of-the-art and the road ahead for the model and non-model fishes
Barman, H. K., Rasal, K. D., Chakrapani, V., Ninawe, A. S., Vengayil, D. T., Asrafuzzaman, S., Sundaray, J. K., & Jayasankar, P. (2017) · Transgenic Research · doi:10.1007/s11248-017-0030-5 · Cited by 35
Functional Interrogation of Primary Human T Cells via CRISPR Genetic Editing
Chen, X., Kozhaya, L., Taştan, C., Placek, L., Dogan, M., Horne, M., Abblett, R. L., Karhan, E., Vaeth, M., Feske, S., et al. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.1701616 · Cited by 35
“through targeting promoter or noncoding regions (13, 14).”
BackgroundMethodApplication of CRISPR/Cas to Understand Cis- and Trans-Regulatory Elements in Plants
Wolter, F., & Puchta, H. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8657-6_2 · Cited by 35
Overexpression of GPR35 confers drug resistance in NSCLC cells by β-arrestin/Akt signaling
Wang, W., Han, T., Tong, W., Zhao, J., & Qiu, X. (2018) · OncoTargets and Therapy · doi:10.2147/ott.s175606 · Cited by 36
“Recent study using genome-wide Crispr-cas9 activation screen has shown that GPR35 was involved in BRAF inhibitor resistance.(33) Collectively, it suggested that GPR35 may potentiate a broad-spectrum resistance to chemodrugs.”
Translatable gene therapy for lung cancer using Crispr CAS9—an exploratory review
Nair, J., Nair, A., Veerappan, S., & Sen, D. (2019) · Cancer Gene Therapy · doi:10.1038/s41417-019-0116-8 · Cited by 36
Chemical Biology Framework to Illuminate Proteostasis
Sebastian, R. M., & Shoulders, M. D. (2020) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-013118-111552 · Cited by 35
Nakatake, Y., Ko, S. B. H., Sharov, A. A., Wakabayashi, S., Murakami, M., Sakota, M., Chikazawa-Nohtomi, N., Ookura, C., Sato, S., Ito, N., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107655 · Cited by 34
Strong and tunable anti‐CRISPR/Cas activities in plants
Calvache, C., Vázquez‐Vilar, M., Selma, S., Uranga, M., Fernández‐del‐Carmen, A., Daròs, J., & Orzáez, D. (2021) · Plant Biotechnology Journal · doi:10.1111/pbi.13723 · Cited by 36
“1 comprises three elements, each of them encoded in a different TU: (i) a modified gRNA scaffold, which includes anchoring sites for the phage MS2 coat protein (MCP; Konermann et al., 2015); (ii) a dCas9 fused to the EDLL plant activator domain and (iii) a MCP fused to the synthetic VP64-p65-Rta (VPR) activator domain.”
BackgroundYeap, W., Khan, N. C. M., Jamalludin, N., Muad, M. R., Appleton, D. R., & Kulaveerasingam, H. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.773656 · Cited by 37
Zhou, T., Zhu, X., Ye, Z., Wang, Y., Yao, C., Xu, N., Zhou, M., Ma, J., Qin, Y., Shen, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29514-y · Cited by 36
Translating Lung Function Genome-Wide Association Study (GWAS) Findings
Kheirallah, A. K., Miller, S., Hall, I. P., & Sayers, I. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2015.12.002 · Cited by 36
Sun, Z., Zhao, W., Li, Y., Si, C., Sun, X., Zhong, Q., & Yang, S. (2022) · Foods · doi:10.3390/foods11203248 · Cited by 36
“However, new editing technologies allow us to make genetic edits very efficiently to achieve big data-assisted targeted breeding [59,60].”
BackgroundCRISPR-assisted transcription activation by phase-separation proteins
Liu, J., Chen, Y., Nong, B., Luo, X., Cui, K., Li, Z., Zhang, P., Tan, W., Yang, Y., Ma, W., et al. (2023) · Protein & Cell · doi:10.1093/procel/pwad013 · Cited by 37
“…mice ( Dmd gene loss-of-function mutant mice) to treat muscular dystrophy (Liao et al., 2017), etc. Low efficiency remains a major roadblock for CRISPRa systems in basic and clinical applications and much effort has been devoted to combating this issue (Konermann et al., 2015; Zhou et al., 2018).”
BackgroundMethodResultInfluentialCouto, J., Vulin, M., Jehanno, C., Coissieux, M.-M., Hamelin, B., Schmidt, A., Ivanek, R., Sethi, A., Bräutigam, K., Frei, A., et al. (2023) · EMBO Journal · doi:10.15252/embj.2022112559 · Cited by 31
A modular dCas9-based recruitment platform for combinatorial epigenome editing
Swain, T., Pflueger, C., Freytag, S., Poppe, D., Pflueger, J., Nguyen, T. V., Li, J. K., & Lister, R. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1108 · Cited by 42
Exonuclease-enhanced prime editors
Truong, D. J., Geilenkeuser, J., Wendel, S. V., Wilming, J. C. H., Armbrust, N., Binder, E. M. H., Santl, T. H., Siebenhaar, A., Gruber, C., Phlairaharn, T., et al. (2024) · Nature Methods · doi:10.1038/s41592-023-02162-w · Cited by 35
“2b), we reasoned that a direct fusion of the exonuclease might not Article https://doi.org/10.1038/s41592-023-02162-w be an optimal configuration and therefore opted for aptamer-based recruitment 10 .”
BackgroundInfluentialRamberger, E., Sapozhnikova, V., Ng, Y. L. D., Dolnik, A., Ziehm, M., Popp, O., Sträng, E., Kull, M., Grünschläger, F., Krüger, J., et al. (2024) · Nature Cancer · doi:10.1038/s43018-024-00784-3 · Cited by 47
“Lentiviral plasmid dCAS-VP64_Blast was a gift from Feng Zhang (Addgene plasmid #61425) 69 and was used to stably transduce MM.1S cells.”
MethodCRISPR/Cas genome editing in soybean: challenges and new insights to overcome existing bottlenecks
Alves, N. S. F., Pinto, C. E. M., Távora, F. T. P. K., de Melo, B. P., Arraes, F. B. M., Lourenço‐Tessutti, I. T., de Moura, S. M., de Oliveira, A. C., Morgante, C. V., Qi, Y., et al. (2024) · Journal of Advanced Research · doi:10.1016/j.jare.2024.08.024 · Cited by 41
“In contrast, gRNAs for CRISPRa target promoter regions to increase gene expression by recruiting transcriptional activation effectors, as dCas9 or gRNAs can be fused to transcriptional activation domains [91].”
Functional interrogation of non-coding DNA through CRISPR genome editing
Canver, M. C., Bauer, D. E., & Orkin, S. H. (2017) · Methods · doi:10.1016/j.ymeth.2017.03.008 · Cited by 36
One-Step piggyBac Transposon-Based CRISPR/Cas9 Activation of Multiple Genes
Li, S., Zhang, A., Xue, H., Li, D., & Liu, Y. (2017) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2017.06.007 · Cited by 35
“For each gene, all three sgRNAs were designed to target 200–+1 bp upstream of its transcription start site (TSS).(16) To quickly test the activation efficiency, we first co-transfected the 293FT-SAM cell line with all three sgRNAs.”
MethodInfluentialEmerging Approaches for Spatiotemporal Control of Targeted Genome with Inducible CRISPR-Cas9
Nihongaki, Y., Otabe, T., & Sato, M. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04757 · Cited by 35
Direct and indirect approaches to identify drug modes of action
Tulloch, L. B., Menzies, S. K., Coron, R. P., Roberts, M. D., Florence, G. J., & Smith, T. (2017) · IUBMB Life · doi:10.1002/iub.1697 · Cited by 36
“Another study has engineered Cas9 to act as a sgRNAmediated DNA-binding protein to upregulate specific gene expression (29), and it is likely that this system will be valuable for drug target identification in eukaryotic overexpression libraries in the future.”
BackgroundMouse medulloblastoma driven by CRISPR activation of cellular Myc
Vo, B. T., Kwon, J. A., Li, C., Finkelstein, D., Xu, B., Orr, B. A., Sherr, C. J., & Roussel, M. F. (2018) · Scientific Reports · doi:10.1038/s41598-018-24956-1 · Cited by 36
Garza, J. C., Qi, X., Gjeluci, K., Leussis, M. P., Basu, H., Reis, S. A., Zhao, W. N., Piguel, N. H., Penzes, P., Haggarty, S. J., et al. (2018) · Translational Psychiatry · doi:10.1038/s41398-018-0182-y · Cited by 37
Tong, Z., Sathe, A., Ebner, B., Pan, Q., Veltkamp, C., Gschwend, J. E., Holm, P. S., & Nawroth, R. (2019) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-019-1322-9 · Cited by 36
RETRACTED: lncRNA RMST Enhances DNMT3 Expression through Interaction with HuR
Peng, W.-X., Koirala, P., Zhang, W., Ni, C., Zheng, W., Yang, L., & Mo, Y.-Y. (2019) · Molecular Therapy · doi:10.1016/j.ymthe.2019.09.024 · Cited by 35
“Oligonucleotides carrying each gRNAwere synthesized as amixed pool; theywere amplified by PCR and then cloned into lenti single guide RNA (sgRNA) (MS2)_zeo backbone (Lenti-MS2) (Addgene, plasmid 61427), as described previously.(19)”
MethodRetractedMAUDE: inferring expression changes in sorting-based CRISPR screens
de Boer, C. G., Ray, J. P., Hacohen, N., & Regev, A. (2020) · Genome biology · doi:10.1186/s13059-020-02046-8 · Cited by 39
“For instance, CRISPR interference (CRIS-PRi) and CRISPR activation (CRISPRa) have been used to respectively repress or activate elements in a targeted cis -regulatory region and identify enhancers of a gene ’ s expression [2, 4, 8, 9].”
BackgroundMethodYamulla, R. J., Nalubola, S., Flesken‐Nikitin, A., Nikitin, A. Y., & Schimenti, J. C. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108086 · Cited by 35
Yao, H., Hannum, D. F., Zhai, Y., Hill, S. F., Albanus, R. D., Lou, W., Skidmore, J. M., Sanchez, G. J., Saiakhova, A., Bielas, S. L., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-74537-4 · Cited by 37
Delivery Platforms for CRISPR/Cas9 Genome Editing of Glial Cells in the Central Nervous System
Meneghini, V., Peviani, M., Luciani, M., Zambonini, G., & Gritti, A. (2021) · Frontiers in Genome Editing · doi:10.3389/fgeed.2021.644319 · Cited by 36
“Transcriptional activators are usually directed upstream of the TSS (from −1,000 to +1 bp) with the highest levels of activity observed by targeting the region from −200 to +1 bp in the promoter (Konermann et al., 2015).”
BackgroundProteasomal degradation of the tumour suppressor FBW7 requires branched ubiquitylation by TRIP12
Khan, O. M., Almagro, J., Nelson, J. K., Horswell, S. D., Encheva, V., Keyan, K. S., Clurman, B. E., Snijders, A. P., & Behrens, A. (2021) · Nature Communications · doi:10.1038/s41467-021-22319-5 · Cited by 34
Kcam, M. C. V., Tsong, A. J., & Chappell, J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab211 · Cited by 36
“Unlike eukaryotic CRISPRa systems that have largely relied upon a handful of ADs (29,37,38) to achieve activation in diverse genetic and cellular contexts (37), bacterial CRISPRa systems likely require a greater repertoire of components and it remains unclear if an optimal AD has been identified.”
BackgroundZhu, G., Yu, J., Sun, Z., Chen, Y., Zheng, H., Lin, M.-L., Ouyang, S., Liu, G.-L., Zhang, J., & Shao, F. (2021) · Cell Death and Disease · doi:10.1038/s41419-021-04000-3 · Cited by 36
Nanoparticle delivery systems for substance use disorder
Kasina, V., Mownn, R. J., Bahal, R., & Sartor, G. C. (2022) · Neuropsychopharmacology · doi:10.1038/s41386-022-01311-7 · Cited by 39
“In a technique called CRISPR activation and interference (CRISPRa and CRISPRi), a catalytically inactive Cas9 is fused to a transcription activator or repressor domain, and when combined with sgRNAs, this method allows for gene-specific activation or repression [154].”
MethodDevelopment of Light‐Activated CRISPR Using Guide RNAs with Photocleavable Protectors
Jain, P., Ramanan, V., Schepers, A. G., Dalvie, N. S., Panda, A., Fleming, H. E., & Bhatia, S. N. (2016) · Angewandte Chemie · doi:10.1002/ange.201606123 · Cited by 35
Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities
Esposito, R., Polidori, T., Meise, D. F., Pulido-Quetglas, C., Chouvardas, P., Forster, S., Schaerer, P., Kobel, A., Schlatter, J., Kerkhof, E., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100171 · Cited by 35
An engineered xCas12i with high activity, high specificity and broad PAM range
Zhang, H., Kong, X., Xue, M., Hu, J., Wang, Z., Wei, Y., Wang, H., Zhou, J., Zhang, W., Xu, M., et al. (2022) · Protein & Cell · doi:10.1093/procel/pwac052 · Cited by 35
CRISPR/Cas9: a historical and chemical biology perspective of targeted genome engineering
Singh, A., Chakraborty, D., & Maiti, S. (2016) · Chemical Society Reviews · doi:10.1039/c6cs00197a · Cited by 35
Furuhata, Y., Nihongaki, Y., Sato, M., & Yoshimoto, K. (2017) · ACS Synthetic Biology · doi:10.1021/acssynbio.7b00246 · Cited by 35
Suzuki, M., Ikeda, A., & Bartlett, J. D. (2017) · Archives of Toxicology · doi:10.1007/s00204-017-2135-2 · Cited by 37
Wu, Z., Sun, D., & Pu, H. (2023) · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy · doi:10.1016/j.saa.2023.123121 · Cited by 34
Multi-gene engineering in plants with RNA-guided Cas9 nuclease
Raitskin, O., & Patron, N. J. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2015.11.008 · Cited by 38
Development and potential applications of CRISPR-Cas9 genome editing technology in sarcoma
Liu, T., Shen, J. K., Li, Z., Choy, E., Hornicek, F. J., & Duan, Z. (2016) · Cancer Letters · doi:10.1016/j.canlet.2016.01.030 · Cited by 30
Interferons and beyond: Induction of antiretroviral restriction factors
Hotter, D., & Kirchhoff, F. (2017) · Journal of Leukocyte Biology · doi:10.1002/jlb.3mr0717-307r · Cited by 36
Applications of the CRISPR/Cas system beyond gene editing
Anton, T., Karg, E., & Bultmann, S. (2018) · Biology Methods and Protocols · doi:10.1093/biomethods/bpy002 · Cited by 32
Genetically modified immune cells targeting tumor antigens
Poorebrahim, M., Abazari, M. F., Sadeghi, S., Mahmoudi, R., Kheirollahi, A., Askari, H., Wickström, S. L., Poortahmasebi, V., Lundqvist, A., Kiessling, R. W., et al. (2020) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2020.107603 · Cited by 36
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
