The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index; none of the 5 sources its claims cite is checked for support yet.
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
Open accessAbstract
The genetic interrogation and reprogramming of cells requires methods for robust and precise targeting of genes for expression or repression. The CRISPR-associated catalytically inactive dCas9 protein offers a general platform for RNA-guided DNA targeting. Here, we show that fusion of dCas9 to effector domains with distinct regulatory functions enables stable and efficient transcriptional repression or activation in human and yeast cells, with the site of delivery determined solely by a coexpressed short guide (sg)RNA. Coupling of dCas9 to a transcriptional repressor domain can robustly silence expression of multiple endogenous genes. RNA-seq analysis indicates that CRISPR interference (CRISPRi)-mediated transcriptional repression is highly specific. Our results establish that the CRISPR system can be used as a modular and flexible DNA-binding platform for the recruitment of proteins to a target DNA sequence, revealing the potential of CRISPRi as a general tool for the precise regulation of gene expression in eukaryotic cells.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
0 of 5 cited sources checked · 0 supported · 0 flagged
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Here we show that fusion of dCas9 to effector domains with distinct regulatory functions enables stable and efficient transcriptional repression or activation in human and yeast cells with the site of delivey determined solely by a co-expressed short guide (sg)RNA.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > Abstract
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In this experiment we found that we can simultaneously knock down endogenous expression of CD71 and CXCR4 (Figure 3E).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi can silence endogenous human genes
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: The fluorescent antibodies used to stain CD71 and CXCR4 are specific for those proteins.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Without dCas9, rtTA strongly activated the reporter, but this induction can be effectively blocked by dCas9 (115 fold repression, Figure 4B).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi as a tool for mapping and perturbing regulatory elements
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our data show CD71 and CXCR4 can be efficiently and stably knocked down (Figure 3C–D), providing evidence that CRISPRi can be used like RNAi to suppress endogenous gene expression.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi can silence endogenous human genes
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: The fluorescent antibodies used to stain CD71 and CXCR4 are specific for those proteins.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Interestingly, a strong correlation exists between the degree of knockdown for dCas9 and dCas9-KRAB for endogenous genes”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi can silence endogenous human genes
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes- Rests on an assumption: The fluorescent antibodies used to stain CD71 and CXCR4 are specific for those proteins.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Furthermore, we observed few changes in gene expression in the negative control sample, suggesting that the negative control sgRNA triggers minimal off-target effects (Figure 2 and Figure S3A).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi-mediated gene knockdown is highly specific to the target gene
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our results revealed that both dCas9-VP64 and dCas9-p65AD can effectively activate reporter gene expression, suggesting that dCas9 can serve as a generic and modular platform for different types of transcriptional control including both repression and activation (Figure 1E).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > dCas9 fusion proteins can efficiently activate or silence transcription
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found that we can robustly silence GFP expression in HEK293 cells when both the RNA and protein components of CRISPRi are stably expressed in human cells (Figure 1D).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > dCas9 fusion proteins can efficiently activate or silence transcription
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Interestingly, we also observed that blocking the AP1 enhancer caused a stronger silencing effect than blocking the SP1 enhancer within the SV40 promoter (Figure 4A)”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi as a tool for mapping and perturbing regulatory elements
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our results also revealed a linear relationship between the level of expression from the sgRNA vector and the level of GFP remaining within a cell (Figure S2A).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > dCas9 fusion proteins can efficiently activate or silence transcription
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- It may state two separate claims as one. 14
- Probably not a substantial claim. 7
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found that cells expressing the dCas9-KRAB fusion protein show a 5-fold decrease in GFP signal while cells expressing dCas9 alone, dCas9-CS or dCas9-WRPW show a 2-fold decrease in GFP signal”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > dCas9 fusion proteins can efficiently activate or silence transcription
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We also found no evidence for significant on- or off-target effects due to expression of either sgGAL4 or sgGFP-NT1 alone (Figure S3B).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi-mediated gene knockdown is highly specific to the target gene
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found that while dCas9 alone had no effect on transcription, we efficiently repressed GFP expression with dCas9-KRAB (Figure 4A).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi as a tool for mapping and perturbing regulatory elements
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We observed that 6 out of 9 sgRNAs targeting GFP knocked down GFP expression by at least 75% with a ~15-fold repression for the best sgRNA (NT1) (Table S1).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > dCas9 fusion proteins can efficiently activate or silence transcription
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found that stable dCas9-KRAB expression is sufficient to silence GFP with substantial knockdown 3 days following transfection (Figure S1A–B) and strong silencing 6 days following transfection (Figure 1C).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > dCas9 fusion proteins can efficiently activate or silence transcription
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our results show that CRISPRi is highly specific as GFP is the only gene that is significantly suppressed by the GFP-targeting sgRNA (Figure 2 and Figure S3A). If we average the data from two independent biological replicates, no gene other than GFP changes by more than 1.5 fold.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi-mediated gene knockdown is highly specific to the target gene
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“With dCas9 alone, we observed 18-fold repression, which is increased to 53-fold with addition of the Mxi1 domain (Figure 3F).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi is a general method for silencing transcription of endogenous genes in eukaryotes
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We sequenced the GFP reporter locus in these cells to confirm that dCas9 is completely nucleolytically inactive. Here, GFP retained a wild type sequence with no detectable indels in GFP knockdown cells.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > dCas9 fusion proteins can efficiently activate or silence transcription
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In this experiment we found that both dCas9 and dCas9-KRAB proteins can knock down endogenous expression of CD71 and CXCR4 (Figure 3A–B), with 3 out of 10 sgRNAs for each gene showing significant repression (60–80% repression).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi can silence endogenous human genes
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: The fluorescent antibodies used to stain CD71 and CXCR4 are specific for those proteins.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“While we are able to target dCas9 to both endogenous and reporter genes, not all sgRNA targeting constructs work efficiently.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > DISCUSSION > Future optimization for CRISPRi technology
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“arguing that the design of the fusion protein or fusion partner is an important parameter for future optimization efforts.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > dCas9 fusion proteins can efficiently activate or silence transcription
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This suggests that while dCas9 may not be able to directly block the initiation of transcription, dCas9 fusion proteins can silence proximal regulatory elements within a promoter by recruiting chromatin modifiers.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > RESULTS > CRISPRi as a tool for mapping and perturbing regulatory elements
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The specificity of CRISPRi remains to be determined across a broad range of sgRNA sequences.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > DISCUSSION > CRISPRi efficiently and specifically represses transcription in human cells
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“In human cells, previous work has demonstrated that local chromatin context is a crucial determinant of KRAB mediated silencing.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > DISCUSSION > CRISPRi efficiently and specifically represses transcription in human cells
What the sources say
- Not checked yetcites Groner et al., 2010 source
Strength:boosted· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Nonetheless, it may be substantially easier to specifically modulate transcription as only a small fraction of the human genome is transcribed or required for controlling transcription thus binding of catalytically inactive dCas9, and it is derivatives, at near cognate sites will often not impact transcription.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > DISCUSSION > CRISPRi efficiently and specifically represses transcription in human cells
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
- Rests on an assumption: Only a small fraction of the human genome is transcribed or required for controlling transcription.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As an exogenous system, CRISPRi does not compete with endogenous machinery such as microRNA expression or function.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > DISCUSSION > CRISPRi provides an alternative strategy to RNAi for gene regulation
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✗ Based: failsProbably not a substantial claim. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“as we show that promoters and in theory introns can also be targeted.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > DISCUSSION > CRISPRi provides an alternative strategy to RNAi for gene regulation
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✗ Based: failsProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
In the paper
“For example, recruitment of the KRAB domain to adjacent genomic regions can have no effect or can completely silence transcription (Groner et al., 2010).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > DISCUSSION > CRISPRi efficiently and specifically represses transcription in human cells
What the sources say
- Not checked yetcites Groner et al., 2010 source
Strength:plain· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
In the paper
“Nonetheless, an exon trapping strategy in which Tet binding sites were randomly inserted in the genome allowing recruitment of a Tetracycline repressor-KRAB fusion protein revealed that ~80% of genes tested can be silenced by KRAB-mediated recruitment of Kap1 and HP1 proteins (Groner et al., 2010).”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > DISCUSSION > CRISPRi efficiently and specifically represses transcription in human cells
What the sources say
- Not checked yetcites Groner et al., 2010 source
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Triplicate cultures were measured for each experiment and their standard deviation was indicated as the error bar.”
§ CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes > METHODS > Strain construction and fluorescence measurements for CRISPRi in yeast
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper relies on this without support.
The fluorescent antibodies used to stain CD71 and CXCR4 are specific for those proteins.
“We designed sgRNAs to target genes encoding cell surface transmembrane proteins, enabling us to use flow cytometry with directly conjugated fluorescent antibodies to quantify gene expression at the single-cell level.”
The paper relies on this without support.
Only a small fraction of the human genome is transcribed or required for controlling transcription.
“only a small fraction of the human genome is transcribed or required for controlling transcription”
The paper relies on this without support.
CRISPRi acts at the DNA level.
“because CRISPRi acts at the DNA level”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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 [23]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“such as fusing dCas9 to direct or indirect transcription activators (such as VP64), to increase the expression of a specific DNA sequence”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [130]
The cited source says what the claim attributes to it.
In the citing paper
“or transcription repressors (such as KRAB), to increase the efficiency of dCas9-mediated transcription inhibition [130,131].”
From CRISPR-Cas: Converting A Bacterial Defence Mechanism into A State-of-the-Art Genetic Manipulation Tool (2019) · cites this paper as [130]
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“The National Institute of Standards and Technology (NIST) manages a scientific consortium aimed at measuring and standardizing such outcomes as genome editing technology advances 100 .”
From The promise and challenge of therapeutic genome editing (2020) · cites this paper as [100]
Experimental — accuracy not yet measuredIn the citing paper
“Clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 is a naturally occurring bacterial immune system that uses a novel nuclease system to protect bacteria from phage infection (6-9), and it has recently been harnessed for a variety of genome-engineering applications (10)(11)(12)(13)(14)(15)(16)(17).”
From RNA-guided endonuclease provides a therapeutic strategy to cure latent herpesviridae infection (2014) · cites this paper as [15]
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
Self-citationMultiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339 · cited 2×
“Recently, several groups have shown that a modified type II CRISPR (Clustered Regularly Interspaced Palindromic Repeats) system can be targeted to DNA using RNA, enabling genetic editing of any region of the genome in a variety of organisms (Cho et al., 2013; Cong et al., 2013; Dicarlo et al., 2013; Gratz et al., 2013…”
BackgroundEnzymatic assembly of DNA molecules up to several hundred kilobases
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 10,088
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 · cited 4×
“However, the remarkable success in using RNA-guided Cas9 to enable DNA cutting for many genes in distinct organisms argues that Cas9 can bind to target DNA sites in a broad range of genes or regulatory regions (Cho et al., 2013; Cong et al., 2013; DiCarlo et al., 2013; Gratz et al., 2013; Hwang et al., 2013; Jiang et…”
BackgroundInfluentialRepurposing 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 · cited 3×
“dCas9 Fusion Proteins Can Efficiently Activate or Silence Transcription We have shown recently that CRISPRi can decrease gene expression in human cells (Qi et al., 2013).”
BackgroundInfluentialSelf-citationTight control of gene expression in mammalian cells by tetracycline-responsive promoters.
Gossen, M., & Bujard, H. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.12.5547 · Cited by 4,943
Global analysis of protein localization in budding yeast
Huh, W.-K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., & O'Shea, E. K. (2003) · Nature · doi:10.1038/nature02026 · Cited by 4,248
Self-citationWang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.04.025 · Cited by 3,495 · cited 2×
“…distinct organisms argues that Cas9 can bind to target DNA sites in a broad range of genes or regulatory regions (Cho et al., 2013; Cong et al., 2013; DiCarlo et al., 2013; Gratz et al., 2013; Hwang et al., 2013; Jiang et al., 2013; Jinek et al., 2012, 2013; Mali et al., 2013; Wang et al., 2013).”
BackgroundHigh-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells
Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2623 · Cited by 3,292
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937
Flagged first, then by citations
Cited by
Sorted by citations
Genome engineering using the CRISPR-Cas9 system
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133
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
“Specifically, fusion of dCas9 to effector domains including VP64 or KRAB allowed stable and efficient transcriptional activation or repression, respectively, in human and yeast cells (129).”
Self-citationDevelopment 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
“This CRISPR-based interference, or CRISPRi, works efficiently in prokaryotic genomes but is less effective in eukaryotic cells (Gilbert et al., 2013).”
InfluentialGenome-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
CRISPR-Cas systems for editing, regulating and targeting genomes
Sander, J. D., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2842 · Cited by 3,153
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
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., et al. (2015) · Nature · doi:10.1038/nature14136 · Cited by 2,825
Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation
Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., Guimaraes, C., Panning, B., Ploegh, H. L., Bassik, M. C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.029 · Cited by 2,728
“Wepackaged this tiling library of sgRNAs into lentiviral particles and transduced K562 human myeloid leukemia cells stably expressing dCas9 or a dCas9-KRAB fusion protein, which we have previously described (Gilbert et al., 2013).”
BackgroundResultInfluentialSelf-citationCrystal structure of Cas9 in complex with guide RNA and target DNA
Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306
“Moreover, a catalytically inactive Cas9 can serve as an RNA-guided DNA-binding platform to target effector domains and modulate endogenous transcription (Gilbert et al., 2013; Konermann et al., 2013; Maeder et al., 2013; Perez-Pinera et al., 2013; Qi et al., 2013).”
BackgroundCHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing
Labun, K., Montague, T. G., Krause, M., Cleuren, Y. N. T., Tjeldnes, H., & Valen, E. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz365 · Cited by 2,075
“For instance, CRISPR–Cas has been used to introduce new sequences into the genome (1–3), activate (4,5) or repress (6) transcription, as an enrichment tool for sequencing (7,8), for targeted hypermutation (9), as a diagnostic tool (10), to perform whole-organism lineage tracing (11), to target RNA molecules for destru…”
MethodImproving CRISPR-Cas nuclease specificity using truncated guide RNAs
Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2808 · Cited by 1,993
“…to implement with applications involving multiplex 12–14 or genome-wide libraries of gRNAs 15, 16 and, unlike the paired nickase strategy, can also be used to improve the specificities of dCas9 25 or dCas9 fusions to heterologous effector domains such as transcriptional regulatory domains 17–19 .”
MethodDynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System
Chen, B., Gilbert, L. A., Cimini, B. A., Schnitzbauer, J., Zhang, W., Li, G., Park, J. S., Blackburn, E. H., Weissman, J. S., Qi, L. S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.12.001 · Cited by 1,988
“Furthermore, a repurposed, nuclease-deactivated Cas9 (dCas9) protein has been used to regulate endogenous gene expression by controlling the RNA polymerase activity or by modulating promoter accessibility when fused with transcription factors (Gilbert et al., 2013; Qi et al., 2013).”
Self-citationHilton, I. B., D’Ippolito, A. M., Vockley, C. M., Thakore, P. I., Crawford, G. E., Reddy, T. E., & Gersbach, C. A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3199 · Cited by 1,931
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. A. (2014) · Nature · doi:10.1038/nature13011 · Cited by 1,822
Self-citationThe CRISPR tool kit for genome editing and beyond
Adli, M. (2018) · Nature Communications · doi:10.1038/s41467-018-04252-2 · Cited by 1,545
Highly efficient Cas9-mediated transcriptional programming
Chavez, A., Scheiman, J., Vora, S., Pruitt, B. W., Tuttle, M., P R Iyer, E., Lin, S., Kiani, S., Guzman, C. D., Wiegand, D. J., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3312 · Cited by 1,622
Yang, H., Wang, H., Shivalila, C. S., Cheng, A. W., Shi, L., & Jaenisch, R. (2013) · Cell · doi:10.1016/j.cell.2013.08.022 · Cited by 1,596
“Because the binding of Cas9 is guided by the simple base-pair complementarities between the engineered single-guide RNA (sgRNA) and a target genomic DNA sequence, it is possible to direct Cas9 to any genomic locus by providing the engineered sgRNA (Cho et al., 2013; Cong et al., 2013; Gilbert et al., 2013; Hwang et al…”
A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging
Tanenbaum, M. E., Gilbert, L. A., Qi, L. S., Weissman, J. S., & Vale, R. D. (2014) · Cell · doi:10.1016/j.cell.2014.09.039 · Cited by 1,611
Self-citationBoosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system
Xie, K., Minkenberg, B., & Yang, Y. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1420294112 · Cited by 1,557
“For example, PTG could be used with Cas9 nickase to improve targeting fidelity (13, 33, 34), or with deactivated Cas9 transcriptionalactivator or -repressor to manipulate multiple gene expression (35, 36).”
MethodTranscriptional enhancers: from properties to genome-wide predictions
Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356
“Through these domains, transcriptional activators (part Aa ), repressive transcription factors (TFs) 117,137,139 (part Ab ) or chromatin-modifying domains 138,139 (part Ac ) can be recruited to genomic regulatory regions to modulate the transcription of target genes.”
BackgroundThe next generation of CRISPR–Cas technologies and applications
Pickar-Oliver, A., & Gersbach, C. A. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0131-5 · Cited by 1,459
Dunbar, C. E., High, K. A., Joung, J. K., Kohn, D. B., Ozawa, K., & Sadelain, M. (2018) · Science · doi:10.1126/science.aan4672 · Cited by 1,410
“A number of clever strategies that could eventually be applied clinically involve the use of RNA-guided catalytically inactive Cas9 (“dead Cas9” or dCas9) to turn genes on and off by blocking transcriptional machinery or recruiting epigenetic regulators (59, 60).”
Engineering Cellular Metabolism
Nielsen, J., & Keasling, J. D. (2016) · Cell · doi:10.1016/j.cell.2016.02.004 · Cited by 1,400
Morris, K. V., & Mattick, J. S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3722 · Cited by 1,447
RNA-guided gene activation by CRISPR-Cas9-based transcription factors
Perez-Pinera, P., Kocak, D. D., Vockley, C. M., Adler, A. F., Kabadi, A. M., Polstein, L. R., Thakore, P. I., Glass, K. A., Ousterout, D. G., Leong, K. W., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2600 · Cited by 1,328
Drug delivery systems for RNA therapeutics
Paunovska, K., Loughrey, D., & Dahlman, J. E. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-021-00439-4 · Cited by 1,349
Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease
Anders, C., Niewoehner, O., Duerst, A., & Jinek, M. (2014) · Nature · doi:10.1038/nature13579 · Cited by 1,323
Genome-scale CRISPR-Cas9 Knockout and Transcriptional Activation Screening
Joung, J., Konermann, S., Gootenberg, J. S., Abudayyeh, O. O., Platt, R. J., Brigham, M. D., Sanjana, N. E., & Zhang, F. (2017) · Nature Protocols · doi:10.1038/nprot.2017.016 · Cited by 1,243
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111
“We assumed the gRNAs targeting the TSS of the assayed gene have a “true” effect size of 85% (based on previous observations that show CRISPRi effects of 80–90% across a panel of genes 8 ), but that some portion of the FlowFISH signal is due to non-specific binding of the probe.”
MethodOff-target Effects in CRISPR/Cas9-mediated Genome Engineering
Zhang, X.-H., Tee, L. Y., Wang, X.-G., Huang, Q.-S., & Yang, S.-H. (2015) · Molecular Therapy - Nucleic Acids · doi:10.1038/mtna.2015.37 · Cited by 1,273
Editing DNA Methylation in the Mammalian Genome
Liu, X. S., Wu, H., Ji, X., Stelzer, Y., Wu, X., Czauderna, S., Shu, J., Dadon, D., Young, R. A., & Jaenisch, R. (2016) · Cell · doi:10.1016/j.cell.2016.08.056 · Cited by 1,224
“…activator/suppressor, chromatin modifier, and green fluorescence protein to regulate gene expression, to modify chromatin, and to image genomic loci respectively (Chen et al., 2013; Gilbert et al., 2013; Hilton et al., 2015; Jinek et al., 2012; Konermann et al., 2015; Qi et al., 2013).”
Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors
Konermann, S., Lotfy, P., Brideau, N. J., Oki, J., Shokhirev, M. N., & Hsu, P. D. (2018) · Cell · doi:10.1016/j.cell.2018.02.033 · Cited by 1,164
“…benchmark CasRx against more established technologies for transcript knockdown or repression, comparing CasRx-mediated RNA interference to dCas9-mediated CRISPR interference (Gilbert et al., 2013, 2014) and spacer sequence-matched small hairpin RNAs (shRNAs) via transient transfection (Figure 5C).”
High-throughput functional genomics using CRISPR-Cas9
Shalem, O., Sanjana, N. E., & Zhang, F. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3899 · Cited by 1,233
Structures of Cas9 endonucleases reveal RNA-mediated conformational activation
Jinek, M., Jiang, F., Taylor, D. W., Sternberg, S. H., Kaya, E., Ma, E., Anders, C., Hauer, M., Zhou, K., Lin, S., et al. (2014) · Science · doi:10.1126/science.1247997 · Cited by 1,230
Self-citationAdamson, B., Norman, T. M., Jost, M., Cho, M. Y., Nuñez, J. K., Chen, Y., Villalta, J. E., Gilbert, L. A., Horlbeck, M. A., Hein, M. Y., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.048 · Cited by 1,193
“…as activity against genomically integrated GFP (using sgGFP, an sgRNA programmed with the previously validated EGFP-NT2 protospacer (Table S1) (Gilbert et al., 2013)) was robust and comparable to that from a previously validated sgRNA expression construct (95.4% and 96.2% repression of GFP…”
MethodResultInfluentialSelf-citationCas9 as a versatile tool for engineering biology
Mali, P., Esvelt, K. M., & Church, G. M. (2013) · Nature Methods · doi:10.1038/nmeth.2649 · Cited by 1,197
The CRISPR/Cas9 system for plant genome editing and beyond
Bortesi, L., & Fischer, R. (2014) · Biotechnology Advances · doi:10.1016/j.biotechadv.2014.12.006 · Cited by 1,289
“If it is expressed as a fusion protein with the transactivation or transrepression domain of a transcription factor, the precise and reversible transcriptional control of target genes becomes possible (Gilbert et al., 2013; Maeder et al., 2013b).”
BackgroundCRISPR RNA–guided activation of endogenous human genes
Maeder, M. L., Linder, S. J., Cascio, V. M., Fu, Y., Ho, Q. H., & Joung, J. K. (2013) · Nature Methods · doi:10.1038/nmeth.2598 · Cited by 1,249
“In addition, fusions of dCas9 to effector domains have been used to activate reporter genes in E. coli and human cells 9,10 and to repress endogenous genes in human cells 10 .”
BackgroundResultThe promise and challenge of therapeutic genome editing
Doudna, J. A. (2020) · Nature · doi:10.1038/s41586-020-1978-5 · Cited by 1,126
Self-citationCRISPR/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
“Alternatively, dCas9 can be fused to a repressor domain such as KRAB to enhance repression (37).”
BackgroundMethodInfluentialSelf-citationOptimized libraries for CRISPR-Cas9 genetic screens with multiple modalities
Sanson, K. R., Hanna, R. E., Hegde, M., Donovan, K. F., Strand, C., Sullender, M. E., Vaimberg, E. W., Goodale, A., Root, D. E., Piccioni, F., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07901-8 · Cited by 1,043
Thakore, P. I., D'Ippolito, A. M., Song, L., Safi, A., Shivakumar, N. K., Kabadi, A. M., Reddy, T. E., Crawford, G. E., & Gersbach, C. A. (2015) · Nature Methods · doi:10.1038/nmeth.3630 · Cited by 1,012
“…to DNA, KRAB recruits a heterochromatin-forming complex that causes histone methylation and deacetylation 25–28 . dCas9-KRAB fusions have effectively silenced non-coding RNAs and single genes when targeted to promoter regions, 5’ untranslated regions, and proximal enhancer elements 6, 9, 16, 18 .”
InfluentialRoles, Functions, and Mechanisms of Long Non-Coding RNAs in Cancer
Fang, Y., & Fullwood, M. J. (2016) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.09.006 · Cited by 1,094
“In addition, CRISPR can be modified for other purposes such as upregulating gene expression by combining a Cas9 unable to cleave nucleic acids with transcription activators such as VP64 activator domains [110,112,113].”
BackgroundCRISPR technology: A decade of genome editing is only the beginning
Wang, J. Y., & Doudna, J. A. (2023) · Science · doi:10.1126/science.add8643 · Cited by 1,105
“As a result, the first examples of engineered CRISPR-Cas involved transcriptional repression or activation to silence or up-regulate specific genes (8, 9).”
BackgroundSelf-citationHorlbeck, M. A., Gilbert, L. A., Villalta, J. E., Adamson, B., Pak, R. A., Chen, Y., Fields, A. P., Park, C. Y., Corn, J. E., Kampmann, M., et al. (2016) · eLife · doi:10.7554/elife.19760 · Cited by 894
Self-citationCRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes
Komor, A. C., Badran, A. H., & Liu, D. R. (2016) · Cell · doi:10.1016/j.cell.2016.10.044 · Cited by 1,037
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
Wu, X., Scott, D. A., Kriz, A. J., Chiu, A. C., Hsu, P. D., Dadon, D. B., Cheng, A. W., Trevino, A. E., Konermann, S., Chen, S., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2889 · Cited by 944
Applications of CRISPR technologies in research and beyond
Barrangou, R., & Doudna, J. A. (2016) · Nature Biotechnology · doi:10.1038/nbt.3659 · Cited by 1,005
Self-citationPrinciples of genetic circuit design
Brophy, J. A. N., & Voigt, C. A. (2014) · Nature Methods · doi:10.1038/nmeth.2926 · Cited by 965
Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds
Zalatan, J. G., Lee, M. E., Almeida, R., Gilbert, L. A., Whitehead, E. H., La Russa, M., Tsai, J. C., Weissman, J. S., Dueber, J. E., Qi, L. S., et al. (2015) · Cell · doi:10.1016/j.cell.2014.11.052 · Cited by 938
“domain (Gilbert et al., 2013), a potent transcriptional repressor that recruits chromatin modifiers to silence target genes (Groner et al.”
InfluentialSelf-citationCRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity
Barrangou, R., & Marraffini, L. A. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.03.011 · Cited by 832
“In mammalian cells, dCas9 can be fused to transcriptional activators such as VP64 and the p65 activator domain (Figure 3) (Gilbert et al., 2013; Maeder et al., 2013; Mali et al., 2013a).”
BackgroundInfluentialApplications of CRISPR–Cas in agriculture and plant biotechnology
Zhu, H., Li, C., & Gao, C. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00288-9 · Cited by 870
Yin, H., Song, C.-Q., Dorkin, J. R., Zhu, L. J., Li, Y., Wu, Q., Park, A., Yang, J., Suresh, S., Bizhanova, A., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3471 · Cited by 876
Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation
Dominguez, A. A., Lim, W. A., & Qi, L. S. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.2 · Cited by 832
Self-citationConcerning RNA-guided gene drives for the alteration of wild populations
Esvelt, K. M., Smidler, A. L., Catteruccia, F., & Church, G. M. (2014) · eLife · doi:10.7554/elife.03401 · Cited by 889
Enhanced prime editing systems by manipulating cellular determinants of editing outcomes
Chen, P. J., Hussmann, J. A., Yan, J., Knipping, F., Ravisankar, P., Chen, P.-F., Chen, C.-D., Nelson, J. W., Newby, G. A., Şahin, M., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.018 · Cited by 841
“We transduced a Repair-seq library of 1,513 sgRNAs targeting 476 genes (enriched for roles in DNA repair and associated processes; Figure S1G) and 60 non-targeting control sgRNAs into human K562 and HeLa CRISPRi cell lines (Gilbert et al., 2014; Gilbert et al., 2013; Hussmann et al., 2021) (Figure 1B; Table S1).”
BackgroundMethodSelf-citationControl of protein stability by post-translational modifications
Lee, J. M., Hammarén, H. M., Savitski, M. M., & Baek, S. H. (2023) · Nature Communications · doi:10.1038/s41467-023-35795-8 · Cited by 896
Orthogonal Cas9 proteins for RNA-guided gene regulation and editing
Esvelt, K. M., Mali, P., Braff, J. L., Moosburner, M., Yaung, S. J., & Church, G. M. (2013) · Nature Methods · doi:10.1038/nmeth.2681 · Cited by 786
In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9
Swiech, L., Heidenreich, M., Banerjee, A., Habib, N., Li, Y., Trombetta, J., Sur, M., & Zhang, F. (2015) · Nature Biotechnology · doi:10.1038/nbt.3055 · Cited by 772
Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing
Nuñez, J. K., Chen, J., Pommier, G. C., Cogan, J. Z., Replogle, J. M., Adriaens, C., Ramadoss, G. N., Shi, Q., Hung, K. L., Samelson, A. J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.025 · Cited by 760
Self-citationCheng, A. W., Wang, H., Yang, H., Shi, L., Yarden Katz, A., Theunissen, T. W., Rangarajan, S., Shivalila, C., Dadon, D. B., & Jaenisch, R. (2013) · Cell Research · doi:10.1038/cr.2013.122 · Cited by 768
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells
Liu, S. J., Horlbeck, M. A., Cho, S. W., Birk, H. S., Malatesta, M., He, D. X., Attenello, F. J., Villalta, J. E., Cho, M. Y., Chen, Y., et al. (2016) · Science · doi:10.1126/science.aah7111 · Cited by 756
Self-citationCRISPR/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
“revealed that dCas9 interacts with effectors related to transcriptional regulation, such as VP64 and KRAB, to coregulate gene expression, which is currently the most common use of dCas9.(59)”
BackgroundInfluentialInterpreting the language of histone and DNA modifications
Rothbart, S. B., & Strahl, B. D. (2014) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2014.03.001 · Cited by 792
“Our ability to now site-specifically modify the chromatin landscape in complex eukaryotic systems using re-purposed genome editing tools like zinc-finger (ZF) nuclease, TALE nuclease, and clustered regulatory interspaced short palindromic repeat (CRISPR) technologies [228–231] is an important step towards tackling thi…”
BackgroundA CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation
Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., Voytas, D. F., Hsieh, T.-F., Zhang, Y., & Qi, Y. (2015) · Plant Physiology · doi:10.1104/pp.15.00636 · Cited by 707
“…such as VP16 or VP64 (Sadowski et al., 1988; Beerli et al., 1998) to a deactivated Cas9 (dCas9) lacking endonuclease activity can up-regulate endogenous gene expression in human cells (Cheng et al., 2013; Gilbert et al., 2013; Maeder et al., 2013; Mali et al., 2013a; Perez-Pinera et al., 2013).”
BackgroundInfluentialXiong, Y., Zhang, J., Yang, Z., Mou, Q., Ma, Y., Xiong, Y., & Lu, Y. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b09211 · Cited by 687
CRISPR/Cas9 for genome editing: progress, implications and challenges
Zhang, F., Wen, Y., & Guo, X. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu125 · Cited by 720
“fused repressive or activating effector domains to dCas9, which together with gRNA could implement precise and stable transcriptional control of target genes, including transcription repression and activation (59).”
BackgroundDiverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems
Mohanraju, P., Makarova, K. S., Zetsche, B., Zhang, F., Koonin, E. V., & John van der, O. O. S. T. (2016) · Science · doi:10.1126/science.aad5147 · Cited by 692
“The dCas9 has been used for transcriptional activation and repression [134-137], for localizing fluorescent protein labels [138], and for recruiting histone modifying enzymes [139, 140].”
MethodFunctional annotation of native enhancers with a Cas9–histone demethylase fusion
Kearns, N. A., Pham, H., Tabak, B., Genga, R. M., Silverstein, N. J., Garber, M., & Maehr, R. (2015) · Nature Methods · doi:10.1038/nmeth.3325 · Cited by 656
Synthetic lethality and cancer
O’Neil, N. J., Bailey, M. L., & Hieter, P. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.47 · Cited by 689
Genome editing in the human malaria parasite Plasmodium falciparum using the CRISPR-Cas9 system
Ghorbal, M., Gorman, M., MacPherson, C. R., Martins, R. M., Scherf, A., & Lopez-Rubio, J.-J. (2014) · Nature Biotechnology · doi:10.1038/nbt.2925 · Cited by 674
Systematic mapping of functional enhancer–promoter connections with CRISPR interference
Fulco, C. P., Munschauer, M., Anyoha, R., Munson, G., Grossman, S. R., Perez, E. M., Kane, M., Cleary, B., Lander, E. S., & Engreitz, J. M. (2016) · Science · doi:10.1126/science.aag2445 · Cited by 643
“1B), but, because recruitment of KRAB-dCas9 to these sites may directly interfere with transcription (9), we focused on distal regulatory elements in subsequent analysis.”
BackgroundA light-inducible CRISPR-Cas9 system for control of endogenous gene activation
Polstein, L. R., & Gersbach, C. A. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1753 · Cited by 630
Sequence determinants of improved CRISPR sgRNA design
Xu, H., Xiao, T., Chen, C.-H., Li, W., Meyer, C. A., Wu, Q., Wu, D., Cong, L., Zhang, F., Liu, J. S., et al. (2015) · Genome Research · doi:10.1101/gr.191452.115 · Cited by 625
“Alternatively, in the CRISPRi/a systems, catalytically inactive Cas9 (dCas9) proteins guided by sgRNAs enable the localization of effector domains to repress or activate gene transcription without modifying DNA (Gilbert et al. 2013; Qi et al. 2013).”
Harnessing genomics to fast-track genetic improvement in aquaculture
Houston, R. D., Bean, T. P., Macqueen, D. J., Gundappa, M. K., Jin, Y. H., Jenkins, T. L., Selly, S.-L. C., Martín, S., Stevens, J. R., Santos, E. M., et al. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0227-y · Cited by 659
A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain
Kleaveland, B., Shi, C. Y., Stefano, J., & Bartel, D. P. (2018) · Cell · doi:10.1016/j.cell.2018.05.022 · Cited by 610
Past, present, and future of CRISPR genome editing technologies
Pacesa, M., Pelea, O., & Jinek, M. (2024) · Cell · doi:10.1016/j.cell.2024.01.042 · Cited by 609
“196 To suppress gene expression in eukaryotic cells, nuclease-inactive Cas9 can be fused to various transcriptional and epigenetic modulators, for example, the KRAB transcriptional repressor domain, 197,198 and targeted to promoter regions of actively transcribed genes.”
Bock, C., Datlinger, P., Chardon, F. M., Coelho, M. A., Dong, M. B., Lawson, K. A., Lu, T., Maroc, L., Norman, T. M., Song, B., et al. (2022) · Nature Reviews Methods Primers · doi:10.1038/s43586-021-00093-4 · Cited by 626
“In CRISPRi, dCas9 is fused with a Krüppel associated box (KRAB) domain, which represses gene expression when targeted to promoter regions 63,68–71 .”
BackgroundSelf-citationGenomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
Aguirre, A. J., Meyers, R. M., Weir, B. A., Vázquez, F., Zhang, C., Ben‐David, U., Cook, A., Ha, G., Harrington, W. F., Doshi, M. B., et al. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-0154 · Cited by 580
“Furthermore, nuclease-dead versions of Cas9 (dCas9) can also be fused to transcriptional activator or repressor domains to modulate gene expression at specific sites in the genome (13-17).”
Liu, Q., Gao, R., Li, J., Lin, L., Zhao, J., Sun, W., & Tian, C. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-016-0693-9 · Cited by 583
Choi, K. R., Jang, W. D., Yang, D., Cho, J. S., Park, D., & Lee, S. Y. (2019) · Trends in biotechnology · doi:10.1016/j.tibtech.2019.01.003 · Cited by 579
The CRISPR-Cas immune system: Biology, mechanisms and applications
Rath, D., Amlinger, L., Rath, A., & Lundgren, M. (2015) · Biochimie · doi:10.1016/j.biochi.2015.03.025 · Cited by 471
CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs
Mandegar, M. A., Huebsch, N., Frolov, E. B., Shin, E., Truong, A., Olvera, M. P., Chan, A. H., Miyaoka, Y., Holmes, K., Spencer, C. I., et al. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.01.022 · Cited by 525
Self-citationWang, H.-X., Li, M., Lee, C. M., Chakraborty, S., Kim, H.-W., Bao, G., & Leong, K. W. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00799 · Cited by 560
Ishino, Y., Krupovic, M., & Forterre, P. (2018) · Journal of Bacteriology · doi:10.1128/jb.00580-17 · Cited by 558
Multiplexed CRISPR technologies for gene editing and transcriptional regulation
McCarty, N. S., Graham, A. E., Studená, L., & Ledesma‐Amaro, R. (2020) · Nature Communications · doi:10.1038/s41467-020-15053-x · Cited by 567
Increased demand for NAD(+) relative to ATP drives aerobic glycolysis
Luengo, A., Li, Z., Gui, D. Y., Sullivan, L. B., Zagorulya, M., Do, B. T., Ferreira, R., Naamati, A., Ali, A., Lewis, C. A., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.12.012 · Cited by 547
Genome Engineering with Targetable Nucleases
Carroll, D. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060713-035418 · Cited by 568
“A nuclease-dead version of the Cas9 protein, when linked to such a domain, becomes an RNA-guided TF (109, 110).”
BackgroundCRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons
Tian, R., Gachechiladze, M. A., Ludwig, C. H., Laurie, M. T., Hong, J. Y., Nathaniel, D., Prabhu, A. V., Fernandopulle, M. S., Patel, R., Abshari, M., et al. (2019) · Neuron · doi:10.1016/j.neuron.2019.07.014 · Cited by 543
Ribosome profiling reveals the what, when, where and how of protein synthesis
Brar, G. A., & Weissman, J. S. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4069 · Cited by 559
Self-citationBCAA catabolism in brown fat controls energy homeostasis through SLC25A44
Yoneshiro, T., Wang, Q., Tajima, K., Matsushita, M., Maki, H., Igarashi, K., Dai, Z., White, P. J., McGarrah, R. W., Ilkayeva, O., et al. (2019) · Nature · doi:10.1038/s41586-019-1503-x · Cited by 553
“…Hipp11 (H11) locus expressing the nuclease-deficient Cas9 fused to the zinc-finger protein 10 (ZNF10) Krüppel-Associated Box (KRAB) repressor domain 31 , together with mCherry and the puromycin resistance cassette. dCas9-KRAB mice were backcrossed with wild-type C57BL/6J mice, and subsequently…”
CRISPR-Based Therapeutic Genome Editing: Strategies and In Vivo Delivery by AAV Vectors
Wang, D., Zhang, F., & Gao, G. (2020) · Cell · doi:10.1016/j.cell.2020.03.023 · Cited by 539
“In mammalian cells, robust gene repression was achieved by fusing a nuclease-deactivated Cas9 (dCas9) to a repressor domain like the Krüppel-associated box (KRAB) domain and targeting it to the transcription start site (Gilbert et al., 2014; Gilbert et al., 2013) (Figure 2A).”
Comparison 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
“These nuclease-null, or “dead,” Cas9 (dCas9) variants can then be fused to effector domains, allowing users to precisely direct a given functional activity to any arbitrary locus within the genome 7,9,10,11 .”
Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR
Boettcher, M., & McManus, M. T. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.028 · Cited by 539
Genome Engineering Using CRISPR-Cas9 System
Cong, L., & Zhang, F. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1862-1_10 · Cited by 536
Engineering mesoporous silica nanoparticles for drug delivery: where are we after two decades?
Vallet‐Regí, M., Schüth, F., Lozano, D., Colilla, M., & Manzano, M. (2022) · Chemical Society Reviews · doi:10.1039/d1cs00659b · Cited by 537
Genetically engineered mouse models in oncology research and cancer medicine
Kersten, K., de Visser, K. E., van Miltenburg, M. H., & Jonkers, J. (2017) · EMBO Molecular Medicine · doi:10.15252/emmm.201606857 · Cited by 502
“The CRISPR/Cas9 system has recently been modified to induce target gene repression (CRISPRi) or activation (CRISPRa) (Gilbert et al , 2013).”
Gonzãlez, F., Zhu, Z., Shi, Z., Lelli, K. M., Verma, N., Li, Q. V., & Huangfu, D. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.05.018 · Cited by 504
“, nCas9, dCas9, or dCas9-KRAB) (Gilbert et al., 2013; Mali et al., 2013a; Qi et al., 2013; Ran et al., 2013b), one may repurpose iCRISPR for additional tasks such as gene regulation.”
BackgroundStructure-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
Classification and evolution of type II CRISPR-Cas systems
Chylinski, K., Makarova, K. S., Charpentier, E., & Koonin, E. V. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku241 · Cited by 498
An enhanced CRISPR repressor for targeted mammalian gene regulation
Yeo, N. C., Chavez, A., Lance‐Byrne, A., Chan, Y., Menn, D. J., Milanova, D., Kuo, C., Guo, X., Sharma, S., Tung, A., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0048-5 · Cited by 489
Metadata
- Authors
- Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., Lim, W. A., Weissman, J. S., & Qi, L. S.
- Affiliations
- QB3 (US)
- Howard Hughes Medical Institute (US)
- Peking University (CN)
- Corresponding author
- Weissman, Jonathan S.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-07
- Volume
- 154
- Issue
- 2
- Pages
- 442-451
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3770145
- OpenAlex
- W2101749257
- Cited by
- 3,696
- References
- 46
- Citations by year
- 2026: 195 · 2025: 260 · 2024: 298 · 2023: 286 · 2022: 316 · 2021: 374 · 2020: 387 · 2019: 332 · 2018: 328 · 2017: 286 · 2016: 256 · 2015: 187 · 2014: 161 · 2013: 28
- FWCI
- 94.43
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (U01 CA168370, P50 GM102706, 0540879)
- Howard Hughes Medical Institute
- National Institutes of Health (GM102706, GM081879)
- University of California, San Francisco (GM081879)
- National Cancer Institute (U01CA168370)
- National Institute of General Medical Sciences (P50GM081879, P50GM102706, GM081879, F32GM100611, GM102706)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- CRISPR interference, dCas9, transcriptional repression, transcriptional activation, gene silencing, CRISPR/Cas9
- MeSH terms
- Bacterial Proteins, HeLa Cells, Humans, Saccharomyces cerevisiae, Streptococcus pyogenes, Gene Targeting, HEK293 Cells, RNA, Small Untranslated
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.
A language model drew the claims from the paper on 2026-10-05, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-05 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
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
