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.
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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
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Items 501–600 of 1,013
Hamilton, P. J., Burek, D. J., Lombroso, S. I., Neve, R. L., Robison, A. J., Nestler, E. J., & Heller, E. A. (2018) · Neuropsychopharmacology · doi:10.1038/npp.2017.88 · Cited by 113
“This mode of gene regulation drives physiologically relevant changes in expression level (~1.2– 2.0-fold) (Gilbert et al, 2013; Heller et al, 2014, 2016) that are lower than that seen with exogenous gene expression or gene knockout (Chen et al, 1998).”
BackgroundInfluentialCRISPR/Cas9-mediated genome engineering of CHO cell factories: application and perspectives
Lee, J. S., Grav, L. M., Lewis, N. E., & Faustrup Kildegaard, H. (2015) · Biotechnology Journal · doi:10.1002/biot.201500082 · Cited by 117
Precision cancer mouse models through genome editing with CRISPR-Cas9
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Spell Checking Nature: Versatility of CRISPR/Cas9 for Developing Treatments for Inherited Disorders
Wojtal, D., Kemaladewi, D. U., Malam, Z., Abdullah, S., Wong, T. W. Y., Hyatt, E., Baghestani, Z., Pereira, S., Stavropoulos, J., Mouly, V., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.012 · Cited by 121
Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system
Kipniss, N. H., Dingal, P. C. D. P., Abbott, T. R., Gao, Y., Wang, H., Dominguez, A. A., Labanieh, L., & Qi, L. S. (2017) · Nature Communications · doi:10.1038/s41467-017-02075-1 · Cited by 113
“Substituting equations (12), (13), (14) into Equation (15) yields a steady-state formula for GFP as a function of CNO ligand and ARRB2-dCas9,”
BackgroundSelf-citationGenome editing for horticultural crop improvement
Xu, J., Hua, K., & Lang, Z. (2019) · Horticulture Research · doi:10.1038/s41438-019-0196-5 · Cited by 117
Current and future prospects for CRISPR‐based tools in bacteria
Luo, M. L., Leenay, R. T., & Beisel, C. L. (2015) · Biotechnology and Bioengineering · doi:10.1002/bit.25851 · Cited by 116
“The most notable advance has been the development of protein fusions to drive gene activation and repression (Gilbert et al., 2013; Maeder et al., 2013; Mali et al., 2013a; Perez-Pinera et al., 2013) (Fig.”
BackgroundCarleton, J. B., Berrett, K. C., & Gertz, J. (2017) · Cell Systems · doi:10.1016/j.cels.2017.08.011 · Cited by 113
“In addition to the original form of CRISPRi (Gilbert et al., 2013), which uses the KRAB repressive domain to recruit KAP1 and deposit heterochromatin at targeted sites (Groner et al., 2010), we also investigated the repressive capacity of the SIN3A interacting domain of MAD1, also known as the SID domain (Ayer et al.,…”
BackgroundInfluentialCRISPR/Cas approach: A new way of looking at plant-abiotic interactions
Mushtaq, M., Bhat, J. A., Mir, Z. A., Sakina, A., Ali, S., Singh, A. K., Tyagi, A., Salgotra, R. K., Dar, A. A., & Bhat, R. (2018) · Journal of Plant Physiology · doi:10.1016/j.jplph.2018.04.001 · Cited by 113
Magill, S. T., Vasudevan, H. N., Seo, K., Villanueva-Meyer, J. E., Choudhury, A., Liu, S. J., Pekmezci, M., Findakly, S., Hilz, S., Lastella, S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18582-7 · Cited by 114
How specific is CRISPR/Cas9 really?
O’Geen, H., Yu, A. S., & Segal, D. J. (2015) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2015.10.001 · Cited by 108
“A modest number of offtarget bindings might also be acceptable when using dCas9 to regulate transcription without altering the genetic content [18-20,23], even in clinical applications.”
Conditional Degrons for Controlling Protein Expression at the Protein Level
Natsume, T., & Kanemaki, M. T. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-120116-024656 · Cited by 113
Hanewich-Hollatz, M. H., Chen, Z., Hochrein, L. M., Huang, J., & Pierce, N. A. (2019) · ACS Central Science · doi:10.1021/acscentsci.9b00340 · Cited by 111
Inoue, F., Kreimer, A., Ashuach, T., Ahituv, N., & Yosef, N. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.09.010 · Cited by 109
“As an additional validation, we used CRISPR activation (CRIPSRa) (Gilbert et al., 2013) to target three CRSs detected in our study at the SOX1, IRX3, and OTX2 loci in hESCs.”
MethodCRISPR guide RNA design for research applications
Mohr, S. E., Hu, Y., Ewen‐Campen, B., Housden, B. E., Viswanatha, R., & Perrimon, N. (2016) · FEBS Journal · doi:10.1111/febs.13777 · Cited by 112
Deaner, M., & Alper, H. S. (2017) · Metabolic Engineering · doi:10.1016/j.ymben.2017.01.012 · Cited by 110
Cellular Biosensors with Engineered Genetic Circuits
Saltepe, B., Kehribar, E. Ş., YİRMİBEŞOĞLU, S. S. S., & Şeker, U. Ö. Ş. (2017) · ACS Sensors · doi:10.1021/acssensors.7b00728 · Cited by 110
The CRISPR /Cas revolution reaches the RNA world: Cas13, a new Swiss Army knife for plant biologists
Wolter, F., & Puchta, H. (2018) · The Plant Journal · doi:10.1111/tpj.13899 · Cited by 113
“By fusing this nuclease “dead” Cas9 (dCas9) directly or indirectly to an effector domain, it can then be used to guide diverse enzymatic functions to any specific site in the genome (Gilbert et al., 2013; Konermann et al., 2015).”
BackgroundPrediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network
Xue, L., Tang, B., Chen, W., & Luo, J. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00368 · Cited by 113
Engineering of monosized lipid-coated mesoporous silica nanoparticles for CRISPR delivery
Noureddine, A., Maestas-Olguin, A., Saada, E. A., LaBauve, A. E., Agola, J. O., Baty, K. E., Howard, T. A., Sabo, J. K., Espinoza, C. R. S., Doudna, J. A., et al. (2020) · Acta Biomaterialia · doi:10.1016/j.actbio.2020.07.027 · Cited by 113
Self-citationLiu, Z., Hu, X., Liang, Y., Yu, J., Li, H., Shokhirev, M. N., & Zheng, Y. (2022) · Nature Immunology · doi:10.1038/s41590-022-01244-9 · Cited by 117
Self-citationDrugging the epigenome in the age of precision medicine
Feehley, T., O’Donnell, C. W., Mendlein, J. D., Karande, M., & McCauley, T. (2023) · Clinical Epigenetics · doi:10.1186/s13148-022-01419-z · Cited by 119
CRISPR-mediated Activation of Latent HIV-1 Expression
Limsirichai, P., Gaj, T., & Schaffer, D. V. (2015) · Molecular Therapy · doi:10.1038/mt.2015.213 · Cited by 112
Programmable control of bacterial gene expression with the combined CRISPR and antisense RNA system
Lee, Y. J., Hoynes-O’Connor, A., Leong, M. C., & Moon, T. S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw056 · Cited by 106
Lin, J., Wagner, J. M., & Alper, H. S. (2017) · Biotechnology Advances · doi:10.1016/j.biotechadv.2017.07.005 · Cited by 110
A Robust CRISPR Interference Gene Repression System in Pseudomonas
Tan, S. Z., Reisch, C. R., & Prather, K. L. J. (2018) · Journal of Bacteriology · doi:10.1128/jb.00575-17 · Cited by 106
“pyogenes provides robust repression in hosts such as Escherichia coli (10), Bacillus subtilis (12), and mammalian cells (13).”
BackgroundA glance at genome editing with CRISPR–Cas9 technology
Barman, A., Deb, B., & Chakraborty, S. (2019) · Current Genetics · doi:10.1007/s00294-019-01040-3 · Cited by 107
Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair
Wienert, B., Nguyen, D. N., Guenther, A., Feng, S. J., Locke, M. N., Wyman, S. K., Shin, J. J., Kazane, K. R., Gregory, G. L., Carter, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15845-1 · Cited by 102
Pramanik, D., Shelake, R. M., Kim, M. J., & Kim, J. (2020) · Molecular Plant · doi:10.1016/j.molp.2020.11.002 · Cited by 110
Targeting Cdk11 in osteosarcoma cells using the CRISPR‐cas9 system
Feng, Y., Sassi, S. O., Shen, J. K., Yang, X., Gao, Y., Osaka, E., Zhang, J., Yang, S., Cao, Y., Mankin, H. J., et al. (2014) · Journal of Orthopaedic Research® · doi:10.1002/jor.22745 · Cited by 108
“Another RNA-seq showed GFP to be the only gene product that was significantly suppressed by the GFP-targeting sgRNA.(12) Using microarray experiments to compare genome-wide gene expression profiles also revealed that the CRISPRCas9 system is highly specific.”
BackgroundResultInfluentialMouse Genome Engineering via CRISPR-Cas9 for Study of Immune Function
Pelletier, S. W., Gingras, S., & Green, D. R. (2015) · Immunity · doi:10.1016/j.immuni.2015.01.004 · Cited by 108
CRISPR/Cas9 in zebrafish: an efficient combination for human genetic diseases modeling
Liu, J., Zhou, Y., Qi, X., Chen, J., Chen, W., Qiu, G., Wu, Z., & Wu, N. (2016) · Human Genetics · doi:10.1007/s00439-016-1739-6 · Cited by 110
“…repair of targeted DSBs, catalytically inactive Cas9 (dCas9) proteins guided by sgRNAs have been used to repress or activate gene transcription without introducing irreversible mutations to the genome, which are commonly referred to as CRISPRi/a systems (Qi et al. 2013; Gilbert et al. 2013).”
BackgroundMultiplexed CRISPR/Cas9 Genome Editing and Gene Regulation Using Csy4 in Saccharomyces cerevisiae
Ferreira, R., Skrekas, C., Nielsen, J., & David, F. (2017) · ACS Synthetic Biology · doi:10.1021/acssynbio.7b00259 · Cited by 108
CRISPR/Cas9 library screening for drug target discovery
Kurata, M., Yamamoto, K., Moriarity, B. S., Kitagawa, M., & Largaespada, D. A. (2017) · Journal of Human Genetics · doi:10.1038/s10038-017-0376-9 · Cited by 108
“For the downregulation of targeted genes, CRISPR-dCas9KRAB (CRISPRi) can interfere with or silence a transcription [4, 5].”
BackgroundCRISPR-based technologies: prokaryotic defense weapons repurposed
Terns, R. M., & Terns, M. P. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.01.003 · Cited by 112
Functional genetics for all: engineered nucleases, CRISPR and the gene editing revolution
Gilles, A. F., & Averof, M. (2014) · EvoDevo · doi:10.1186/2041-9139-5-43 · Cited by 110
“For example, catalytically inactive versions of Cas9 have been used to interfere with transcription [138,139], coupled with transcriptional activators, repressors or chromatin modifiers to generate artificial transcriptional regulators [117,139-143], or linked with fluorescent proteins to reveal…”
Genome Editing Tools in Plants
Mohanta, T. K., Bashir, T., Hashem, A., Allah, E. F. A., & Bae, H. (2017) · Genes · doi:10.3390/genes8120399 · Cited by 109
“Expression of dead Cas9 as a fusion protein with the activation or repression domains of transcription factors can lead to reversible transcriptional control of target genes [106,107].”
BackgroundThe Ftx Noncoding Locus Controls X Chromosome Inactivation Independently of Its RNA Products.
Furlan, G., Hernandez, N. G., Huret, C., Galupa, R., van Bemmel, J. V., Romito, A., Heard, E., Morey, C., & Rougeulle, C. (2018) · Molecules and Cells · doi:10.1016/j.molcel.2018.03.024 · Cited by 106
Advancements and Obstacles of CRISPR-Cas9 Technology in Translational Research
You, L., Tong, R., Li, M., Liu, Y., Xue, J., & Lü, Y. (2019) · Molecular Therapy — Methods & Clinical Development · doi:10.1016/j.omtm.2019.02.008 · Cited by 112
Applications of CRISPR/Cas9 in the Synthesis of Secondary Metabolites in Filamentous Fungi
Jiang, C., Lv, G., Tu, Y., Cheng, X., Duan, Y., Zeng, B., & He, B. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.638096 · Cited by 111
“, KRAB/Kox1), has been used to negatively regulate the transcription of specific genomic loci (Gilbert et al., 2013; Leitão et al., 2017).”
BackgroundMethoddCas9: A Versatile Tool for Epigenome Editing
Brocken, D. J. W., Tark‐Dame, M., & Dame, R. T. (2017) · Current Issues in Molecular Biology · doi:10.21775/cimb.026.015 · Cited by 113
“repressor domains (KRAB, SID) have been fused to dCas9 to specifically increase or decrease target gene expression (Gilbert et al., 2013; Maeder et al., 2013b; Perez-Pinera et al., 2013; Lawhorn et al., 2014).”
BackgroundInfluentialCRISPR-assisted multi-dimensional regulation for fine-tuning gene expression in Bacillus subtilis
Lu, Z., Yang, S., Yuan, X., Shi, Y., Ouyang, L., Jiang, S., Li, Y., & Zhang, G. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz072 · Cited by 106
Kotani, H., Taimatsu, K., Ohga, R., Ota, S., & Kawahara, A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0128319 · Cited by 106
CRISPR/Cas9-Enabled Multiplex Genome Editing and Its Application
Minkenberg, B., Wheatley, M. S., & Yang, Y. (2017) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2017.05.003 · Cited by 107
Molecular biology at the cutting edge: A review on CRISPR/CAS9 gene editing for undergraduates
Thurtle‐Schmidt, D. M., & Lo, T. (2018) · Biochemistry and Molecular Biology Education · doi:10.1002/bmb.21108 · Cited by 103
Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity
Nguyen, D., Miyaoka, Y., Gilbert, L. A., Mayerl, S. J., Lee, B. H., Weissman, J. S., Conklin, B. R., & Wells, J. A. (2016) · Nature Communications · doi:10.1038/ncomms12009 · Cited by 107
Self-citationChen, F., Li, X., Aquadro, E., Haigh, S. B., Zhou, J., Stepp, D. W., Weintraub, N. L., Barman, S. A., & Fulton, D. J. (2016) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2016.08.003 · Cited by 105
Progress in Genome Editing Technology and Its Application in Plants
Zhang, K., Raboanatahiry, N. H., Zhu, B., & Li, M. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.00177 · Cited by 105
“(2013) demonstrated 93% repression of GFP reporter gene expression when dCas9 was fused with a Krüppel-associated box repressor in human cells (Gilbert et al., 2013).”
BackgroundFu, X., Zhu, X., Qin, F., Zhang, Y., Lin, J., Ding, Y., Yang, Z., Shang, Y., Wang, L., Zhang, Q., et al. (2018) · Molecular Cancer · doi:10.1186/s12943-018-0783-3 · Cited by 105
“For Linc00210 depletion, dCas9-Krab CRISPRi strategy was used [45].”
MethodRetractedGenome-wide analysis of somatic noncoding mutation patterns in cancer
Dietlein, F., Wang, A. B., Fagre, C. R., Tang, A., Besselink, N. J. M., Cuppen, E. P. J. G., Li, C., Sunyaev, S. R., Neal, J. T., & Allen, E. M. V. (2022) · Science · doi:10.1126/science.abg5601 · Cited by 103
Marqués, M.-C., Sánchez-Vicente, J., Ruiz, R., Montagud‐Martínez, R., Márquez‐Costa, R., Gómez, G., Carbonell, A., Daròs, J., & Rodrigo, G. (2022) · ACS Synthetic Biology · doi:10.1021/acssynbio.2c00090 · Cited by 105
Modeling Disease In Vivo With CRISPR/Cas9
Dow, L. E. (2015) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2015.07.006 · Cited by 111
“In addition, nuclease-inactive ‘dead’ Cas9 (dCas9) has been adapted to enable suppression of gene transcription (CRISPRi) or activation of endogenous gene expression (CRISPRa) [87–92].”
Resources for the design of CRISPR gene editing experiments
Graham, D. B., & Root, D. E. (2015) · Genome biology · doi:10.1186/s13059-015-0823-x · Cited by 108
Systematic identification of regulatory variants associated with cancer risk
Liu, S., Liu, Y., Zhang, Q., Wu, J., Liang, J., Yu, S., Wei, G., White, K. P., & Wang, X. (2017) · Genome biology · doi:10.1186/s13059-017-1322-z · Cited by 100
“To validate that the rs11055880-containing region endogenously regulates ATF7IP expression, we used the CRISPR interference (CRISPRi) system to alter the chromatin state at the rs11055880 site through recruitment of a KRAB effector domain fused to catalytically dead Cas9 [36].”
MethodInfluentialCRISPR technologies for stem cell engineering and regenerative medicine
Hsu, M., Chang, Y., Truong, V. A., Lai, P., Nguyen, T. K. N., & Hu, Y. (2019) · Biotechnology Advances · doi:10.1016/j.biotechadv.2019.107447 · Cited by 106
The miniature CRISPR-Cas12m effector binds DNA to block transcription
Wu, W. Y., Mohanraju, P., Liao, C., Adiego-Pérez, B., Creutzburg, S. C. A., Makarova, K. S., Keessen, K., Lindeboom, T. A., Khan, T. S., Prinsen, S. H. P., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.11.003 · Cited by 102
Enabling functional genomics with genome engineeringPreprint
Hilton, I. B., & Gersbach, C. A. (2015) · Genome Research · doi:10.1101/gr.190124.115 · Cited by 106
“However, when fused to repressive domains, such as the KRAB domain (Margolin et al. 1994), the inhibitory effect of ZFs (Beerli et al. 1998), TALEs (Cong et al. 2012), or dCas9 (Gilbert et al. 2013) on transcription is markedly enhanced.”
BackgroundMethodInfluentialDesignable DNA-binding domains enable construction of logic circuits in mammalian cells
Gaber, R., Lebar, T., Majerle, A., Šter, B., Dobnikar, A., Benčina, M., & Jerala, R. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1433 · Cited by 103
Recent applications of synthetic biology tools for yeast metabolic engineering
Jensen, M. K., & Keasling, J. D. (2014) · FEMS Yeast Research · doi:10.1111/1567-1364.12185 · Cited by 106
“1a) (Farzadfard et al., 2013; Gilbert et al., 2013).”
CRISPR/Cas9 for Human Genome Engineering and Disease Research
Xiong, X., Chen, M., Lim, W. A., Zhao, D., & Qi, L. S. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022258 · Cited by 111
Self-citationEmerging roles for long noncoding RNAs in skeletal biology and disease
Huynh, N. P. T., Anderson, B. A., Guilak, F., & McAlinden, A. (2016) · Connective Tissue Research · doi:10.1080/03008207.2016.1194406 · Cited by 105
“This includes, but not limited to, dCas9-KRAB (253,254) for gene repression and dCas9-VP48 (255), dCas9-VP64 (256) (257), dCas9-p300 (258), dCas9-VP64/p65 (259) for gene activation.”
BackgroundKim, S. K., Seong, W., Han, G. H., Lee, D., & Lee, S. (2017) · Microbial Cell Factories · doi:10.1186/s12934-017-0802-x · Cited by 103
“Recently, CRISPR interference (CRISPRi) was developed for DNA-sequence-specific gene regulation and used to repress multiple genes simultaneously in bacteria, yeast, plants, and animals [13, 21, 22].”
BackgroundAdvances and challenges in genetic engineering of microalgae
Fajardo, C., Donato, M. D., Carrasco-Reinado, R., Martı́nez-Rodrı́guez, G., Mancera, J. M., & Fernández‐Acero, F. J. (2019) · Reviews in Aquaculture · doi:10.1111/raq.12322 · Cited by 105
Harnessing CRISPR-Cas9 immunity for genetic engineering
Charpentier, E., & Marraffini, L. A. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.07.001 · Cited by 107
The synthetic biology toolbox for tuning gene expression in yeast
Redden, H., Morse, N. J., & Alper, H. S. (2014) · FEMS Yeast Research · doi:10.1111/1567-1364.12188 · Cited by 103
“By removing endonuclease activity of the RNA-guided Cas9, dCas9 can be used for gene silencing (Gilbert et al., 2013).”
MethodNotch regulates BMP responsiveness and lateral branching in vessel networks via SMAD6
Mouillesseaux, K. P., Wiley, D. S., Saunders, L. M., Wylie, L. A., Kushner, E. J., Chong, D. C., Citrin, K. M., Barber, A. T., Park, Y., Kim, J., et al. (2016) · Nature Communications · doi:10.1038/ncomms13247 · Cited by 102
CRISPR screens in plants: approaches, guidelines, and future prospects
Gaillochet, C., Develtere, W., & Jacobs, T. B. (2021) · The Plant Cell · doi:10.1093/plcell/koab099 · Cited by 102
Exploration of Epigenetics for Improvement of Drought and Other Stress Resistance in Crops: A Review
Sun, C., Ali, K., Yan, K., Fiaz, S., Dormatey, R., Bi, Z., & Bai, J. (2021) · Plants · doi:10.3390/plants10061226 · Cited by 108
Natural products from resurrection plants: Potential for medical applications
Gechev, T., Hille, J., Woerdenbag, H. J., Benina, M., Mehterov, N. H., Toneva, V., Fernie, A. R., & Mueller‐Roeber, B. (2014) · Biotechnology Advances · doi:10.1016/j.biotechadv.2014.03.005 · Cited by 104
Making designer mutants in model organisms
Peng, Y., Clark, K. J., Campbell, J. M., Panetta, M. R., Guo, Y., & Ekker, S. C. (2014) · Development · doi:10.1242/dev.102186 · Cited by 103
Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation
Braun, C. J., Bruno, P. M., Horlbeck, M. A., Gilbert, L. A., Weissman, J. S., & Hemann, M. T. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600582113 · Cited by 104
“To determine whether this extent of TRP53 loss was significant enough to impact the speed of tumor development and response to chemotherapy, we transplanted Eμ-Myc p19 cells expressing dCas9 and either a control sgRNA (Gal4) or either of two sgRNAs targeting Trp53 (T2, T3) into syngeneic C57BL/6J mice (25).”
BackgroundSelf-citationTransforming plant biology and breeding with CRISPR /Cas9, Cas12 and Cas13
Schindele, P., Wolter, F., & Puchta, H. (2018) · FEBS Letters · doi:10.1002/1873-3468.13073 · Cited by 110
Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids
D’Ippolito, A. M., McDowell, I. C., Barrera, A., Hong, L. K., Leichter, S. M., Bartelt, L. C., Vockley, C. M., Majoros, W. H., Safi, A., Song, L., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2018.06.007 · Cited by 106
lncRNA KHPS1 Activates a Poised Enhancer by Triplex-Dependent Recruitment of Epigenomic Regulators
Blank-Giwojna, A., Postepska‐Igielska, A., & Grummt, I. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.02.059 · Cited by 102
A neuroscientist’s guide to transgenic mice and other genetic tools
Navabpour, S., Kwapis, J. L., & Jarome, T. J. (2019) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.12.013 · Cited by 108
Gao, J., Wei, B., Liu, M., Hirsova, P., Sehrawat, T. S., Cao, S., Hu, X., Xue, F., Yaqoob, U., Kang, N., et al. (2021) · Hepatology · doi:10.1002/hep.31617 · Cited by 100
Himeda, C. L., Jones, T. I., & Jones, P. L. (2015) · Molecular Therapy · doi:10.1038/mt.2015.200 · Cited by 102
Genome Editing Technologies: Defining a Path to Clinic
Corrigan‐Curay, J., O’Reilly, M., Kohn, D. B., Cannon, P. M., Bao, G., Bushman, F. D., Carroll, D., Cathomen, T., Joung, J. K., Roth, D. B., et al. (2015) · Molecular Therapy · doi:10.1038/mt.2015.54 · Cited by 101
Metabolic engineering for enhancing microbial biosynthesis of advanced biofuels
Das, M., Patra, P., & Ghosh, A. (2019) · Renewable and Sustainable Energy Reviews · doi:10.1016/j.rser.2019.109562 · Cited by 100
Genetic glycoengineering in mammalian cells
Narimatsu, Y., Büll, C., Chen, Y., Wandall, H. H., Yang, Z., & Clausen, H. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100448 · Cited by 103
“Utilization of catalytically inactive (dead) dCas9 allows to fully repress target gene expression through fusion with transcription repressors (CRISPR interference, CRISPRi) and recruitment to the promoter region of a target gene (92).”
BackgroundSensitive cells: enabling tools for static and dynamic control of microbial metabolic pathways
Cress, B. F., Trantas, E., Ververidis, F., Linhardt, R. J., & Koffas, M. A. G. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2015.09.007 · Cited by 99
“cerevisiae [35,36 ], and mammalian cells [37].”
Advancing chimeric antigen receptor T cell therapy with CRISPR/Cas9
Ren, J., & Zhao, Y. (2017) · Protein & Cell · doi:10.1007/s13238-017-0410-x · Cited by 103
“…including gene editing and gene expression regulation, epigenetic modification, and genome imaging (Cheng et al., 2013; DiCarlo et al., 2013; Gilbert et al., 2013; Hwang et al., 2013; Li et al., 2013; Maeder et al., 2013; Nekrasov et al., 2013; Perez-Pinera et al., 2013; Qi et al., 2013;…”
BackgroundLane, S., Xu, H., Oh, E. J., Kim, H., Lesmana, A., Jeong, D., Zhang, G.-C., Tsai, C., Jin, Y., & Kim, S. R. (2018) · Scientific Reports · doi:10.1038/s41598-018-20804-4 · Cited by 98
Hua, X., Li, B., Song, L., Hu, C., Li, X., Wang, D., Xiong, Y., Zhao, P., He, H., Xia, Q., et al. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra117.000194 · Cited by 101
“To exclude off-target effects of RNAi, we used the CRISPRi system (24), in which dCas9 was fused to effector domains to serve as an RNA-guided DNA-binding protein to target gene expression (Fig.”
MethodModel-based understanding of single-cell CRISPR screening
Duan, B., Zhou, C., Zhu, C., Yu, Y., Li, G., Zhang, S., Zhang, C., Ye, X., Ma, H., Qu, S., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10216-x · Cited by 98
Functional Genomics via CRISPR–Cas
Ford, K. M., McDonald, D., & Mali, P. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.06.034 · Cited by 103
Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability
Hansen, M. M. K., Desai, R. V., Simpson, M. L., & Weinberger, L. S. (2018) · Cell Systems · doi:10.1016/j.cels.2018.08.002 · Cited by 88
Xu, L., Zhao, L., Gao, Y., Xu, J., & Han, R. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1048 · Cited by 91
Wierzbicki, M. P., Maloney, V., Mizrachi, E., & Myburg, A. A. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00176 · Cited by 101
CRISPR/Cas System and Factors Affecting Its Precision and Efficiency
Javaid, N., & Choi, S. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.761709 · Cited by 106
Sequence-specific inhibition of microRNA via CRISPR/CRISPRi system
Zhao, Y., Dai, Z., Yang, L. H., Yin, M., Ma, K., He, M., Ouyang, H., & Teng, C. (2014) · Scientific Reports · doi:10.1038/srep03943 · Cited by 96
Genetic screens and functional genomics using CRISPR /Cas9 technology
Hartenian, E., & Doench, J. G. (2015) · FEBS Journal · doi:10.1111/febs.13248 · Cited by 100
Piotrowski, J. S., Zhang, Y., Bates, D. M., Keating, D. H., Sato, T. K., Ong, I. M., & Landick, R. C. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00090 · Cited by 95
“Genome editing and optimization techniques such as CRISPR/Cas9 and MAGE allows rapid, detailed genome editing in both bacteria and eukaryotes (Wang et al., 2012; Cong et al., 2013; DiCarlo et al., 2013; Gilbert et al., 2013).”
Zhen, S., Ling, H., Liu, Y., Sun, X., Jiang, M., Chen, W., Zhao, L., & Li, X. (2016) · Oncotarget · doi:10.18632/oncotarget.14176 · Cited by 96
Kimberland, M. L., Hou, W., Alfonso-Pecchio, A. R., Wilson, S. P., Rao, Y., Zhang, S., & Lu, Q. (2018) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2018.08.007 · Cited by 99
A Chromatin Accessibility Atlas of the Developing Human Telencephalon
Markenscoff-Papadimitriou, E., Whalen, S., Przytycki, P. F., Thomas, R., Binyameen, F., Nowakowski, T. J., Kriegstein, A. R., Sanders, S., State, M. W., Pollard, K. S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.002 · Cited by 91
Xiong, F., Wang, R., Lee, J.-H., Li, S., Chen, S.-F., Liao, Z., Hasani, L. A., Nguyen, P. T.-M., Zhu, X., Krakowiak, J., et al. (2021) · Cell Research · doi:10.1038/s41422-021-00515-8 · Cited by 107
RANKL-responsive epigenetic mechanism reprograms macrophages into bone-resorbing osteoclasts
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“Advances in gene editing technology, such as CRISPR‒Cas9, have enabled direct manipulation of SEs in human cells [88, 89].”
BackgroundPlant genome engineering in full bloom
Lozano‐Juste, J., & Cutler, S. R. (2014) · Trends in Plant Science · doi:10.1016/j.tplants.2014.02.014 · Cited by 95
CRISPR-mediated genome editing and human diseases
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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 ›
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