The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
Open accessAbstract
Bacterial type II CRISPR-Cas9 systems have been widely adapted for RNA-guided genome editing and transcription regulation in eukaryotic cells, yet their in vivo target specificity is poorly understood. Here we mapped genome-wide binding sites of a catalytically inactive Cas9 (dCas9) from Streptococcus pyogenes loaded with single guide RNAs (sgRNAs) in mouse embryonic stem cells (mESCs). Each of the four sgRNAs we tested targets dCas9 to between tens and thousands of genomic sites, frequently characterized by a 5-nucleotide seed region in the sgRNA and an NGG protospacer adjacent motif (PAM). Chromatin inaccessibility decreases dCas9 binding to other sites with matching seed sequences; thus 70% of off-target sites are associated with genes. Targeted sequencing of 295 dCas9 binding sites in mESCs transfected with catalytically active Cas9 identified only one site mutated above background levels. We propose a two-state model for Cas9 binding and cleavage, in which a seed match triggers binding but extensive pairing with target DNA is required for cleavage.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“| Delivery methods improvement | Application in cell culture [89–94] | Viral transduction | May cause accumulation of off-target mutations |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [93]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“| Delivery methods improvement | Application in cell culture [89–94] | Plasmid transfection | May cause accumulation of off-target mutations |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [93]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“| Delivery methods improvement | Application in cell culture [89–94] | RNP electroporation: Rapid transfection and turnover | Eliminate off-target effects |”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as [93]
Experimental — accuracy not yet measuredIn the citing paper
“A key feature of our system is the transient expression of the nuclease Cas9, through delivery of mRNA. This allowed for sufficient exposure to the nuclease for gene repair and reduced concerns associated with long-term nuclease exposure34.”
From Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo (2016) · cites this paper as [34]
In the citing paper
“And moreover, DNA binding and cleavage by Cas9 are in some cases uncoupled, that is, Cas9 can bind to but not cleave DNA sequences that are partially complementary to sgRNA 49 and exert epigenomic regulatory effects, 43 44 which is unpredictable by silicon methods relying on base pairing.”
From CRISPR-Cas9: a new and promising player in gene therapy (2015) · cites this paper as [49]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
MicroRNAs: Target Recognition and Regulatory Functions
Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.01.002 · Cited by 20,068
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339
Self-citationWebLogo: A Sequence Logo Generator: Figure 1Preprint
Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,418
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
Genome-scale CRISPR-Cas9 knockout screening in human cells
Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X., Scott, D. A., Mikkelsen, T. S., Heckl, D., Ebert, B. L., Root, D. E., Doench, J. G., et al. (2014) · Science · doi:10.1126/science.1247005 · Cited by 5,234
Self-citationRepurposing 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
DNA targeting specificity of RNA-guided Cas9 nucleases
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741
Flagged first, then by citations
Cited by
Sorted by citations
Items 901–944 of 944
Ashok, K. R., Ellango, R., Rajendran, V., Bhargava, C. N., Pavithran, S., Dhawane, Y., Manamohan, M., Jha, G. K., & Asokan, R. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.148735
Harnessing CRISPR-Cas for Stress Tolerance and Yield Improvement in Cotton
Rajan, A. R., Raveendran, M., Varanavasiappan, S., Subramanian, A., Mannu, J., & Kokiladevi, E. (2025) · ACS Agricultural Science & Technology · doi:10.1021/acsagscitech.5c00415
Search-and-remove genome editing allows selection of cells by DNA sequence
Fast, L., Omar, M., Kanis, P., Schaffer, T., Chowdhury, D. T., Rakava, E., Pääbo, S., & Riesenberg, S. (2025) · Nature Communications · doi:10.1038/s41467-025-66896-1 · Cited by 1
Widjaya, M. A., Lee, S.-D., & Ho, Y. (2021) · Figshare · doi:10.6084/m9.figshare.15001312
Shaigani, P., Fuchs, T., Graban, P., Prem, S., Haack, M., Masri, M. A., Mehlmer, N., & Brueck, T. (2024) · Figshare · doi:10.6084/m9.figshare.26567228
Marinov, G. K., Kim, S. H., Bagdatli, S. T., Higashino, S. I., Trevino, A. E., Tycko, J., Wu, T., Bintu, L., Bassik, M. C., He, C., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22678208
Marinov, G. K., Kim, S. H., Bagdatli, S. T., Higashino, S. I., Trevino, A. E., Tycko, J., Wu, T., Bintu, L., Bassik, M. C., He, C., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22678205
Additional file 3 of BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models
Zarate, O. A., Yang, Y., Wang, X., & Wang, J.-P. (2022) · Figshare · doi:10.6084/m9.figshare.21406993
Mak, J. K., Störtz, F., & Mináry, P. (2024) · Figshare · doi:10.6084/m9.figshare.26550874
Li, J., Kong, D., Ke, Y., Zeng, W., & Miki, D. (2024) · Figshare · doi:10.6084/m9.figshare.25017975
Additional file 2 of BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models
Zarate, O. A., Yang, Y., Wang, X., & Wang, J.-P. (2022) · Figshare · doi:10.6084/m9.figshare.21406990
Additional file 1 of Eukaryotic-driven directed evolution of Cas9 nucleases
Ruta, G. V., Ciciani, M., Kheir, E., Gentile, M. D., Amistadi, S., Casini, A., & Cereseto, A. (2024) · Figshare · doi:10.6084/m9.figshare.26697428
Additional file 2 of Eukaryotic-driven directed evolution of Cas9 nucleases
Ruta, G. V., Ciciani, M., Kheir, E., Gentile, M. D., Amistadi, S., Casini, A., & Cereseto, A. (2024) · Figshare · doi:10.6084/m9.figshare.26697431
Additional file 3 of Eukaryotic-driven directed evolution of Cas9 nucleases
Ruta, G. V., Ciciani, M., Kheir, E., Gentile, M. D., Amistadi, S., Casini, A., & Cereseto, A. (2024) · Figshare · doi:10.6084/m9.figshare.26697434
Widjaya, M. A., Lee, S.-D., & Ho, Y. (2021) · Figshare · doi:10.6084/m9.figshare.15001309
Li, J., Kong, D., Ke, Y., Zeng, W., & Miki, D. (2024) · Figshare · doi:10.6084/m9.figshare.25017788
Shaigani, P., Fuchs, T., Graban, P., Prem, S., Haack, M., Masri, M. A., Mehlmer, N., & Brueck, T. (2024) · Figshare · doi:10.6084/m9.figshare.26567222
Additional file 1 of BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models
Zarate, O. A., Yang, Y., Wang, X., & Wang, J.-P. (2022) · Figshare · doi:10.6084/m9.figshare.21406987
Shaigani, P., Fuchs, T., Graban, P., Prem, S., Haack, M., Masri, M. A., Mehlmer, N., & Brueck, T. (2024) · Figshare · doi:10.6084/m9.figshare.26567225
Li, J., Kong, D., Ke, Y., Zeng, W., & Miki, D. (2024) · Figshare · doi:10.6084/m9.figshare.26668953
Li, J., Kong, D., Ke, Y., Zeng, W., & Miki, D. (2024) · Figshare · doi:10.6084/m9.figshare.26668956
CRISPR-Based Synthetic Gene Circuits for Industrial and Therapeutic Applications
Raue, J. M. (2024) · Academic International Journal of Engineering Science · doi:10.59675/e224
Towards whole-cell mapping of single-molecule dynamics
Beheiry, M. E. (2015) · theses.fr (ABES) · doi:10.70675/582d8fdaz0f52z45e5z92e1z6b130a96353b
Understanding the mechanisms of histone modifications in vivo
Kalaivani, N. P. (2016) · theses.fr (ABES) · doi:10.70675/f2af210dz8793z41a5z9c2eza555f78ea60b
Galupa, R. (2017) · theses.fr (ABES) · doi:10.70675/04cc3b8cz6ea7z4c6fzb501z4b35e97f7a72
Development of targeted methylome modifications in mammal cells
Lleida, A. A. (2018) · theses.fr (ABES) · doi:10.70675/6e05a7d8z70caz4650zb774z4d6156ab4205
Insights into the embryo/endosperm interface in Zea Mays and Arabidopsis thaliana
Doll, N. M. (2019) · theses.fr (ABES) · doi:10.70675/f88d2d38z4303z4e72z83a2zac50b238dff8
Dissection of coordinated interferon response by promoter elements with enhancer activity
Santiago‐Algarra, D. (2020) · theses.fr (ABES) · doi:10.70675/a064ee17zbea2z412azb9b6z12839deb2851
CRISPRi screens in bacterial genomics
Rousset, F. (2020) · theses.fr (ABES) · doi:10.70675/b0192b7fzcd2az4a96z8d07z108b9a663eae
AviTag-seq unifies nucleotide-resolution maps of CRISPR off-targets and AAV vector integrations
Li, J.-X., Zhang, S.-M., Ma, X.-Y., Deng, D.-H., Bai, P.-D., Zhao, J.-J., Gong, A., Shan-Chen, P. A. N. G., Dong, F., Wang, S.-D., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-10298-6
Joyce, C. M., Kramer, G. D., Vu, J. T., Tavasoli, K. U., Gardner, B. M., & Richardson, C. D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.01.729390
CRISPR Learns to Read the Epigenome
Black, J. B., & Gersbach, C. A. (2026) · The CRISPR Journal · doi:10.1177/25731599261460335
Advances in AI-Guided CRISPR-Cas9 Engineering Strategies for Microbial Biotechnology
Delgado-Nungaray, J. A., Pérez-Ponce, D. A., Figueroa-Yáñez, L. J., Delgado, E. R., García-Ramírez, M. A., & González‐Reynoso, O. (2026) · Journal of Genome Biotechnology and Genetics · doi:10.3390/jgbg1020010
Direct comparison of CRISPR knockout and interference with Perturb-seqPreprint
Drepanos, L. M., Velasco, B. E., Chase, A., Srikanth, S., Gatzen, M., Rickner, H., Dubinsky, D., Navia, A. W., Shibue, T., Yates, K. B., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.04.736492
Genome editing for aquaculture breeding: established applications and emerging directions
Wu, Y. N., Yang, L., Zhang, Y., Wu, M., Huang, S., Guo, X., Wang, D., Xu, J., & Zhou, L. J. (2026) · Water Biology and Security · doi:10.1016/j.watbs.2026.100683
Sun, Y.-D., Song, L.-J., Liu, B., Cheng, C.-Y., Zhang, L., Zhang, J.-P., & Zhang, X.-B. (2026) · The CRISPR Journal · doi:10.1177/25731599261470587
Zhu, W., Tian, M., Duan, Y., Reisman, S. J., Miller, S. E., Corden, E., ter Weele, M. A., Song, L., Blount, J., Safi, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.10.743836
Optimized parameters for CRISPR-Cas9 interference library design
Srikanth, S., Zheng, F., Drepanos, L. M., Shah, S. T., Kaplan, E. L., Gibson, D., Lynch, G. O., Uebele, A., Reint, G., Merzouk, S., et al. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101338 · Cited by 2
AI for accurate prediction of on-target efficiency and minimization of off-targets in plants
Cheng, M., Previtera, D. A., Zhang, Y., & Gong, Z. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-44079-3.00002-4
Zu, Y., Wang, H., Han, X., Wu, X., & Chen, L. (2026) · Genetics · doi:10.1093/genetics/iyag245
CRISPR-Based Genome Editing and Delivery Systems: Advances, Challenges and Future Directions
Kaur, A., Chanan, R., Sharma, M., Sharma, S., & Sharma, D. (2026) · IntechOpen eBooks · doi:10.5772/intechopen.1016405
Edición genética: una valoración científica y bioética del primer caso en seres humanos en el Perú
Paredes-Moscosso, S. R., Villegas-Llerena, C., & Carbajal, C. Ñ. (2026) · Medicina y Ética · doi:10.36105/mye.2026v37n4.01
Metadata
- Authors
- 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., Jaenisch, R., Zhang, F., & Sharp, P. A.
- Affiliations
- Koch Institute for Integrative Cancer Research At MIT (US)
- Broad Institute (US)
- Massachusetts Institute of Technology (US)
- Whitehead Institute for Biomedical Research (US)
- Corresponding author
- Zhang, Feng
- Sharp, Phillip A
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2014-04-20
- Volume
- 32
- Issue
- 7
- Pages
- 670-676
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC4145672
- OpenAlex
- W1506494596
- Cited by
- 944
- References
- 47
- Citations by year
- 2026: 26 · 2025: 42 · 2024: 56 · 2023: 61 · 2022: 73 · 2021: 63 · 2020: 75 · 2019: 80 · 2018: 81 · 2017: 97 · 2016: 123 · 2015: 111 · 2014: 54
- FWCI
- 52.65
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- eScholarship (California Digital Library) (submittedVersion)
- PMC
- Funders
- Howard Hughes Medical Institute
- National Institute of Mental Health (DP1MH100706)
- National Cancer Institute (R01CA133404, P01CA042063, P30CA014051, P30-CA-14051, P01 CA 42063)
- National Institute of General Medical Sciences (R01GM034277, R01 GM34277, R37GM034277, T32GM007287)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK097768)
- National Center for Chronic Disease Prevention and Health Promotion (1DP1-MH100706)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R37HD045022)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- Cas9, CRISPR/Cas9, dCas9, genome-wide binding sites, single guide RNA, Streptococcus pyogenes, mouse embryonic stem cells, off-target binding, seed sequence, protospacer adjacent motif, chromatin accessibility, DNA cleavage, target specificity
- MeSH terms
- Animals, Base Sequence, Binding Sites, Cells, Cultured, Deoxyribonuclease I, DNA-Binding Proteins, Models, Genetic, Molecular Sequence Data, Protein Binding, Genome, Mice, Embryonic Stem Cells, CRISPR-Cas Systems
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
