RNA virus interference via CRISPR/Cas13a system in plants
Open accessPublished version of a preprint
Abstract
BACKGROUND: CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants. RESULTS: CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana. CRISPR RNA (crRNAs) targeting the HC-Pro and GFP sequences exhibit better interference than those targeting other regions such as coat protein (CP) sequence. Cas13a can also process pre-crRNAs into functional crRNAs. CONCLUSIONS: Our data indicate that CRISPR/Cas13a can be used for engineering interference against RNA viruses, providing a potential novel mechanism for RNA-guided immunity against RNA viruses and for other RNA manipulations in plants.
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
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?
New systems such as Cas12, Cas13a, and Cas13b are in the pipeline.
“CRISPR/Cas9 is the most widely used system, but new systems such as Cas12, Cas13a, and Cas13b are in the pipeline (Smargon et al., 2017;Zaidi et al., 2017;Aman et al., 2018).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Aman et al., 2018
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Jones, J. D. G., & Dangl, J. L. (2006) · Nature · doi:10.1038/nature05286 · Cited by 13,177 · see citing works
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 6,304 · see citing works
Repurposing 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 1× · see citing works
“However, like dCas9, dCas13a retains its ability to bind specifically to the target RNA and therefore can function as an RNA-guided RNA-binding protein [11, 14].”
BackgroundCpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Zetsche, B., Gootenberg, J. S., Abudayyeh, O. O., Slaymaker, I. M., Makarova, K. S., Essletzbichler, P., Volz, S. E., Joung, J., John van der, O. O. S. T., Regev, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.038 · Cited by 4,750 · see citing works
Nucleic acid detection with CRISPR-Cas13a/C2c2
Gootenberg, J. S., Abudayyeh, O. O., Lee, J. W., Essletzbichler, P., Dy, A. J., Joung, J., Verdine, V. K., Donghia, N. M., Daringer, N. M., Freije, C. A., et al. (2017) · Science · doi:10.1126/science.aam9321 · Cited by 3,887 · see citing works
Evolution and classification of the CRISPR–Cas systems
Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J. J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F. J. M., Wolf, Y. I., Yakunin, A. F., et al. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2577 · Cited by 2,512 · see citing works
An updated evolutionary classification of CRISPR–Cas systems
Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., et al. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3569 · Cited by 2,504 · see citing works
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
Abudayyeh, O. O., Gootenberg, J. S., Konermann, S., Joung, J., Slaymaker, I. M., Cox, D. B. T., Shmakov, S., Makarova, K. S., Semenova, E., Станиславович, М. Л., et al. (2016) · Science · doi:10.1126/science.aaf5573 · Cited by 2,328 · see citing works
RNA targeting with CRISPR–Cas13
Abudayyeh, O. O., Gootenberg, J. S., Essletzbichler, P., Han, S., Joung, J., Belanto, J. J., Verdine, V., Cox, D. B. T., Kellner, M. J., Regev, A., et al. (2017) · Nature · doi:10.1038/nature24049 · Cited by 2,093 · see citing works
RNA-guided genetic silencing systems in bacteria and archaea
Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012) · Nature · doi:10.1038/nature10886 · Cited by 1,851 · see citing works
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
Shmakov, S., Abudayyeh, O. O., Makarova, K. S., Wolf, Y. I., Gootenberg, J. S., Semenova, E., Станиславович, М. Л., Joung, J., Konermann, S., Severinov, K., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.008 · Cited by 1,221 · see citing works
Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection
East-Seletsky, A., O’Connell, M. R., Knight, S. C., Burstein, D. E., Cate, J. H. D., Tjian, R., & Doudna, J. A. (2016) · Nature · doi:10.1038/nature19802 · Cited by 1,180 · see citing works
Diversity and evolution of class 2 CRISPR–Cas systems
Shmakov, S., Smargon, A. A., Scott, D. A., Cox, D. B. T., Pyzocha, N., Yan, W. X., Abudayyeh, O. O., Gootenberg, J. S., Makarova, K. S., Wolf, Y. I., et al. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.184 · Cited by 1,056 · see citing works
Understanding the Functions of Plant Disease Resistance Proteins
Martin, G. B., Bogdanove, A. J., & Sessa, G. (2003) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.54.031902.135035 · Cited by 915 · see citing works
CRISPR-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 907 · see citing works
Induction and suppression of RNA silencing: insights from viral infections
Voinnet, O. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1555 · Cited by 836 · see citing works
Unravelling the structural and mechanistic basis of CRISPR–Cas systems
John van der, O. O. S. T., Westra, E. R., Jackson, R. N., & Wiedenheft, B. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3279 · Cited by 715 · see citing works
RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence
Pumplin, N., & Voinnet, O. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3120 · Cited by 644 · see citing works
Smargon, A. A., Cox, D. B. T., Pyzocha, N. K., Zheng, K., Slaymaker, I. M., Gootenberg, J. S., Abudayyeh, O. A., Essletzbichler, P., Shmakov, S., Makarova, K. S., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2016.12.023 · Cited by 575 · see citing works
CRISPR/Cas9-mediated viral interference in plants
Ali, Z., Abulfaraj, A. A., Idris, A. M., Ali, S., Tashkandi, M., & Mahfouz, M. M. (2015) · Genome biology · doi:10.1186/s13059-015-0799-6 · Cited by 507 · see citing works
Self-citationThe Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a
Liu, L., Li, X., Ma, J., Li, Z., You, L., Wang, J., Wang, M., Zhang, X., & Wang, Y. (2017) · Cell · doi:10.1016/j.cell.2017.06.050 · Cited by 506 · see citing works
Genetics of Plant Virus Resistance
Kang, B., Yeam, I., & Jahn, M. (2005) · Annual Review of Phytopathology · doi:10.1146/annurev.phyto.43.011205.141140 · Cited by 502 · see citing works
Coat Protein-Mediated Resistance Against Virus Infection
Beachy, R. N., Loesch-Fries, S., & Tumer, N. E. (1990) · Annual Review of Phytopathology · doi:10.1146/annurev.py.28.090190.002315 · Cited by 444 · see citing works
Mechanisms of Pathogen-Derived Resistance to Viruses in Transgenic Plants.
Baulcombe, D. C. (1996) · The Plant Cell · doi:10.1105/tpc.8.10.1833 · Cited by 429 · see citing works
Crop immunity against viruses: outcomes and future challenges
Nicaise, V. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00660 · Cited by 386 · see citing works
Efficient Virus-Mediated Genome Editing in Plants Using the CRISPR/Cas9 System
Ali, Z., Abulfaraj, A. A., Li, L., Ghosh, N., Piatek, M. J., Mahjoub, A., Aouida, M., Piatek, A., Baltes, N. J., Voytas, D. F., et al. (2015) · Molecular Plant · doi:10.1016/j.molp.2015.02.011 · Cited by 368 · see citing works
Self-citationMechanisms of plant resistance to viruses
Soosaar, J. L. M., Burch‐Smith, T. M., & Dinesh‐Kumar, S. P. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1239 · Cited by 350 · see citing works
Potyviruses and the Digital Revolution
Gibbs, A. J., & Ohshima, K. (2010) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-073009-114404 · Cited by 290 · see citing works
Anantharaman, V., Makarova, K. S., Burroughs, A. M., Koonin, E. V., & Aravind, L. (2013) · Biology Direct · doi:10.1186/1745-6150-8-15 · Cited by 263 · see citing works
Molecular Ecology and Emergence of Tropical Plant Viruses
Fargette, D., Konaté, G., Fauquet, C., et al. (2006) · Annual Review of Phytopathology · doi:10.1146/annurev.phyto.44.120705.104644 · Cited by 219 · see citing works
Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity
Jiang, W., Samai, P., & Marraffini, L. A. (2016) · Cell · doi:10.1016/j.cell.2015.12.053 · Cited by 198 · see citing works
RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding
Younis, A., Siddique, M. I., Kim, C.-K., & Lim, K. (2014) · International Journal of Biological Sciences · doi:10.7150/ijbs.10452 · Cited by 190 · see citing works
Optimized cDNA libraries for virus-induced gene silencing (VIGS) using tobacco rattle virus
Liu, E., & Page, J. E. (2008) · Plant Methods · doi:10.1186/1746-4811-4-5 · Cited by 150 · see citing works
Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation
Mahas, A., Stewart, C. N., & Mahfouz, M. M. (2017) · Biotechnology Advances · doi:10.1016/j.biotechadv.2017.11.008 · Cited by 121 · see citing works
Self-citationAntiviral strategies in plants based on RNA silencing
Simón‐Mateo, C., & Garcı́a, J. A. (2011) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2011.05.011 · Cited by 113 · see citing works
DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes
Plagens, A., Richter, H., Charpentier, E., & Randau, L. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuv019 · Cited by 110 · see citing works
Improving crop disease resistance: lessons from research on Arabidopsis and tomato
Piquerez, S. J. M., Harvey, S. E., Beynon, J., & Ntoukakis, V. E. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00671 · Cited by 99 · see citing works
Boosting plant immunity with CRISPR/Cas
Chaparro‐Garcia, A., Kamoun, S., & Nekrasov, V. (2015) · Genome biology · doi:10.1186/s13059-015-0829-4 · Cited by 68 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Hafemeister, C., & Satija, R. (2019) · Genome Biology · doi:10.1186/s13059-019-1874-1 · Cited by 4,479 · see citing works
CRISPR-Cas guides the future of genetic engineering
Knott, G. J., & Doudna, J. A. (2018) · Science · doi:10.1126/science.aat5011 · Cited by 1,410 · see citing works
Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation
Brunner, A., Thielert, M., Vasilopoulou, C., Ammar, C., Coscia, F., Mund, A., Hoerning, O. B., Bache, N., Apalategui, A., Lubeck, M., et al. (2022) · Molecular Systems Biology · doi:10.15252/msb.202110798 · Cited by 544 · see citing works
CRISPR/Cas system: recent advances and future prospects for genome editing
Manghwar, H., Lindsey, K., Zhang, X., & Jin, S. (2019) · Trends in Plant Science · doi:10.1016/j.tplants.2019.09.006 · Cited by 529 · see citing works
Novel antigen-presenting cell imparts Treg-dependent tolerance to gut microbiota
Akagbosu, B., Tayyebi, Z., Shibu, G., Paucar Iza, Y. A., Deep, D., Parisotto, Y. F., Fisher, L., Pasolli, H. A., Thevin, V., Elmentaite, R., et al. (2022) · Nature · doi:10.1038/s41586-022-05309-5 · Cited by 273 · see citing works
Clapp, J., & Ruder, S.-L. (2020) · Global Environmental Politics · doi:10.1162/glep_a_00566 · Cited by 251 · see citing works
High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effects
Tong, H., Huang, J., Xiao, Q., He, B., Dong, X., Liu, Y., Yang, X., Han, D., Wang, Z., Wang, X., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01419-7 · Cited by 230 · see citing works
BiT age: A transcriptome‐based aging clock near the theoretical limit of accuracy
Meyer, D. H., & Schumacher, B. (2021) · Aging Cell · doi:10.1111/acel.13320 · Cited by 165 · see citing works
DNA language models are powerful predictors of genome-wide variant effects
Benegas, G., Batra, S. S., & Song, Y. S. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2311219120 · Cited by 157 · see citing works
Detection of Deleterious On-Target Effects after HDR-Mediated CRISPR Editing
Weisheit, I., Kroeger, J. A., Malik, R., Klimmt, J., Crusius, D., Dannert, A., Dichgans, M., & Paquet, D. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107689 · Cited by 125 · see citing works
RNA-Targeting CRISPR-Cas systems and their applications
Burmistrz, M., Krakowski, K., & Krawczyk-Balska, A. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21031122 · Cited by 125 · see citing works
A panoramic view of cell population dynamics in mammalian aging
Zhang, Z., Schaefer, C., Jiang, W., Lu, Z., Lee, J., Sziraki, A., Abdulraouf, A., Wick, B., Haeussler, M., Li, Z., et al. (2025) · Science · doi:10.1126/science.adn3949 · Cited by 95 · see citing works
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq
Wessels, H.-H., Méndez-Mancilla, A., Hao, Y., Papalexi, E., Mauck, W. M., Lu, L., Morris, J. A., Mimitou, E. P., Smibert, P., Sanjana, N. E., et al. (2023) · Nature Methods · doi:10.1038/s41592-022-01705-x · Cited by 79 · see citing works
Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis
Mantri, M., Hinchman, M. M., McKellar, D. W., Wang, M. F. Z., Cross, S. T., Parker, J. S. L., & De Vlaminck, I. (2022) · Nature Cardiovascular Research · doi:10.1038/s44161-022-00138-1 · Cited by 74 · see citing works
Evaluating the Utilities of Foundation Models in Single-cell Data Analysis
Liu, T., Li, K., Wang, Y., Li, H., & Zhao, H. (2023) · doi:10.1101/2023.09.08.555192 · Cited by 62 · see citing works
CRISPR/Cas systems: opportunities and challenges for crop breeding
Biswas, S., Zhang, D., & Shi, J. (2021) · Plant Cell Reports · doi:10.1007/s00299-021-02708-2 · Cited by 58 · see citing works
Viñas Torné, R., Wiatrak, M., Piran, Z., Fan, S., Jiang, L., Teichmann, S. A., Nitzan, M., & Brbić, M. (2026) · Nature Biotechnology · doi:10.1038/s41587-025-02777-8 · Cited by 58 · see citing works
Concerns regarding ‘off-target’activity of genome editing endonucleases
Kadam, U. S., Shelake, R. M., Chavhan, R. L., & Suprasanna, P. (2018) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2018.03.027 · Cited by 47 · see citing works
Ma, C., Chitra, U., Zhang, S., & Raphael, B. J. (2022) · Cell Systems · doi:10.1016/j.cels.2022.09.002 · Cited by 27 · see citing works
scELMo: Embeddings from Language Models are Good Learners for Single-cell Data Analysis
Liu, T., Chen, T., Zheng, W., Luo, X., Chen, Y., & Zhao, H. (2023) · doi:10.1101/2023.12.07.569910 · Cited by 30 · see citing works
Yaish, O., Asif, M., & Orenstein, Y. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac157 · Cited by 19 · see citing works
Karunarathne, S., Walker, E., Sharma, D., Li, C., & Han, Y. (2023) · Journal of Zhejiang University-SCIENCE B · doi:10.1631/jzus.b2200552 · Cited by 18 · see citing works
“CRISPR/Cas9 is the most widely used system, but new systems such as Cas12, Cas13a, and Cas13b are in the pipeline (Smargon et al., 2017; Zaidi et al., 2017; Aman et al., 2018).”
CRISPR/cas-mediated genome editing in sorghum — recent progress, challenges and prospects
Parikh, A., Brant, E. J., Baloglu, M. C., & Altpeter, F. (2021) · In Vitro Cellular & Developmental Biology - Plant · doi:10.1007/s11627-021-10215-y · Cited by 18 · see citing works
MultiCPA: Multimodal Compositional Perturbation Autoencoder
Inecik, K., Uhlmann, A., Lotfollahi, M., & Theis, F. (2022) · doi:10.1101/2022.07.08.499049 · Cited by 16 · see citing works
Measuring expression heterogeneity of single-cell cytoskeletal protein complexes
Vlassakis, J., Hansen, L. L., Higuchi-Sanabria, R., Zhou, Y., Tsui, C. K., Dillin, A., Huang, H., & Herr, A. E. (2020) · doi:10.1101/2020.09.12.294801 · Cited by 16 · see citing works
Zinati, Y., Takiddeen, A., & Emad, A. (2023) · doi:10.1101/2023.07.25.550225 · Cited by 36 · see citing works
- Authors
- Aman, R., Ali, Z., Butt, H., Mahas, A., Aljedaani, F., Khan, M. Z., Ding, S., & Mahfouz, M.
- Affiliations
- King Abdullah University of Science and Technology (SA)
- Corresponding author
- Mahfouz, Magdy
- ORCID
- Venue
- Genome Biology
- Published
- 2018-01-04
- Volume
- 19
- Issue
- 1
- Pages
- 1-1
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC5755456
- OpenAlex
- W2765284830
- Cited by
- 1,497
- References
- 38
- Citations by year
- 2026: 126 · 2025: 271 · 2024: 244 · 2023: 220 · 2022: 238 · 2021: 187 · 2020: 117 · 2019: 73 · 2018: 21
- FWCI
- 35.21
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) (submittedVersion, cc-by)
- Funders
- King Abdullah University of Science and Technology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Virus Research Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Transgenic Plants and Applications
- Keywords
- CRISPR-Cas13a, turnip mosaic virus, plant antiviral immunity, HC-Pro, Nicotiana benthamiana
- MeSH terms
- Genetic Engineering, Ribonucleases, RNA, Nicotiana, Potyvirus, RNA Interference, Green Fluorescent Proteins, CRISPR-Cas Systems, CRISPR-Associated Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
