ArticleGenome biology2018
A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
158 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Systematic synthesis of CRISPR/Cas applications for enhancing salt tolerance in crops: a decade of progress and challenges.BMC plant biology · 2026Pooled it
- Pooled it
- Metabolic reprogramming in plant defense: linking signaling networks to metabolomics-driven insights.Plant signaling & behavior · 2026Review
- Medicinal-plant immunity and specialized metabolism in plant-pathogen interactions: mechanisms and applications.Planta · 2026Review
- Enhanced exonuclease-Cas9 systems promote multiple nucleotide deletions with higher efficiency and broader targeting scope in plants.Journal of integrative plant biology · 2026Article
- SpacerScope: binary-vectorized, genome-wide off-target profiling for RNA-guided nucleases without prior candidate-site bias.Briefings in bioinformatics · 2026Article
- Coupling of both a transactivation module and a double-stranded DNA-binding domain boosts Cas12i3 variant-based cytosine and adenine editing in plants.Journal of integrative plant biology · 2026Article
- Enhancing CRISPR-Cas12a base editing in plants with LbCas12a variants and introns.Journal of integrative plant biology · 2026Article
- Wheat Biofortification for Enhancing Iron, Zinc, and Protein: The Role of Mutation Breeding.Plants (Basel, Switzerland) · 2026Review
- Read-mapping signatures for molecular characterization of transgenic DNA insertions in paired-end Illumina data.BMC biotechnology · 2026Article
- RiSpy: a feature selection-based fingerprinting framework for accurate identification of genome-edited rice lines.Briefings in bioinformatics · 2026Article
- Beyond CRISPR/Cas9: emerging genome editing technologies for next-generation crop improvement.Molecular biology reports · 2026Review
- Removal of Transgenes and Evaluation of Yield Penalties in Genome Edited Bacterial Blight Resistant Rice Varieties.Plant biotechnology journal · 2026Article
- Impact of wheat GRF4-GIF1 morphogenic regulators on transformation and genome editing efficiency in elite barley cultivars.Frontiers in plant science · 2026Article
- Design principle of successful genome editing applications using CRISPR-based toolkits.Journal of applied genetics · 2025Review
- Engineering and comparison of cas12a-based genome editing systems in plants.The Plant journal : for cell and molecular biology · 2025Article
- CRISPR/Cas system-mediated transgene-free or DNA-free genome editing in plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Review
- Cas9-Rep fusion tethers donor DNA in vivo and boosts the efficiency of HDR-mediated genome editing.Plant biotechnology journal · 2025Article
- Conditional knockdown of gene expression in plants via 3' UTR editing.Plant communications · 2025Article
98 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
backgroundTargeting specificity has been a barrier to applying genome editing systems in functional genomics, precise medicine and plant breeding. In plants, only limited studies have used whole-genome sequencing (WGS) to test off-target effects of Cas9. The cause of numerous discovered mutations is still controversial. Furthermore, WGS-based off-target analysis of Cpf1 (Cas12a) has not been reported in any higher organism to date.
resultsWe conduct a WGS analysis of 34 plants edited by Cas9 and 15 plants edited by Cpf1 in T0 and T1 generations along with 20 diverse control plants in rice. The sequencing depths range from 45× to 105× with read mapping rates above 96%. Our results clearly show that most mutations in edited plants are created by the tissue culture process, which causes approximately 102 to 148 single nucleotide variations (SNVs) and approximately 32 to 83 insertions/deletions (indels) per plant. Among 12 Cas9 single guide RNAs (sgRNAs) and three Cpf1 CRISPR RNAs (crRNAs) assessed by WGS, only one Cas9 sgRNA resulted in off-target mutations in T0 lines at sites predicted by computer programs. Moreover, we cannot find evidence for bona fide off-target mutations due to continued expression of Cas9 or Cpf1 with guide RNAs in T1 generation.
conclusionsOur comprehensive and rigorous analysis of WGS data across multiple sample types suggests both Cas9 and Cpf1 nucleases are very specific in generating targeted DNA modifications and off-targeting can be avoided by designing guide RNAs with high specificity.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.