ArticlePloS one2017
Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 37 citations in OpenAlex.
- MEIOSIN retains a STRA8-independent activity that contributes to meiotic gene activation across vertebrates.Genes & development · 2026Article
- An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.Bioinformatics (Oxford, England) · 2026Article
- PCdb: A comprehensive plant genome-editing database integrating sgRNA efficiency, off-target predictions, and epigenomic landscapes.Plant communications · 2026Article
- Establishment of a zebrafish inbred strain, M-AB, capable of regular breeding and genetic manipulation.Scientific reports · 2024Article
- Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering.Nucleic acids research · 2023Article
- Trichostatin A for Efficient CRISPR-Cas9 Gene Editing of Human Pluripotent Stem Cells.The CRISPR journal · 2023Article
- Article
- Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity.BMC genomics · 2022Article
- A Machine Learning Approach to Identify the Importance of Novel Features for CRISPR/Cas9 Activity Prediction.Biomolecules · 2022Article
- SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish.Nature communications · 2022Article
- Wuschel2 enables highly efficient CRISPR/Cas-targeted genome editing during rapid de novo shoot regeneration in sorghum.Communications biology · 2022Article
- Sycp1 Is Not Required for Subtelomeric DNA Double-Strand Breaks but Is Required for Homologous Alignment in Zebrafish Spermatocytes.Frontiers in cell and developmental biology · 2021Article
- Site-directed targeting of transcriptional activation-associated proteins to repressed chromatin restores CRISPR activity.APL bioengineering · 2020Article
- Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish.Epigenetics & chromatin · 2020Article
- Sycp2 is essential for synaptonemal complex assembly, early meiotic recombination and homologous pairing in zebrafish spermatocytes.PLoS genetics · 2020Article
- Computational Analysis Concerning the Impact of DNA Accessibility on CRISPR-Cas9 Cleavage Efficiency.Molecular therapy : the journal of the American Society of Gene Therapy · 2020Article
- Genome Editing Fidelity in the Context of DNA Sequence and Chromatin Structure.Frontiers in cell and developmental biology · 2020Review
- LION: a simple and rapid method to achieve CRISPR gene editing.Cellular and molecular life sciences : CMLS · 2019Article
- Evaluation of the effects of sequence length and microsatellite instability on single-guide RNA activity and specificity.International journal of biological sciences · 2019Article
- Ionizing radiation induces transgenerational effects of DNA methylation in zebrafish.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gRNAs is especially important for zebrafish mutant construction. Besides the sequence features, local chromatin structures may have effects on CRISPR/Cas9 efficiency, which remain largely unexplored. In the only related study in zebrafish, nucleosome organization was not found to have an effect on CRISPR/Cas9 efficiency, which is inconsistent with recent studies in vitro and in mammalian cell lines. To understand the effects of local chromatin structure on CRISPR/Cas9 efficiency in zebrafish, we first determined that CRISPR/Cas9 introduced genome editing mainly before the dome stage. Based on this observation, we reanalyzed our published nucleosome organization profiles and generated chromatin accessibility profiles in the 256-cell and dome stages using ATAC-seq technology. Our study demonstrated that chromatin accessibility showed positive correlation with CRISPR/Cas9 efficiency, but we did not observe a clear correlation between nucleosome organization and CRISPR/Cas9 efficiency. We constructed an online database for zebrafish gRNA selection based on local chromatin structure features that could prove beneficial to zebrafish homozygous mutant construction via CRISPR/Cas9.
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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.