ArticleMolecular therapy : the journal of the American Society of Gene Therapy2020
Computational Analysis Concerning the Impact of DNA Accessibility on CRISPR-Cas9 Cleavage Efficiency.
Article in Molecular therapy : the journal of the American Society of Gene Therapy, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Efficient Endogenous Tagging in the Sea Urchin,bioRxiv : the preprint server for biology · 2026Article
- CRISPR/Cas9-Based Genome Editing: Understanding Differences in DNA Repair Pathways, Profiles, and Outcomes.International journal of molecular sciences · 2026Review
- Overcoming breeding barriers with genome editing in autopolyploid crops.BMC plant biology · 2026Review
- Article
- Breaking into HIV-1's Epigenetic Vault: Cure Strategies to Eliminate the Viral Reservoir.Viruses · 2026Review
- Extracellular vesicle-mediated delivery of CRISPR machinery silences androgen receptor in castration-resistant prostate cancer cells.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Multiplex CRISPR/Cas9 Editing of Rice Prolamin and GluA Glutelin Genes Reveals Subfamily-Specific Effects on Seed Protein Composition.Plants (Basel, Switzerland) · 2025Article
- A toolkit for facilitating markerless integration of expression cassettes in Komagataella phaffii via CRISPR/Cas9.Microbial cell factories · 2025Article
- Harnessing haploid-inducer mediated genome editing for accelerated maize variety development.Plant biotechnology journal · 2025Article
- Rescue of the disease-associated phenotype in CRISPR-corrected hiPSCs as a therapeutic approach for inherited retinal dystrophies.Molecular therapy. Nucleic acids · 2025Article
- Impact of chromatin on HIV-1 latency: a multi-dimensional perspective.Epigenetics & chromatin · 2025Review
- Targeted sequencing ofmSystems · 2025Article
- CATS: a bioinformatic tool for automated Cas9 nucleases activity comparison in clinically relevant contexts.Frontiers in genome editing · 2025Article
- Article
- Genetic confounds of transgenerational epigenetic inheritance in mice.Epigenetics · 2024Article
- Usefulness of current sgRNA design guidelines and in vitro cleavage assays for plant CRISPR/Cas genome editing: a case targeting the polyphenol oxidase gene family in eggplant (Solanum melongena L.).Transgenic research · 2023Article
- An optimized SpCas9 high-fidelity variant for direct protein delivery.Molecular therapy : the journal of the American Society of Gene Therapy · 2023Article
- Immunomodulatory Effects of Non-Thermal Plasma in a Model for Latent HIV-1 Infection: Implications for an HIV-1-Specific Immunotherapy.Biomedicines · 2023Article
- Assessment of anti-HIV-1 guide RNA efficacy in cells containing the viral target sequence, corresponding gRNA, and CRISPR/Cas9.Frontiers in genome editing · 2023Article
- How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances.Pharmaceutics · 2022Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Defining the variables that impact the specificity of CRISPR/Cas9 has been a major research focus. Whereas sequence complementarity between guide RNA and target DNA substantially dictates cleavage efficiency, DNA accessibility of the targeted loci has also been hypothesized to be an important factor. In this study, functional data from two genome-wide assays, genome-wide, unbiased identification of DSBs enabled by sequencing (GUIDE-seq) and circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq), have been computationally analyzed in conjunction with DNA accessibility determined via DNase I-hypersensitive sequencing from the Encyclopedia of DNA Elements (ENCODE) Database and transcriptome from the Sequence Read Archive to determine whether cellular factors influence CRISPR-induced cleavage efficiency. CIRCLE-seq and GUIDE-seq datasets were selected to represent the absence and presence of cellular factors, respectively. Data analysis revealed that correlations between sequence similarity and CRISPR-induced cleavage frequency were altered by the presence of cellular factors that modulated the level of DNA accessibility. The above-mentioned correlation was abolished when cleavage sites were located in less accessible regions. Furthermore, CRISPR-mediated edits were permissive even at regions that were insufficient for most endogenous genes to be expressed. These results provide a strong basis to dissect the contribution of local chromatin modulation markers on CRISPR-induced cleavage efficiency.
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