ArticleNature protocols2021
Identifying genome-wide off-target sites of CRISPR RNA-guided nucleases and deaminases with Digenome-seq.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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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.
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Who cites it
29 citing papers in PubMed, 35 citations in OpenAlex.
- Digenome-Detect: Accurate, statistics-based analysis software for identifying off-target cleavage sites in genome editing.Molecular therapy. Advances · 2026Article
- Engineered Transformer Base Editor with Enhanced Editing Efficiency.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Treatment of Huntington's disease with a pan-HTT-targeting CRISPR nuclease.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- CRISPR-Cas9-based therapies for Huntington's disease and Friedreich's ataxia: mechanisms, advances, and future perspectives.Neurogenetics · 2026Review
- The evolution of AI-integrated genome editing and its challenges.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Review
- Article
- Structure-Guided Engineering of a Cas12i Nuclease Unlocks Near-PAMless Genome Editing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A Stable and Rapid Protoplast-Based CRISPR/Cas9-Ribonucleoprotein Complex Screening System for Octoploid Strawberry (Plants (Basel, Switzerland) · 2026Article
- Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity using CHANGE-seq-BE.Nature biotechnology · 2026Article
- Treatment of Huntington's disease with a pan-HTT-targeting CRISPR nuclease.bioRxiv : the preprint server for biology · 2025Article
- Design principle of successful genome editing applications using CRISPR-based toolkits.Journal of applied genetics · 2025Review
- Unveiling the cut-and-repair cycle of designer nucleases in human stem and T cells via CLEAR-time dPCR.Nature communications · 2025Article
- The multiple layers of RNA response in double-strand break repair.Experimental & molecular medicine · 2025Review
- Variant-aware Cas-OFFinder: web-based in silico variant-aware potential off-target site identification for genome editing applications.Nucleic acids research · 2025Article
- Predicting CRISPR-Cas9 off-target effects in human primary cells using bidirectional LSTM with BERT embedding.Bioinformatics advances · 2025Article
- CRISPR technology in human diseases.MedComm · 2024Review
- PAM-flexible Engineered FnCas9 variants for robust and ultra-precise genome editing and diagnostics.Nature communications · 2024Article
- CRISPR-Cas and CRISPR-based screening system for precise gene editing and targeted cancer therapy.Journal of translational medicine · 2024Review
- CRISPR in Targeted Therapy and Adoptive T Cell Immunotherapy for Hepatocellular Carcinoma.Journal of hepatocellular carcinoma · 2024Review
- Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Digested genome sequencing (Digenome-seq) is a highly sensitive, easy-to-carry-out, cell-free method for experimentally identifying genome-wide off-target sites of programmable nucleases and deaminases (also known as base editors). Genomic DNA is digested in vitro using clustered regularly interspaced short palindromic repeats ribonucleoproteins (RNPs; plus DNA-modifying enzymes to cleave both strands of DNA at sites containing deaminated base products, in the case of base editors) and subjected to whole-genome sequencing (WGS) with a typical sequencing depth of 30×. A web-based program is available to map in vitro cleavage sites corresponding to on- and off-target sites. Chromatin DNA, in parallel with histone-free genomic DNA, can also be used to account for the effects of chromatin structure on off-target nuclease activity. Digenome-seq is more sensitive and comprehensive than cell-based methods for identifying off-target sites. Unlike other cell-free methods, Digenome-seq does not involve enrichment of DNA ends through PCR amplification. The entire process other than WGS, which takes ~1-2 weeks, including purification and preparation of RNPs, digestion of genomic DNA and bioinformatic analysis after WGS, takes about several weeks.
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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.