ArticleNucleic acids research2021
Deploying MMEJ using MENdel in precision gene editing applications for gene therapy and functional genomics.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Improvement of chicken genome editing efficiency in vitro using ribonucleoprotein-mediated CRISPR/Cas9 delivery.Journal of animal science and biotechnology · 2026Article
- Leveraging DNA repair mechanisms in genetically engineered biocontrol.Current opinion in insect science · 2026Review
- Novel allogeneic CAR T-cell platform involving microhomology-mediated end joining repair and low off-targeting potential.Molecular therapy. Nucleic acids · 2025Article
- Mammalian synthetic gene circuits for biopharmaceutical development & manufacture.NPJ systems biology and applications · 2025Review
- The editable landscape of the yeast genome reveals hotspots of structural variant formation.Science advances · 2025Article
- Extrachromosomal circular DNA drives dynamic genome plasticity: emerging roles in disease progression and clinical potential.Theranostics · 2025Review
- A long journey towards genome editing technologies in plants: a technical and critical review of genome editing technologies.Frontiers in genome editing · 2025Review
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- Application of an F0-based genetic assay in adult zebrafish to identify modifier genes of an inherited cardiomyopathy.Disease models & mechanisms · 2023Article
- Targeting DNA repair pathways with B02 and Nocodazole small molecules to improve CRIS-PITCh mediated cassette integration in CHO-K1 cells.Scientific reports · 2023Article
- ACE2 knockout hinders SARS-CoV-2 propagation in iPS cell-derived airway and alveolar epithelial cells.Frontiers in cell and developmental biology · 2023Article
- CRISPR-Cas-Based Engineering of Probiotics.Biodesign research · 2023Review
- Characterization of sequence contexts that favor alternative end joining at Cas9-induced double-strand breaks.Nucleic acids research · 2022Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Gene-editing experiments commonly elicit the error-prone non-homologous end joining for DNA double-strand break (DSB) repair. Microhomology-mediated end joining (MMEJ) can generate more predictable outcomes for functional genomic and somatic therapeutic applications. We compared three DSB repair prediction algorithms - MENTHU, inDelphi, and Lindel - in identifying MMEJ-repaired, homogeneous genotypes (PreMAs) in an independent dataset of 5,885 distinct Cas9-mediated mouse embryonic stem cell DSB repair events. MENTHU correctly identified 46% of all PreMAs available, a ∼2- and ∼60-fold sensitivity increase compared to inDelphi and Lindel, respectively. In contrast, only Lindel correctly predicted predominant single-base insertions. We report the new algorithm MENdel, a combination of MENTHU and Lindel, that achieves the most predictive coverage of homogeneous out-of-frame mutations in this large dataset. We then estimated the frequency of Cas9-targetable homogeneous frameshift-inducing DSBs in vertebrate coding regions for gene discovery using MENdel. 47 out of 54 genes (87%) contained at least one early frameshift-inducing DSB and 49 out of 54 (91%) did so when also considering Cas12a-mediated deletions. We suggest that the use of MENdel helps researchers use MMEJ at scale for reverse genetics screenings and with sufficient intra-gene density rates to be viable for nearly all loss-of-function based gene editing therapeutic applications.
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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.