ArticleNature communications2022
Accounting for small variations in the tracrRNA sequence improves sgRNA activity predictions for CRISPR screening.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- CRISPR-HAWK: haplotype- and variant-aware guide design toolkit for CRISPR-Cas.Bioinformatics (Oxford, England) · 2026Article
- Mechanistic machine learning for prediction of prime editing outcomes.Nature biotechnology · 2026Article
- Using CRISPR/Cas9 to investigate the role of candidate human disease gene orthologs in Ciona.bioRxiv : the preprint server for biology · 2026Article
- Balancing off-target and on-target considerations for optimized CRISPR-Cas9 knockout library design.Cell genomics · 2026Article
- BEstimate: a computational tool for the design and interpretation of CRISPR base editing experiments.Genome biology · 2026Article
- Using ngTALEN to improve genome editing efficiency on targets containing 5-methylcytosines.The Plant journal : for cell and molecular biology · 2026Article
- Validated CRISPR/Cas9 guide RNAs targeting neurodevelopmental genes in the tunicatebioRxiv : the preprint server for biology · 2026Article
- The B cell receptor-mTOR signaling axis restricts the accumulation of lung tissue-resident memory B cells after influenza infection.Science immunology · 2026Article
- Mechanistic machine learning enables interpretable and generalizable prediction of prime editing outcomes.bioRxiv : the preprint server for biology · 2026Article
- ViableFrontiers in immunology · 2026Article
- Empirical optimization of dual-sgRNA design for in vivo CRISPR/Cas9-mediated exon deletion in mice.Computational and structural biotechnology journal · 2026Article
- Application of CRISPR-Based Epigenome Editing Tools for Engineering Programmable Embryo Models.Methods in molecular biology (Clifton, N.J.) · 2026Article
- CRISPR-HAWK: Haplotype- and Variant-aware guide design toolkit for CRISPR-Cas.bioRxiv : the preprint server for biology · 2025Article
- Defining the Antitumor Mechanism of Action of a Clinical-stage Compound as a Selective Degrader of the Nuclear Pore Complex.Cancer discovery · 2025Article
- A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording.Nature biotechnology · 2025Article
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Higher resolution pooled genome-wide CRISPR knockout screening in Drosophila cells using integration and anti-CRISPR (IntAC).Nature communications · 2025Article
- CRISPR-BEasy: a free web-based service for designing sgRNA tiling libraries for CRISPR-dependent base editing screens.Nucleic acids research · 2025Article
- Revolutionizing CRISPR technology with artificial intelligence.Experimental & molecular medicine · 2025Review
- CRISPRware: a software package for contextual gRNA library design.BMC genomics · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CRISPR technology is a powerful tool for studying genome function. To aid in picking sgRNAs that have maximal efficacy against a target of interest from many possible options, several groups have developed models that predict sgRNA on-target activity. Although multiple tracrRNA variants are commonly used for screening, no existing models account for this feature when nominating sgRNAs. Here we develop an on-target model, Rule Set 3, that makes optimal predictions for multiple tracrRNA variants. We validate Rule Set 3 on a new dataset of sgRNAs tiling essential and non-essential genes, demonstrating substantial improvement over prior prediction models. By analyzing the differences in sgRNA activity between tracrRNA variants, we show that Pol III transcription termination is a strong determinant of sgRNA activity. We expect these results to improve the performance of CRISPR screening and inform future research on tracrRNA engineering and sgRNA modeling.
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