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Using Sniper-Cas9 to Minimize Off-target Effects of CRISPR-Cas9 Without the Loss of On-target Activity Via Directed Evolution
Published on: February 26, 2019
Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
Josh Tycko1, Michael Wainberg2, Georgi K Marinov1
1Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
Pooled CRISPR screens can identify essential regulatory elements, but off-target effects are a concern. GuideScan specificity scores effectively filter confounding guide RNAs, enabling accurate identification of regulatory elements.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Pooled CRISPR screens are vital for characterizing non-coding regulatory elements.
- Off-target effects of CRISPR tools (Cas9, dCas9, CRISPRi/a) in these screens are not well understood.
- Accurate functional genomics relies on minimizing confounding experimental variables.
Purpose of the Study:
- To systematically evaluate off-target activity of Cas9, dCas9, and CRISPRi/a in pooled screens.
- To identify reliable predictors of sgRNA specificity and confounding effects.
- To develop strategies for filtering libraries to improve the accuracy of regulatory element identification.
Main Methods:
- Genome-scale CRISPR screens were performed in K562 cells to identify essential CTCF loop anchors.
- Analysis of single-guide RNA (sgRNA) effects, focusing on on-target versus off-target activities.
- Utilized the GuideScan specificity score to predict sgRNA performance.
- Conducted parallel screens using CRISPR interference/activation (CRISPRi/a) to assess epigenome editing off-targets.
Main Results:
- sgRNAs with the largest effects in screens were primarily driven by off-target activity, not on-target disruption.
- Off-target activity, while weakly correlated with off-target site number, was predictable using GuideScan scores.
- CRISPRi/a screens revealed distinct off-target effects that confound fitness readouts.
- Filtering CRISPRi libraries with GuideScan specificity scores successfully removed confounding sgRNAs.
Conclusions:
- Off-target effects significantly impact pooled CRISPR screens for regulatory elements.
- GuideScan specificity scores are valuable for predicting and mitigating sgRNA off-target activity.
- Filtering CRISPR libraries based on specificity scores enhances the reliable identification of essential regulatory elements.
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