Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation
QB3 · Howard Hughes Medical Institute · +4 more institutions
Abstract
We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA (Horlbeck et al., 2016). Here, we build on this observation with a comprehensive algorithm that incorporates chromatin, position, and sequence features to accurately predict highly effective single guide RNAs (sgRNAs) for targeting nuclease-dead Cas9-mediated transcriptional repression (CRISPRi) and activation (CRISPRa). We use this algorithm to design next-generation genome-scale CRISPRi and CRISPRa libraries targeting human and mouse genomes. A CRISPRi screen for essential genes in K562 cells demonstrates that the large majority of sgRNAs are highly active. We also find CRISPRi does not exhibit any detectable non-specific toxicity…
Citation impact
- FWCI
- 32.55
- Percentile
- 100%
- References
- 62
Authors
11- MAMax A. HorlbeckCorresponding
QB3, Howard Hughes Medical Institute, University of California, San Francisco
- LALuke A. Gilbert
QB3, Howard Hughes Medical Institute, University of California, San Francisco
- JEJacqueline E. Villalta
QB3, Howard Hughes Medical Institute, University of California, San Francisco
- BABritt Adamson
QB3, Howard Hughes Medical Institute, University of California, San Francisco
- RARyan A. Pak
University of California, San Francisco, Innovative Genomics Institute, University of California, Berkeley
Topics & keywords
- CRISPR
- Cas9
- Guide RNA
- Biology
- Computational biology
- Subgenomic mRNA
- Chromatin
- Genome engineering
Funding
- HHHoward Hughes Medical Institute
- LALeukemia and Lymphoma Society
- LKLi Ka Shing Foundation
- NINational Institutes of HealthAwards: P50 GM102706, U01 CA168370, R01 DA036858
- NCNational Cancer InstituteAward: Pathway to Independence Award, K99 CA204602
- NINational Institute of General Medical SciencesAward: DP2 GM119139