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CRISPR-Cas9 for gene overexpression and down-regulation
The S. pyogenes CRISPR-Cas9 system is commonly used for gene knockout experiments. It consists of a Cas9 nuclease, responsible for creating a double-stranded break (DSB), and guide RNA (gRNA) that is responsible for targeting the nuclease to a specific region in the genome. The cells’ endogenous repair mechanisms imperfectly repair the DSB leading to gene knockout. The CRISPR-Cas9 system has also been adapted to generate technologies called CRISPRi (CRISPR interference) and CRISPRa (CRISPR activation). These utilize deactivated Cas9 nuclease (dCas9) that cannot generate a DSB (Figure 1A), so instead target genomic regions resulting in RNA-directed reversible transcriptional control. CRISPRi1,2 utilizes dCas9 with or without a KRAB effector domain that complexes with gRNA to target promoter regions for transcriptional repression, or knockdown, of the gene. CRISPRa3-8 employs dCas9 fused to different transcriptional activation domains, which can be directed to promoter regions by either standard S. pyogenes gRNA or special gRNAs that recruit additional transcriptional activation domains to upregulate expression of the gene target (Figure 1B).
Figure 1.A. CRISPRi and CRISPRa use deactivated or “dead” Cas9 (dCas9), a nuclease-deficient mutant variant of the Cas9 protein. The schematic of dCas9 shows two point mutations (D10A, H840A) that inactivate the DNA cleavage activity. B. CRISPRi and CRISPRa technologies essentially generate artificial transcription factors by attaching an effector domain to dCas9 to silence or activate transciption.
CRISPRi or CRISPRa requires sgRNA designs in proximity to the gene’s promoter region or the transcriptional start site to result in silencing or activation, respectively.4,6 Designing functional gRNAs can be challenging, as transcriptional start sites are not always well annotated or may be inaccessible due to presence of other protein factors, and cryptic or alternative promoters may be utilized. However, systematic manipulation of gene expression at genome scale utilizing pooled sgRNA screening has enabled development of design algorithms with improved gRNA functionality for CRISPRi and CRISPRa.9
Most CRISPRi and CRISPRa publications to date have used expressed single guide RNA (sgRNA) (e.g., plasmid or lentivirus). Custom S. pyogenes lentiviral sgRNAs for CRISPRi and CRISPRa systems can be ordered through the CRISPR Design Tool using rules defined in the literature.4,8 Our sgRNA vector is compatible with CRISPRi and CRISPRa systems that use simple guide RNA2,3,4,7, but not the systems that use modified effector-binding scaffold sgRNAs.6,7
Authors: Jennifer Abarca is a Technical Support Scientist, Zaklina Strezoska is a Senior Scientist, and Annaleen Vermeulen is a Senior Scientist II at GE Healthcare
Optimized tools for high-confidence genome engineering
CRISPR-Cas9 systems can be used with custom RNA guides for several gene editing applications
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