CRISPRa and CRISPRi: Gene Expression Modulation

What is CRISPRa and CRISPRi?

CRISPR/Cas9 has recently been developed to modulate gene expression, CRISPRa (CRISPR activation) for gene activation and CRISPRi (CRISPR interference) for gene expression interference. In both CRISPRa and CRISPRi systems, the enzymatically deficient Cas9 (dCas9) is fused or interacts with transcriptional effector(s). dCas9 contains mutations in two active endonuclease domains, losing the capability to cut DNA. However dCas9 can still target a specific DNA location when coupled with a gRNA. In CRISPRa system, dCas9 is fused or interacts with transcriptional activators leading to gene expression upregulation. In CRISPRi, dCas9 is fused with transcriptional repressor(s) leading to gene expression repression. OriGene offers genome wide CRISPRa Kits against all human and mouse genes.

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Rules of gRNA design for CRISPRa /CRISPRi

To modulate gene regulation, gRNA is usually designed to target around the promoter region, and the transcriptional start site (TSS) (+1)

OriGene provides fast and cost effective custom gRNA design and cloning service (view details).

Fig. 1. Diagram of CRISPRa and CRISPRi. dCas9 - activator leads to activation; dCas9 - repressor leads to repression.

CRISPRa – Gene activation with CRISPR

CRISPRi – Gene interference with CRISPR

CRISPRa – SAM, CRISPR/Cas9 Synergistic Activation Mediator

CRISPRa SAM is a robust CRISPR gene activation system to activate gene expression using CRISPR technology. The CRISPRa SAM consists of dCas9-VP64, a modified gRNA containing MS2 RNA aptamers, and MS2-p65-HSF1 activation domains. VP64 has four copies of VP16, a viral protein that is used for transcriptional activation. p65 and HSF1 are transcription activation domains when p65 and HSF1 are brought in close proximity to dCAs9-VP64 via interaction of MS2 with MS2 RNA aptamers in gRNA, the three transactivators then synergistically upregulate gene expression. CRISPRa SAM can robustly activate both coding and non-coding RNA (lincRNA).

Features:

• Robust CRISPR gene activation system
• Synergistic activation by three activation domains, VP64, p65 and HSF1
• Two vector system, dCas9-VP64-gRNA(MS2) and MS2-p65-HSF1
• Complement to gene overexpression with cDNA clones

Fig. 2. Diagram of CRISPRa SAM – CRISPR/Cas9 activation system. MS2 in MS2-p65-HSF1 fusion protein binds to MS2 RNA aptamer in the gRNA, bringing p65 and HSF1 to VP64; VP64, p65 and HSF1 then synergistically activate gene expression.

CRISPRa SAM CRISPR/Cas9 Activation Vector Products

1. pCas-Guide-CRISPRa Vector

The all-in-one CRISPRa vector contains U6 driven gRNA expression and CMV driven dCas9-VP64. After gRNA targeting sequence cloning, the vector will express dCas9-VP64 fusion protein and gRNA (containing MS2 binding sequence).

Features:

• Containing gRNA cloning site
• gRNA under U6 promoter
• gRNA modified with MS2 RNA aptamer in the loops
• CMV driven dCas9-VP64
• For robust gene activation, needs to work with pCRISPRa-Enhancer

2. CRISPRa SAM Enhancer Vector

pCRISPRa-Enhancer vector encodes a fusion protein of MS2 coat protein and the transactivation domains of p65 and HSF1. MS2 protein will bind to MS2 RNA aptamer in the gRNA, thus bringing p65 and HSF1 together with dCas9-VP64.

Features:

• CMV driven MS2-p65-HSF1
• Requires pCas-Guide-CRISPRa for gene activation
• MS2-p65-HSF1 synergistically activate gene expression with dCas9-VP64

Gene Activation Kit using CRISPRa SAM

CRISPRa SAM can be used to upregulate gene expression. OriGene offers genome-wide locus specific gene activation kit using CRISPRa. Gene specific gRNA will bring dCas9-VP64 to the specific gene locus. p65 and HSF1 will translocate to gRNA by MS2, therefore robustly activate gene expression.

Features:

• Turn-key solution for activating endogenous genes, with 3 targeting gRNAs, 1 scramble control, and 1 enhancer vector
• Pre-designed gRNA with OriGene’s proprietary algorithm
• Two vector system, dCas9-VP64-gRNA(MS2) and MS2-p65-HSF1
• Alternative to gene overexpression with cDNA clones

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CRISPRa SAM Validation Data

CRISPRa SAM system robustly activates gene expression

Fig. 3. Target specific pCas-Guide-CRISPRa vector (encodes dCas9-VP64 and gRNA targeting HBG1 or ASCL1 locus) and pCRISPRa-Enhancer (encodes MS2-p65-HSF1) were transfected into HEK293T cells using MegaTran 2.0. Cells were harvested 48 hrs post transfection; qPCR was performed to measure gene expression.

dCas9-VP64 alone can significantly activate gene expression

Fig. 4. dCas9-VP64 and gRNA targeting ASCL1 locus without CRISPRa enhancer was transfected into HEK293T cells using MegaTran 2.0. Cells were harvested 48 hrs post transfection; qPCR was performed to measure gene expression.

CRISPRi – dCas9-KRAB-MeCP2 Gene Interference

In this CRISPRi system, dCas9 is fused with KRAB and MeCP2 repression domains to carry out robust gene repression. Krüppel-associated box (KRAB) is a well-known transcriptional repressor domain. MeCP2 has been shown to bind to methylated DNA.

Features:

• All-in-one CRISPRi vector system
• gRNA driven by U6 promoter (after target sequence cloned)
• dCas9-KRAB-MeCP2 fusion protein expression by CMV promoter

CRISPRi Validation Data

dCas9-KRAB-MeCP2 significantly repressed gene expression

Fig. 5. All-in-one CRISPRi vector containing gene specific gRNA and dCas9-KRAB-MeCP2 was transfected into HEK293T cells Using MegaTran 2.0. gRNA scramble control was used as a negative control. Cells were harvested 48 hrs post transfection and qPCR was performed to measure mRNA expression.