CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) use a catalytically dead Cas9 (dCas9, no nuclease activity) fused to a repressor or activator domain, guided by a single gRNA to a chosen DNA site. Nothing is cut — the effect is purely occupancy-based and reversible.
efficacy(x) = exp( -(x - μ)² / (2σ²) )
combined(x,n) = 1 - (1 - efficacy(x))^(1 + 0.5·(n-1))
KRAB (CRISPRi): μ = +150 bp, σ = 250 bp (blocks initiation just past the TSS)
VPR (CRISPRa): μ = -200 bp, σ = 300 bp (recruits Pol II from the promoter-proximal region)
rate(KRAB) = 1 − 0.92 · combined rate(VPR) = 1 + 8 · combined
- dCas9-KRAB recruits the KAP1/SETDB1 heterochromatin pathway. It represses most strongly when the guide targets the region just downstream of the transcription start site (TSS), inside the first few hundred base pairs of the gene body, where it blocks Pol II from clearing the promoter-proximal pause.
- dCas9-VPR (a VP64–p65–Rta tripartite activator) works the opposite way: it recruits transcriptional co-activators most effectively when bound upstream of the TSS, in the promoter/enhancer-proximal region — mimicking a strong endogenous transcription factor.
- The bell-shaped efficacy curve is a simplified fit to the positional screens in Gilbert et al. 2014 (CRISPRi) and Chavez et al. 2015 (VPR/CRISPRa): binding far from each effector's sweet spot has almost no effect on transcription.
- Guide RNAs (1–3) multiplexes several gRNAs at nearby offsets; combined occupancy grows with diminishing returns rather than adding linearly.
- Drag the red/green effector marker directly on the gene diagram, or use the slider — both move the same binding-site position. The lower chart plots the full efficacy-vs-position curve for the active mode and marks where you currently sit on it.
Real-world relevance: this positional dependence is exactly why genome-wide CRISPRi/CRISPRa screens tile many guides per gene rather than picking one — the same gene can be silenced or activated by the same dCas9 fusion depending only on where along the locus it lands.