Cell systemsFeb 28, 2026

Competition for resources influences CRISPR-based gene activation

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗

Updated Mar 1, 2026

Abstract

CRISPR-mediated gene activation is not as modular or scalable as previously thought.

Different guide RNAs (gRNAs) compete for dCas9 and an activator protein, leading to interference among them.
This competition can hinder the effectiveness of the CRISPRa system.
Gene activation shows a biphasic response, where higher gRNA levels may cause target repression instead of activation.
A chemical reaction-network model has been developed to describe these interactions.
The model can improve the dynamic range of CRISPRa systems, aiding in their design and optimization.

Simplified

CRISPR-mediated gene activation (CRISPRa) allows concurrent transcriptional control of many genes and is widely used in genome-wide screening, bioproduction, and therapeutics. Multi-gene control is possible due to the sequence specificity by which guide RNAs (gRNAs) recruit dCas9 and an activator protein to target genes. Still, the optimization of CRISPRa systems remains difficult. Here, we show that, despite sequence specificity, different gRNAs interfere with each other by competing for dCas9 and the activator protein. This competition breaks modularity and hinders CRISPRa. We also discover that gene activation is biphasic, wherein increased level of a gRNA leads to target repression instead of activation. We introduce a chemical reaction-network model that captures these effects and use it for improving the dynamic range of CRISPRa. Our results demonstrate that CRISPRa is not as modular or scalable as previously thought and establish a predictive modeling tool that enables systematic design and optimization of multi-gRNA CRISPRa systems. A record of this paper's transparent peer review process is included in the supplemental information.

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Competing interests

Declaration of interests The authors declare no competing interests.

PubMed

Competition for resources influences CRISPR-based gene activation

Abstract

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Funding

Competing interests

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