Nucleic acids researchFeb 23, 2026

Single-cell analysis shows different roles of alternative gene starters in drug response

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗OA ↗

Updated Jun 27, 2026

Abstract

Essence

Alternative promoters can drive distinct cell programs and drug-response effects rather than simply duplicating gene expression.

Evidence

This functional genomics platform study used CRISPR-dCas9 promoter targeting and Isoform-Specific single-cell Perturb-Seq, finding distinct transcriptional programs in 51.6% of targeted genes and promoter-specific drug effects in breast cancer models.

Caveat

The therapeutic implications are inferred from screening and model-system analyses, including breast cancer models, rather than tested promoter-targeted treatments in patients.

Simplified

(CRISPRi) screens have emerged as powerful tools for dissecting gene function, yet their application to genes with multiple promoters, which comprise over 60% of human genes, remains poorly understood. Here, we demonstrate that CRISPR-dCas9-based screens exhibit widespread promoter specificity, with untargeted promoters often showing compensatory upregulation to maintain gene expression. Leveraging this selective targeting of individual promoters within the same gene, we developed Isoform-Specific single-cell Perturb-Seq to systematically analyse alternative promoter function. Our analysis revealed that alternative promoters in 51.6% of targeted genes drive distinct transcriptional programs. This suggests that promoter selection represents a fundamental mechanism for generating cellular diversity rather than mere transcriptional redundancy. In breast cancer models, this promoter-specific targeting revealed differential effects on drug sensitivity, where distinct estrogen receptor (ESR1) promoters showed opposing influences on tamoxifen response and patient survival. These findings demonstrate the necessity of promoter-level analysis in functional genomics and suggest new strategies for therapeutic intervention through promoter-specific targeting.

Key numbers

51.6%

Distinct Transcriptional Programs

Percentage of targeted genes exhibiting unique transcriptional programs

2.3×

Increased P1 Promoter Usage

Fold increase in P1 promoter usage in tamoxifen-resistant cells compared to parental cells

1.9

Survival Hazard Ratio

Hazard ratio for survival based on P1 promoter expression

Full Text

We can’t show the full text here under this license.

View Full Text ↗

Funding

Competing interests

None declared.

PubMed

Single-cell analysis shows different roles of alternative gene starters in drug response

Abstract

Key numbers

Full Text

Funding

Competing interests

You found one interesting study. We’ll send the next 7.

What Lands in Your Inbox Each Week:

Recent issues from the crispr gene editing brief