Comprehensive assessment of activity, specificity, and safety of hypercompact TnpB systems for gene editing

TL;DR

This paper evaluates different TnpB gene editing systems and finds that ISYmu1 TnpB is a compact, efficient, and safe option for genome editing.

Contribution

The study introduces a standardized framework to assess TnpB systems and identifies ISYmu1 TnpB as a top-performing miniature genome editor.

Findings

TnpB systems show intermediate activity and safety compared to Cas12 and Cas9 tools.

ISYmu1 TnpB demonstrates high editing efficiency and specificity.

ISYmu1 TnpB is identified as a promising candidate for therapeutic genome editing.

Abstract

As the ancestor of CRISPR-Cas12 nucleases, TnpB represents the most compact gene editing tool currently available. Recent studies have identified multiple TnpB systems with gene editing activity in mammalian cells, and the potential of TnpB in treating diseases has been demonstrated in animal models. However, the editing characteristics of various TnpB systems, comparable to CRISPR tools, require more extensive investigation.

Using a standardized evaluation framework, we conduct a thorough analysis of the editing properties of four TnpB variants alongside representative Cas12 and Cas9 tools applications. Overall, TnpBs exhibit intermediate editing activity and safety profiles among all tested systems, with ISYmu1 TnpB demonstrating a good performance in both editing activity and specificity. Considering its compact size, potent editing efficiency and high specificity, ISYmu1 TnpB represents a promising candidate for gene therapy.

By comprehensively analyzing genome editing outcomes, we characterize TnpB systems for genome editing and identify ISYmu1 TnpB as an optimal miniature RNA-guided genome editors with balanced performance, highlighting its potential for therapeutic applications.

The online version contains supplementary material available at 10.1186/s13059-026-03949-8.

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