Cell stem cellFeb 26, 2026

Reducing widespread DNA changes in genome editing helps maintain stem cell identity

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗

Updated Jun 27, 2026

Abstract

Essence

CRISPR-Cas9 cuts can disturb long-range chromatin organization and erode stem cell identity.

Evidence

A preclinical genome-editing study in neural stem cells in vivo and mouse embryonic stem cells in vitro used integrated ATAC/RNA sequencing to map editing-induced chromatin and transcriptional changes.

Caveat

The scope is limited to stem-cell models and refined editing strategies, not clinical gene-editing outcomes across tissues.

Simplified

Although CRISPR-Cas9 holds therapeutic promise, broader application demands an understanding of complications in vast non-coding regions. We found that CRISPR-Cas9 can cause premature differentiation of neural stem cells in vivo and mouse embryonic stem cells in vitro, even when cleavage occurred at distant sites tens of kilobases away from the nearest regulatory elements. To investigate this, we employed an integrated assay for transposase-accessible chromatin (ATAC)/RNA sequencing (AR-seq) approach and identified editing-induced chromatin accessibility changes, with their scale varying by cell type. Cells with stemness are most affected, experiencing perturbations that extend over a hundred kilobases. Furthermore, even local DNA perturbations can disrupt CTCF- and condensate-associated chromatin architecture, causing distal transcriptional rewiring and, ultimately, loss of stemness identity. To minimize chromatin perturbations and preserve cell identity, we refined gene-editing strategies, including distance-aware sgRNA design, pharmacological attenuation of DNA resection, and alternative editing systems. This work paves the way for the safer and broader application of genome-editing technologies.