Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity

Ming Zhu; Junsong Yuan; Qiuchen Meng; Jiawei Yu; Xiaoqing Xu; Mingyue Xu; Xiaoyu Ren; Yanyan Hu; Guoan Wei; Zeran Jia; Guohua Yuan; Lu Zang; Shaorui Liu; Yuanyuan Yang; Yuan Zheng; Jiacheng Wang; Tingting Cong; Wei Xie; Xun Lan; Le Cong; Tianhua Ma; Sheng Ding; Weixiang Guo; Xuegong Zhang; Yinqing Li

doi:10.1016/j.stem.2026.01.015

Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity

Ming Zhu^*
, Junsong Yuan
, Qiuchen Meng
, Jiawei Yu
, Xiaoqing Xu
, Mingyue Xu
, Xiaoyu Ren
, Yanyan Hu
, Guoan Wei
, Zeran Jia
, Guohua Yuan
, Lu Zang
, Shaorui Liu
, Yuanyuan Yang
, Yuan Zheng
, Jiacheng Wang
, Tingting Cong
, Wei Xie
, Xun Lan
, Le Cong

Tianhua Ma, Sheng Ding, Weixiang Guo, Xuegong Zhang^*, Yinqing Li^*

^*Corresponding author for this work

Tsinghua University
CAS - Institute of Genetics and Developmental Biology
University of California at San Francisco
Stanford University

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Zhu et al. report that CRISPR editing displaces CTCF- and condensate-associated distal regulations, rewiring 3D genomic regulation. Even distal cleavage causes stem cell differentiation. The authors propose strategies to minimize chromatin disruption and preserve cell identity.

Original language	English
Pages (from-to)	470-486.e14
Journal	Cell Stem Cell
Volume	33
Issue number	3
DOIs	https://doi.org/10.1016/j.stem.2026.01.015
State	Published - 5 Mar 2026
Externally published	Yes

Keywords

chromatin architecture
chromatin condensate
chromatin perturbation
genome editing
neural stem cell
premature differentiation
somatic stem cell

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10.1016/j.stem.2026.01.015

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@article{75aa2658f7814329b28052ec4bc8307f,

title = "Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity",

abstract = "Zhu et al. report that CRISPR editing displaces CTCF- and condensate-associated distal regulations, rewiring 3D genomic regulation. Even distal cleavage causes stem cell differentiation. The authors propose strategies to minimize chromatin disruption and preserve cell identity.",

keywords = "chromatin architecture, chromatin condensate, chromatin perturbation, genome editing, neural stem cell, premature differentiation, somatic stem cell",

author = "Ming Zhu and Junsong Yuan and Qiuchen Meng and Jiawei Yu and Xiaoqing Xu and Mingyue Xu and Xiaoyu Ren and Yanyan Hu and Guoan Wei and Zeran Jia and Guohua Yuan and Lu Zang and Shaorui Liu and Yuanyuan Yang and Yuan Zheng and Jiacheng Wang and Tingting Cong and Wei Xie and Xun Lan and Le Cong and Tianhua Ma and Sheng Ding and Weixiang Guo and Xuegong Zhang and Yinqing Li",

note = "Publisher Copyright: {\textcopyright} 2026 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.",

year = "2026",

month = mar,

day = "5",

doi = "10.1016/j.stem.2026.01.015",

language = "英语",

volume = "33",

pages = "470--486.e14",

journal = "Cell Stem Cell",

issn = "1934-5909",

publisher = "Cell Press",

number = "3",

}

Zhu, M, Yuan, J, Meng, Q, Yu, J, Xu, X, Xu, M, Ren, X, Hu, Y, Wei, G, Jia, Z, Yuan, G, Zang, L, Liu, S, Yang, Y, Zheng, Y, Wang, J, Cong, T, Xie, W, Lan, X, Cong, L, Ma, T, Ding, S, Guo, W, Zhang, X & Li, Y 2026, 'Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity', Cell Stem Cell, vol. 33, no. 3, pp. 470-486.e14. https://doi.org/10.1016/j.stem.2026.01.015

TY - JOUR

T1 - Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity

AU - Zhu, Ming

AU - Yuan, Junsong

AU - Meng, Qiuchen

AU - Yu, Jiawei

AU - Xu, Xiaoqing

AU - Xu, Mingyue

AU - Ren, Xiaoyu

AU - Hu, Yanyan

AU - Wei, Guoan

AU - Jia, Zeran

AU - Yuan, Guohua

AU - Zang, Lu

AU - Liu, Shaorui

AU - Yang, Yuanyuan

AU - Zheng, Yuan

AU - Wang, Jiacheng

AU - Cong, Tingting

AU - Xie, Wei

AU - Lan, Xun

AU - Cong, Le

AU - Ma, Tianhua

AU - Ding, Sheng

AU - Guo, Weixiang

AU - Zhang, Xuegong

AU - Li, Yinqing

PY - 2026/3/5

Y1 - 2026/3/5

N2 - Zhu et al. report that CRISPR editing displaces CTCF- and condensate-associated distal regulations, rewiring 3D genomic regulation. Even distal cleavage causes stem cell differentiation. The authors propose strategies to minimize chromatin disruption and preserve cell identity.

AB - Zhu et al. report that CRISPR editing displaces CTCF- and condensate-associated distal regulations, rewiring 3D genomic regulation. Even distal cleavage causes stem cell differentiation. The authors propose strategies to minimize chromatin disruption and preserve cell identity.

KW - chromatin architecture

KW - chromatin condensate

KW - chromatin perturbation

KW - genome editing

KW - neural stem cell

KW - premature differentiation

KW - somatic stem cell

UR - https://www.scopus.com/pages/publications/105032796207

U2 - 10.1016/j.stem.2026.01.015

DO - 10.1016/j.stem.2026.01.015

M3 - 文章

C2 - 41742419

AN - SCOPUS:105032796207

SN - 1934-5909

VL - 33

SP - 470-486.e14

JO - Cell Stem Cell

JF - Cell Stem Cell

IS - 3

ER -

Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity

Abstract

Keywords

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