Evidence map›Paper›PMID 40175512›Full record

ArticleNature chemical biology2025

TOPO-seq reveals DNA topology-induced off-target activity by Cas9 and base editors.

Min Duan, Pan Gao, Yi-Zhou Zhang, Yu-Long Hu, Lei Zhou, Zhong-Chen Xu, Hou-Yuan Qiu, Xiao-Han Tong, Rui-Jin Ji, Xin-Lin Lei and 3 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature chemical biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Min Duan *Department of Esophagus, Mediastinum and Lymphatic Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
Pan Gao *Department of Esophagus, Mediastinum and Lymphatic Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
Yi-Zhou Zhang *Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.
Yu-Long HuFrontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.ORCID http://orcid.org/0009-0007-6735-1998
Lei ZhouFrontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.
Zhong-Chen XuCollege of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China.
Hou-Yuan QiuFrontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.
Xiao-Han TongFrontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.ORCID http://orcid.org/0000-0003-3116-4908
Rui-Jin JiFrontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.
Xin-Lin LeiFrontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.ORCID http://orcid.org/0009-0009-1462-3739
Hao YinFrontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, China.ORCID http://orcid.org/0000-0001-9654-5985
Cun-Lan GuoCollege of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China.
Ying ZhangDepartment of Esophagus, Mediastinum and Lymphatic Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China. ying.zhang84@whu.edu.cn.ORCID http://orcid.org/0000-0003-4044-0230

Funding

National Natural Science Foundation of China (National Science Foundation of China) 82450105
6 · The paper itself

Abstract

With the increasing use of CRISPR-Cas9, detecting off-target events is essential for safety. Current methods primarily focus on guide RNA (gRNA) sequence mismatches, often overlooking the impact of DNA topology in regulating off-target activity. Here we present TOPO-seq, a high-throughput and sensitive method that identifies genome-wide off-target effects of Cas9 and base editors while accounting for DNA topology. TOPO-seq revealed that topology-induced off-target sites frequently harbor higher mismatches than the relaxed DNA sequence, with over 50% of off-target sites containing six mismatches, which are usually overlooked using previous methods. Applying TOPO-seq to three therapeutic gRNAs in hematopoietic stem cells identified 47 bona fide off-target loci, six of which are specifically induced by DNA topology. These findings highlight DNA topology as a regulator of off-target editing rates, establish TOPO-seq as a robust method for capturing DNA topology-induced off-target events and underscore its importance in off-target detection for developing safe genome-editing therapies.

Indexed as

CRISPR-Associated Protein 9CRISPR-Cas SystemsDNAGene EditingHigh-Throughput Nucleotide SequencingHumansRNA, Guide, CRISPR-Cas SystemsCRISPR-Associated Protein 9DNARNA, Guide, CRISPR-Cas Systems

Identifiers

PMID40175512

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.